Starting phenix.real_space_refine on Thu Jul 31 08:06:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tco_41156/07_2025/8tco_41156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tco_41156/07_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_41156/07_2025/8tco_41156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tco_41156/07_2025/8tco_41156.map" model { file = "/net/cci-nas-00/data/ceres_data/8tco_41156/07_2025/8tco_41156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tco_41156/07_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.53, per 1000 atoms: 0.65 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: 3.39 Conformation dependent library (CDL) restraints added in 1.7 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: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 93 through 98 removed outlier: 3.510A pdb=" N LEU A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 107 removed outlier: 4.068A pdb=" N PHE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 308 through 326 removed outlier: 3.551A pdb=" N ARG A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N HIS A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 351 Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.138A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 358 " --> pdb=" O GLN A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 358' Processing helix chain 'A' and resid 362 through 385 Processing helix chain 'A' and resid 396 through 408 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 422 through 429 Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.884A pdb=" N LEU A 434 " --> pdb=" O GLN A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.946A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 3.762A pdb=" N HIS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 494 Processing helix chain 'A' and resid 496 through 506 removed outlier: 3.695A pdb=" N THR A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 538 through 539 No H-bonds generated for 'chain 'A' and resid 538 through 539' Processing helix chain 'A' and resid 540 through 544 removed outlier: 3.585A pdb=" N THR A 543 " --> pdb=" O PRO A 540 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 540 through 544' Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'B' and resid 46 through 57 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.627A pdb=" N ARG B 87 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 172 through 176 removed outlier: 4.116A pdb=" N THR B 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 176 " --> pdb=" O ILE B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 176' Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 236 removed outlier: 4.107A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 removed outlier: 3.571A pdb=" N HIS B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 148 through 162 Processing helix chain 'C' and resid 200 through 217 Processing helix chain 'C' and resid 224 through 231 Processing helix chain 'C' and resid 242 through 253 Processing helix chain 'C' and resid 323 through 337 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 363 through 366 Processing helix chain 'C' and resid 379 through 381 No H-bonds generated for 'chain 'C' and resid 379 through 381' Processing helix chain 'C' and resid 415 through 424 Processing helix chain 'C' and resid 424 through 435 removed outlier: 3.820A pdb=" N LEU C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU C 430 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 removed outlier: 4.091A pdb=" N LEU C 458 " --> pdb=" O ASN C 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.890A pdb=" N GLN E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.591A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 100B Processing helix chain 'F' and resid 100G through 100I No H-bonds generated for 'chain 'F' and resid 100G through 100I' Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.871A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 92 removed outlier: 6.991A pdb=" N GLN A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL B 178 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA B 194 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 126 removed outlier: 4.879A pdb=" N VAL A 281 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU A 277 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ARG A 136 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 126 removed outlier: 4.879A pdb=" N VAL A 281 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 247 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN A 193 " --> pdb=" O CYS A 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 184 removed outlier: 3.521A pdb=" N THR A 183 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 361 " --> pdb=" O THR A 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 578 through 581 Processing sheet with id=AA7, first strand: chain 'A' and resid 637 through 638 removed outlier: 7.102A pdb=" N THR A 637 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 665 " --> pdb=" O GLU A 656 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP A 658 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N VAL A 663 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 100 removed outlier: 6.375A pdb=" N VAL B 99 " --> pdb=" O ARG C 236 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 155 removed outlier: 3.675A pdb=" N CYS B 159 " --> pdb=" O HIS C 449 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS C 449 " --> pdb=" O CYS B 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 85 through 87 Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 87 removed outlier: 3.519A pdb=" N GLY C 144 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AB4, first strand: chain 'C' and resid 186 through 191 Processing sheet with id=AB5, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AB6, first strand: chain 'C' and resid 383 through 384 removed outlier: 3.799A pdb=" N TYR C 384 " --> pdb=" O THR C 413 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.758A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.035A pdb=" N MET E 34 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 94 through 95 removed outlier: 3.771A pdb=" N VAL E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 12 removed outlier: 7.728A pdb=" N ILE F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AC6, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.706A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.19 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4229 1.34 - 1.46: 3367 1.46 - 1.59: 5841 1.59 - 1.71: 0 1.71 - 1.83: 99 Bond restraints: 13536 Sorted by residual: bond pdb=" C1 NAG C 505 " pdb=" O5 NAG C 505 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" CB ARG A 329 " pdb=" CG ARG A 329 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.14e+00 bond pdb=" CB PRO C 141 " pdb=" CG PRO C 141 " ideal model delta sigma weight residual 1.506 1.570 -0.064 3.90e-02 6.57e+02 2.73e+00 bond pdb=" CG GLU A 466 " pdb=" CD GLU A 466 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.65e+00 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.49e+00 ... (remaining 13531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 18045 2.02 - 4.05: 310 4.05 - 6.07: 45 6.07 - 8.09: 4 8.09 - 10.12: 4 Bond angle restraints: 18408 Sorted by residual: angle pdb=" CG ARG A 329 " pdb=" CD ARG A 329 " pdb=" NE ARG A 329 " ideal model delta sigma weight residual 112.00 121.09 -9.09 2.20e+00 2.07e-01 1.71e+01 angle pdb=" CB ARG A 329 " pdb=" CG ARG A 329 " pdb=" CD ARG A 329 " ideal model delta sigma weight residual 111.30 103.20 8.10 2.30e+00 1.89e-01 1.24e+01 angle pdb=" N GLU A 466 " pdb=" CA GLU A 466 " pdb=" CB GLU A 466 " ideal model delta sigma weight residual 110.16 115.21 -5.05 1.48e+00 4.57e-01 1.16e+01 angle pdb=" CA PRO C 141 " pdb=" N PRO C 141 " pdb=" CD PRO C 141 " ideal model delta sigma weight residual 111.50 107.24 4.26 1.40e+00 5.10e-01 9.25e+00 angle pdb=" CA LEU C 118 " pdb=" CB LEU C 118 " pdb=" CG LEU C 118 " ideal model delta sigma weight residual 116.30 126.42 -10.12 3.50e+00 8.16e-02 8.36e+00 ... (remaining 18403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.23: 7792 22.23 - 44.45: 415 44.45 - 66.68: 50 66.68 - 88.90: 30 88.90 - 111.13: 8 Dihedral angle restraints: 8295 sinusoidal: 3506 harmonic: 4789 Sorted by residual: dihedral pdb=" CB CYS C 143 " pdb=" SG CYS C 143 " pdb=" SG CYS C 151 " pdb=" CB CYS C 151 " ideal model delta sinusoidal sigma weight residual 93.00 177.02 -84.02 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS A 571 " pdb=" SG CYS A 571 " pdb=" SG CYS A 624 " pdb=" CB CYS A 624 " ideal model delta sinusoidal sigma weight residual -86.00 -153.50 67.50 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CB CYS A 647 " pdb=" SG CYS A 647 " pdb=" SG CYS A 650 " pdb=" CB CYS A 650 " ideal model delta sinusoidal sigma weight residual -86.00 -151.22 65.22 1 1.00e+01 1.00e-02 5.58e+01 ... (remaining 8292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1772 0.057 - 0.114: 300 0.114 - 0.171: 41 0.171 - 0.228: 7 0.228 - 0.285: 3 Chirality restraints: 2123 Sorted by residual: chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 62 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2120 not shown) Planarity restraints: 2339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 602 " -0.049 5.00e-02 4.00e+02 7.35e-02 8.63e+00 pdb=" N PRO A 603 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 603 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 603 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 369 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO C 370 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 370 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 370 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 253 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO A 254 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " -0.029 5.00e-02 4.00e+02 ... (remaining 2336 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 271 2.69 - 3.24: 12878 3.24 - 3.80: 20311 3.80 - 4.35: 27706 4.35 - 4.90: 45861 Nonbonded interactions: 107027 Sorted by model distance: nonbonded pdb=" O TRP C 332 " pdb=" OG1 THR C 335 " model vdw 2.138 3.040 nonbonded pdb=" OE2 GLU A 491 " pdb=" OH TYR A 519 " model vdw 2.204 3.040 nonbonded pdb=" O THR C 174 " pdb=" OG SER C 320 " model vdw 2.212 3.040 nonbonded pdb=" OE1 GLU A 499 " pdb=" OG1 THR A 520 " model vdw 2.244 3.040 nonbonded pdb=" O PHE G 49 " pdb=" OG SER G 53 " model vdw 2.248 3.040 ... (remaining 107022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.210 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: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.660 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: 0.000 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.440 ------------------------------------------------------------------------------- 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 : 1.317 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: 1.1330 time to fit residues: 326.7208 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 : 1.312 ------------------------------------------------------------------------------- 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: 0.8980 chunk 144 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.152905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.134190 restraints weight = 19546.890| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.36 r_work: 0.3784 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 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 = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13566 Z= 0.157 Angle : 0.640 11.137 18483 Z= 0.321 Chirality : 0.044 0.286 2123 Planarity : 0.005 0.048 2329 Dihedral : 8.315 73.320 2109 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.45 % Allowed : 10.37 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1607 helix: 0.32 (0.27), residues: 382 sheet: 0.61 (0.28), residues: 359 loop : -0.17 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 167 HIS 0.007 0.001 HIS A 586 PHE 0.033 0.002 PHE A 462 TYR 0.020 0.002 TYR A 682 ARG 0.005 0.000 ARG A 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 10) link_NAG-ASN : angle 2.39246 ( 30) link_BETA1-4 : bond 0.00310 ( 5) link_BETA1-4 : angle 2.50072 ( 15) hydrogen bonds : bond 0.04651 ( 496) hydrogen bonds : angle 5.79402 ( 1335) SS BOND : bond 0.00334 ( 15) SS BOND : angle 1.16354 ( 30) covalent geometry : bond 0.00367 (13536) covalent geometry : angle 0.62784 (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 279 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 258 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8238 (m-80) cc_final: 0.8030 (m-80) REVERT: A 113 GLU cc_start: 0.7952 (tt0) cc_final: 0.7741 (tt0) REVERT: A 151 GLN cc_start: 0.7289 (pm20) cc_final: 0.6859 (pm20) REVERT: A 231 GLU cc_start: 0.7632 (mp0) cc_final: 0.7308 (mp0) REVERT: A 255 ARG cc_start: 0.7620 (mtp85) cc_final: 0.7393 (mtp85) REVERT: A 296 ASP cc_start: 0.8054 (p0) cc_final: 0.7615 (p0) REVERT: A 426 LEU cc_start: 0.8270 (tp) cc_final: 0.8004 (tm) REVERT: A 491 GLU cc_start: 0.7569 (tt0) cc_final: 0.7336 (tp30) REVERT: A 682 TYR cc_start: 0.8158 (t80) cc_final: 0.7642 (t80) REVERT: A 684 GLU cc_start: 0.7320 (mp0) cc_final: 0.6823 (mp0) REVERT: B 244 ARG cc_start: 0.7135 (tpm170) cc_final: 0.6915 (tpm170) REVERT: C 250 MET cc_start: 0.8173 (tpp) cc_final: 0.7894 (mmm) outliers start: 21 outliers final: 10 residues processed: 261 average time/residue: 1.0775 time to fit residues: 310.5406 Evaluate side-chains 261 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 251 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLN 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 198 VAL 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: 0.7980 chunk 83 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.0040 chunk 152 optimal weight: 1.9990 chunk 124 optimal weight: 0.0670 chunk 133 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.5532 ------------------------------------------------------------------------------- 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** ** 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 = 0.4142 r_free = 0.4142 target = 0.153156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.134849 restraints weight = 19615.484| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.28 r_work: 0.3777 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- 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: 3 | |-----------------------------------------------------------------------------| |-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: 0.7373 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13566 Z= 0.154 Angle : 0.624 11.439 18483 Z= 0.308 Chirality : 0.044 0.275 2123 Planarity : 0.004 0.055 2329 Dihedral : 7.161 55.944 2109 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.63 % Allowed : 12.65 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1607 helix: 0.35 (0.27), residues: 387 sheet: 0.64 (0.28), residues: 363 loop : -0.26 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 167 HIS 0.005 0.001 HIS D 90 PHE 0.026 0.002 PHE A 462 TYR 0.017 0.002 TYR A 682 ARG 0.005 0.000 ARG A 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 10) link_NAG-ASN : angle 2.31307 ( 30) link_BETA1-4 : bond 0.00292 ( 5) link_BETA1-4 : angle 2.73508 ( 15) hydrogen bonds : bond 0.04021 ( 496) hydrogen bonds : angle 5.40806 ( 1335) SS BOND : bond 0.00372 ( 15) SS BOND : angle 1.15738 ( 30) covalent geometry : bond 0.00364 (13536) covalent geometry : angle 0.61122 (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 289 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8363 (m-80) cc_final: 0.8134 (m-80) REVERT: A 113 GLU cc_start: 0.7937 (tt0) cc_final: 0.7723 (tt0) REVERT: A 151 GLN cc_start: 0.7261 (pm20) cc_final: 0.6836 (pm20) REVERT: A 231 GLU cc_start: 0.7579 (mp0) cc_final: 0.7238 (mp0) REVERT: A 296 ASP cc_start: 0.7987 (p0) cc_final: 0.7609 (p0) REVERT: A 303 ASP cc_start: 0.7648 (t0) cc_final: 0.7321 (t0) REVERT: A 561 SER cc_start: 0.8024 (m) cc_final: 0.7681 (p) REVERT: A 682 TYR cc_start: 0.8212 (t80) cc_final: 0.7634 (t80) REVERT: A 684 GLU cc_start: 0.7302 (mp0) cc_final: 0.6811 (mp0) REVERT: B 178 VAL cc_start: 0.7615 (t) cc_final: 0.7410 (p) REVERT: C 250 MET cc_start: 0.8194 (tpp) cc_final: 0.7974 (mmm) REVERT: C 335 THR cc_start: 0.6606 (OUTLIER) cc_final: 0.6376 (p) REVERT: D 100 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6425 (pm20) outliers start: 38 outliers final: 14 residues processed: 264 average time/residue: 1.2566 time to fit residues: 366.6041 Evaluate side-chains 267 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 251 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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 615 ILE Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 10 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: 0.6980 chunk 98 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 74 optimal weight: 0.4980 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: 0.7580 ------------------------------------------------------------------------------- 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** ** 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 = 0.4114 r_free = 0.4114 target = 0.150883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.132443 restraints weight = 19410.171| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.27 r_work: 0.3760 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 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 = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1793 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= 0.190 Angle : 0.637 11.061 18483 Z= 0.313 Chirality : 0.045 0.270 2123 Planarity : 0.005 0.062 2329 Dihedral : 6.460 55.436 2109 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.90 % Allowed : 15.55 % Favored : 81.55 % 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: -0.03 (0.21), residues: 1607 helix: 0.27 (0.26), residues: 387 sheet: 0.63 (0.28), residues: 361 loop : -0.38 (0.22), residues: 859 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 0.022 0.002 PHE A 462 TYR 0.017 0.002 TYR F 27 ARG 0.006 0.000 ARG C 218 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 10) link_NAG-ASN : angle 2.32620 ( 30) link_BETA1-4 : bond 0.00241 ( 5) link_BETA1-4 : angle 2.84449 ( 15) hydrogen bonds : bond 0.03892 ( 496) hydrogen bonds : angle 5.34096 ( 1335) SS BOND : bond 0.00672 ( 15) SS BOND : angle 1.24146 ( 30) covalent geometry : bond 0.00452 (13536) covalent geometry : angle 0.62365 (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 299 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 257 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8432 (m-80) cc_final: 0.8229 (m-80) REVERT: A 113 GLU cc_start: 0.7917 (tt0) cc_final: 0.7704 (tt0) REVERT: A 151 GLN cc_start: 0.7250 (pm20) cc_final: 0.6803 (pm20) REVERT: A 231 GLU cc_start: 0.7687 (mp0) cc_final: 0.7289 (mp0) REVERT: A 296 ASP cc_start: 0.8002 (p0) cc_final: 0.7610 (p0) REVERT: A 303 ASP cc_start: 0.7677 (t0) cc_final: 0.7258 (OUTLIER) REVERT: A 561 SER cc_start: 0.8101 (m) cc_final: 0.7713 (p) REVERT: A 682 TYR cc_start: 0.8215 (t80) cc_final: 0.7712 (t80) REVERT: A 684 GLU cc_start: 0.7308 (mp0) cc_final: 0.6810 (mp0) REVERT: C 250 MET cc_start: 0.8199 (tpp) cc_final: 0.7961 (mmm) REVERT: C 379 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7807 (mmt) REVERT: D 100 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.6380 (pm20) REVERT: E 73 GLU cc_start: 0.6752 (mp0) cc_final: 0.6414 (mp0) outliers start: 42 outliers final: 21 residues processed: 274 average time/residue: 1.1745 time to fit residues: 354.5531 Evaluate side-chains 273 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 520 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 109 VAL 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: 7.9990 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 325 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.150069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.131702 restraints weight = 19632.229| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.27 r_work: 0.3748 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 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 = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2003 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= 0.213 Angle : 0.643 9.609 18483 Z= 0.319 Chirality : 0.046 0.272 2123 Planarity : 0.005 0.069 2329 Dihedral : 6.261 58.058 2109 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.76 % Allowed : 17.07 % 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: 0.20 (0.26), residues: 382 sheet: 0.54 (0.28), residues: 360 loop : -0.45 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 36 HIS 0.007 0.001 HIS C 131 PHE 0.020 0.002 PHE A 503 TYR 0.019 0.002 TYR E 59 ARG 0.007 0.000 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 10) link_NAG-ASN : angle 2.34584 ( 30) link_BETA1-4 : bond 0.00320 ( 5) link_BETA1-4 : angle 2.82676 ( 15) hydrogen bonds : bond 0.03900 ( 496) hydrogen bonds : angle 5.29005 ( 1335) SS BOND : bond 0.00400 ( 15) SS BOND : angle 1.40642 ( 30) covalent geometry : bond 0.00505 (13536) covalent geometry : angle 0.62963 (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 298 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 258 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7229 (pm20) cc_final: 0.6783 (pm20) REVERT: A 231 GLU cc_start: 0.7715 (mp0) cc_final: 0.7249 (mp0) REVERT: A 296 ASP cc_start: 0.7960 (p0) cc_final: 0.7699 (p0) REVERT: A 303 ASP cc_start: 0.7655 (t0) cc_final: 0.7232 (OUTLIER) REVERT: A 561 SER cc_start: 0.8159 (m) cc_final: 0.7771 (p) REVERT: A 667 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7093 (tmm) REVERT: A 676 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8381 (mm) REVERT: A 682 TYR cc_start: 0.8233 (t80) cc_final: 0.7728 (t80) REVERT: A 684 GLU cc_start: 0.7317 (mp0) cc_final: 0.6822 (mp0) REVERT: B 107 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6660 (t70) REVERT: B 204 ARG cc_start: 0.7650 (ptp90) cc_final: 0.7051 (ptp90) REVERT: C 123 LYS cc_start: 0.7603 (ptpp) cc_final: 0.7362 (ptpp) REVERT: C 379 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7896 (mmt) REVERT: D 100 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6355 (pm20) outliers start: 40 outliers final: 25 residues processed: 275 average time/residue: 1.1315 time to fit residues: 342.5045 Evaluate side-chains 285 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 256 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 392 THR 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 615 ILE Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 107 ASP 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 198 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 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 113 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 107 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 115 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 138 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 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 = 0.4112 r_free = 0.4112 target = 0.150834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.132568 restraints weight = 19817.402| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.28 r_work: 0.3761 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 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 = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13566 Z= 0.169 Angle : 0.619 11.490 18483 Z= 0.306 Chirality : 0.044 0.268 2123 Planarity : 0.004 0.069 2329 Dihedral : 6.000 55.212 2109 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.90 % Allowed : 17.62 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1607 helix: 0.30 (0.27), residues: 382 sheet: 0.61 (0.28), residues: 353 loop : -0.43 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 36 HIS 0.007 0.001 HIS C 131 PHE 0.021 0.002 PHE A 105 TYR 0.023 0.002 TYR E 59 ARG 0.007 0.000 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 10) link_NAG-ASN : angle 2.24813 ( 30) link_BETA1-4 : bond 0.00257 ( 5) link_BETA1-4 : angle 2.56808 ( 15) hydrogen bonds : bond 0.03640 ( 496) hydrogen bonds : angle 5.22055 ( 1335) SS BOND : bond 0.00521 ( 15) SS BOND : angle 1.42529 ( 30) covalent geometry : bond 0.00401 (13536) covalent geometry : angle 0.60596 (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 297 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 255 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7214 (pm20) cc_final: 0.6761 (pm20) REVERT: A 231 GLU cc_start: 0.7698 (mp0) cc_final: 0.7233 (mp0) REVERT: A 253 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6286 (pp) REVERT: A 296 ASP cc_start: 0.7962 (p0) cc_final: 0.7759 (p0) REVERT: A 303 ASP cc_start: 0.7615 (t0) cc_final: 0.7188 (OUTLIER) REVERT: A 667 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6878 (tmm) REVERT: A 676 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8359 (mm) REVERT: A 680 ASP cc_start: 0.8205 (m-30) cc_final: 0.7986 (m-30) REVERT: A 682 TYR cc_start: 0.8267 (t80) cc_final: 0.7841 (t80) REVERT: A 684 GLU cc_start: 0.7354 (mp0) cc_final: 0.6860 (mp0) REVERT: B 204 ARG cc_start: 0.7576 (ptp90) cc_final: 0.6985 (ptp90) REVERT: C 250 MET cc_start: 0.8210 (tpp) cc_final: 0.7990 (mmm) REVERT: C 379 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7845 (mmt) REVERT: D 100 GLN cc_start: 0.6875 (OUTLIER) cc_final: 0.6338 (pm20) REVERT: E 83 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7691 (mtp180) outliers start: 42 outliers final: 26 residues processed: 272 average time/residue: 1.2669 time to fit residues: 382.4360 Evaluate side-chains 276 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 245 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 497 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 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 198 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 414 PHE 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 83 ARG Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 107 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 106 optimal weight: 0.0270 chunk 151 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 E 31 GLN ** 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 = 0.4110 r_free = 0.4110 target = 0.150618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.132375 restraints weight = 19681.023| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.27 r_work: 0.3759 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 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 = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13566 Z= 0.170 Angle : 0.616 11.515 18483 Z= 0.307 Chirality : 0.044 0.267 2123 Planarity : 0.004 0.070 2329 Dihedral : 5.891 55.111 2109 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.18 % Allowed : 18.11 % Favored : 78.71 % 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: 0.25 (0.26), residues: 381 sheet: 0.56 (0.28), residues: 353 loop : -0.47 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 36 HIS 0.005 0.001 HIS A 670 PHE 0.021 0.002 PHE A 462 TYR 0.030 0.002 TYR A 595 ARG 0.006 0.000 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 10) link_NAG-ASN : angle 2.24518 ( 30) link_BETA1-4 : bond 0.00247 ( 5) link_BETA1-4 : angle 2.47133 ( 15) hydrogen bonds : bond 0.03675 ( 496) hydrogen bonds : angle 5.20096 ( 1335) SS BOND : bond 0.00418 ( 15) SS BOND : angle 1.31512 ( 30) covalent geometry : bond 0.00405 (13536) covalent geometry : angle 0.60424 (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 297 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7217 (pm20) cc_final: 0.6753 (pm20) REVERT: A 231 GLU cc_start: 0.7728 (mp0) cc_final: 0.7251 (mp0) REVERT: A 253 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6271 (pp) REVERT: A 293 LYS cc_start: 0.7860 (mtpp) cc_final: 0.7610 (mtpp) REVERT: A 303 ASP cc_start: 0.7558 (t0) cc_final: 0.7137 (t0) REVERT: A 486 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7745 (pp20) REVERT: A 676 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8364 (mm) REVERT: A 682 TYR cc_start: 0.8258 (t80) cc_final: 0.7822 (t80) REVERT: A 684 GLU cc_start: 0.7320 (mp0) cc_final: 0.6838 (mp0) REVERT: B 204 ARG cc_start: 0.7314 (ptp90) cc_final: 0.7091 (ptp-110) REVERT: C 341 GLN cc_start: 0.7567 (mt0) cc_final: 0.7342 (mt0) REVERT: C 379 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7888 (mmt) REVERT: D 100 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6349 (pm20) REVERT: E 83 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7694 (mtp180) outliers start: 46 outliers final: 31 residues processed: 269 average time/residue: 1.0301 time to fit residues: 307.2373 Evaluate side-chains 280 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 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 497 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 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 182 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain E residue 2 VAL 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 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: 0.2980 chunk 13 optimal weight: 0.0170 chunk 64 optimal weight: 0.2980 chunk 106 optimal weight: 0.0370 chunk 142 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 137 optimal weight: 0.0770 overall best weight: 0.1454 ------------------------------------------------------------------------------- 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 594 GLN D 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.154875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.136885 restraints weight = 19544.895| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.27 r_work: 0.3799 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13566 Z= 0.110 Angle : 0.602 11.372 18483 Z= 0.296 Chirality : 0.043 0.367 2123 Planarity : 0.004 0.060 2329 Dihedral : 5.571 54.294 2109 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.28 % Allowed : 19.90 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1607 helix: 0.46 (0.27), residues: 381 sheet: 0.52 (0.29), residues: 344 loop : -0.34 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 47 HIS 0.006 0.001 HIS C 131 PHE 0.022 0.002 PHE A 462 TYR 0.019 0.001 TYR E 59 ARG 0.006 0.000 ARG B 171 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 10) link_NAG-ASN : angle 2.12119 ( 30) link_BETA1-4 : bond 0.00450 ( 5) link_BETA1-4 : angle 2.00096 ( 15) hydrogen bonds : bond 0.03260 ( 496) hydrogen bonds : angle 5.05160 ( 1335) SS BOND : bond 0.00754 ( 15) SS BOND : angle 1.36239 ( 30) covalent geometry : bond 0.00249 (13536) covalent geometry : angle 0.59163 (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 294 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 261 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7211 (pm20) cc_final: 0.6733 (pm20) REVERT: A 231 GLU cc_start: 0.7666 (mp0) cc_final: 0.7202 (mp0) REVERT: A 253 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6004 (pp) REVERT: A 293 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7595 (mtpp) REVERT: A 296 ASP cc_start: 0.8077 (p0) cc_final: 0.7844 (p0) REVERT: A 303 ASP cc_start: 0.7427 (t0) cc_final: 0.6995 (t0) REVERT: A 486 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7790 (pp20) REVERT: A 566 PHE cc_start: 0.6796 (m-10) cc_final: 0.6494 (m-10) REVERT: A 676 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8443 (mm) REVERT: A 682 TYR cc_start: 0.8272 (t80) cc_final: 0.7913 (t80) REVERT: A 684 GLU cc_start: 0.7264 (mp0) cc_final: 0.7003 (mp0) REVERT: B 178 VAL cc_start: 0.7519 (t) cc_final: 0.7295 (p) REVERT: C 123 LYS cc_start: 0.7597 (ptpp) cc_final: 0.7373 (ptpp) REVERT: C 325 GLN cc_start: 0.7355 (mt0) cc_final: 0.7153 (mt0) REVERT: C 338 ARG cc_start: 0.8418 (ttp80) cc_final: 0.8060 (ttt90) REVERT: C 341 GLN cc_start: 0.7546 (mt0) cc_final: 0.7319 (mt0) outliers start: 33 outliers final: 20 residues processed: 274 average time/residue: 1.1034 time to fit residues: 333.1404 Evaluate side-chains 273 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 253 LEU Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 237 VAL 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 G residue 7 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 chunk 146 optimal weight: 1.9990 chunk 94 optimal weight: 0.0270 chunk 57 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 263 GLN A 315 ASN A 594 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.154515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.136468 restraints weight = 19363.134| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.27 r_work: 0.3811 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13566 Z= 0.127 Angle : 0.615 11.328 18483 Z= 0.304 Chirality : 0.044 0.271 2123 Planarity : 0.004 0.060 2329 Dihedral : 5.567 54.719 2109 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.07 % Allowed : 19.90 % Favored : 78.02 % 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: 0.56 (0.27), residues: 380 sheet: 0.57 (0.29), residues: 344 loop : -0.36 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 47 HIS 0.005 0.001 HIS C 131 PHE 0.021 0.002 PHE A 462 TYR 0.029 0.001 TYR A 595 ARG 0.007 0.000 ARG F 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 10) link_NAG-ASN : angle 1.89242 ( 30) link_BETA1-4 : bond 0.00270 ( 5) link_BETA1-4 : angle 2.01970 ( 15) hydrogen bonds : bond 0.03341 ( 496) hydrogen bonds : angle 5.05480 ( 1335) SS BOND : bond 0.00336 ( 15) SS BOND : angle 1.40508 ( 30) covalent geometry : bond 0.00301 (13536) covalent geometry : angle 0.60576 (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 280 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7199 (pm20) cc_final: 0.6746 (pm20) REVERT: A 231 GLU cc_start: 0.7646 (mp0) cc_final: 0.7239 (mp0) REVERT: A 293 LYS cc_start: 0.7803 (mtpp) cc_final: 0.7567 (mtpp) REVERT: A 296 ASP cc_start: 0.8070 (p0) cc_final: 0.7777 (p0) REVERT: A 303 ASP cc_start: 0.7393 (t0) cc_final: 0.6972 (t0) REVERT: A 334 ASP cc_start: 0.7501 (m-30) cc_final: 0.7264 (p0) REVERT: A 486 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7764 (pp20) REVERT: A 561 SER cc_start: 0.7987 (m) cc_final: 0.7745 (p) REVERT: A 566 PHE cc_start: 0.6770 (m-10) cc_final: 0.6416 (m-10) REVERT: A 676 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8426 (mm) REVERT: A 682 TYR cc_start: 0.8278 (t80) cc_final: 0.7916 (t80) REVERT: A 684 GLU cc_start: 0.7264 (mp0) cc_final: 0.7000 (mp0) REVERT: C 325 GLN cc_start: 0.7385 (mt0) cc_final: 0.7183 (mt0) REVERT: C 338 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8018 (ttt90) REVERT: F 19 ARG cc_start: 0.7804 (mmm-85) cc_final: 0.7591 (mmm-85) outliers start: 30 outliers final: 22 residues processed: 264 average time/residue: 1.0718 time to fit residues: 314.0491 Evaluate side-chains 269 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 279 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 594 GLN 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 212 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 318 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 109 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 23 optimal weight: 0.0870 chunk 158 optimal weight: 0.0770 chunk 131 optimal weight: 0.0170 chunk 84 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 152 optimal weight: 0.2980 overall best weight: 0.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 315 ASN ** C 341 GLN ** 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 = 0.4164 r_free = 0.4164 target = 0.154920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.136964 restraints weight = 19390.015| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.26 r_work: 0.3802 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13566 Z= 0.118 Angle : 0.622 10.825 18483 Z= 0.307 Chirality : 0.044 0.297 2123 Planarity : 0.004 0.053 2329 Dihedral : 5.524 54.653 2109 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.38 % Allowed : 20.80 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.22), residues: 1607 helix: 0.58 (0.27), residues: 380 sheet: 0.48 (0.29), residues: 345 loop : -0.34 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 47 HIS 0.005 0.001 HIS C 131 PHE 0.023 0.002 PHE A 462 TYR 0.018 0.001 TYR E 59 ARG 0.007 0.000 ARG F 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 10) link_NAG-ASN : angle 1.83344 ( 30) link_BETA1-4 : bond 0.00305 ( 5) link_BETA1-4 : angle 1.91826 ( 15) hydrogen bonds : bond 0.03311 ( 496) hydrogen bonds : angle 5.05392 ( 1335) SS BOND : bond 0.00341 ( 15) SS BOND : angle 1.45992 ( 30) covalent geometry : bond 0.00278 (13536) covalent geometry : angle 0.61370 (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 266 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7222 (pm20) cc_final: 0.6742 (pm20) REVERT: A 231 GLU cc_start: 0.7648 (mp0) cc_final: 0.7177 (mp0) REVERT: A 296 ASP cc_start: 0.8101 (p0) cc_final: 0.7782 (p0) REVERT: A 303 ASP cc_start: 0.7377 (t0) cc_final: 0.6963 (t0) REVERT: A 486 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7783 (pp20) REVERT: A 561 SER cc_start: 0.7931 (m) cc_final: 0.7672 (p) REVERT: A 566 PHE cc_start: 0.6696 (m-10) cc_final: 0.6466 (m-10) REVERT: A 676 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8413 (mm) REVERT: A 682 TYR cc_start: 0.8263 (t80) cc_final: 0.7906 (t80) REVERT: A 684 GLU cc_start: 0.7240 (mp0) cc_final: 0.6976 (mp0) REVERT: B 178 VAL cc_start: 0.7452 (t) cc_final: 0.7239 (p) REVERT: C 325 GLN cc_start: 0.7365 (mt0) cc_final: 0.7122 (mt0) REVERT: C 338 ARG cc_start: 0.8331 (ttp80) cc_final: 0.8125 (ttt90) REVERT: F 19 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7588 (mmm-85) outliers start: 20 outliers final: 18 residues processed: 255 average time/residue: 1.4148 time to fit residues: 400.2148 Evaluate side-chains 259 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 2.477 ------------------------------------------------------------------------------- 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 279 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 595 TYR 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 212 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 7 SER 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: 2.9990 chunk 3 optimal weight: 2.9990 chunk 83 optimal weight: 0.0570 chunk 122 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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 ** 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 = 0.4117 r_free = 0.4117 target = 0.150915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.132560 restraints weight = 19753.815| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.29 r_work: 0.3766 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- 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: 0.7392 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13566 Z= 0.183 Angle : 0.672 13.673 18483 Z= 0.330 Chirality : 0.046 0.268 2123 Planarity : 0.004 0.057 2329 Dihedral : 5.684 55.049 2109 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.66 % Allowed : 20.73 % Favored : 77.61 % 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: 0.55 (0.29), residues: 341 loop : -0.46 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 35 HIS 0.007 0.001 HIS D 90 PHE 0.025 0.002 PHE A 317 TYR 0.025 0.002 TYR A 424 ARG 0.007 0.000 ARG F 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 10) link_NAG-ASN : angle 1.98480 ( 30) link_BETA1-4 : bond 0.00272 ( 5) link_BETA1-4 : angle 2.22702 ( 15) hydrogen bonds : bond 0.03639 ( 496) hydrogen bonds : angle 5.15717 ( 1335) SS BOND : bond 0.00376 ( 15) SS BOND : angle 1.58268 ( 30) covalent geometry : bond 0.00440 (13536) covalent geometry : angle 0.66215 (18408) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13361.02 seconds wall clock time: 237 minutes 30.46 seconds (14250.46 seconds total)