Starting phenix.real_space_refine on Thu Sep 18 07:51:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xi3_38369/09_2025/8xi3_38369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xi3_38369/09_2025/8xi3_38369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xi3_38369/09_2025/8xi3_38369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xi3_38369/09_2025/8xi3_38369.map" model { file = "/net/cci-nas-00/data/ceres_data/8xi3_38369/09_2025/8xi3_38369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xi3_38369/09_2025/8xi3_38369.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 111 5.16 5 C 9583 2.51 5 N 2590 2.21 5 O 2876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15162 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 1902 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 235, 1897 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 4, 'TRANS': 230} Conformer: "B" Number of residues, atoms: 235, 1897 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 4, 'TRANS': 230} bond proxies already assigned to first conformer: 1920 Chain: "D" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1897 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 4, 'TRANS': 230} Chain: "A" Number of atoms: 7572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7572 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 26, 'TRANS': 935} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3072 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 371} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 719 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Time building chain proxies: 3.49, per 1000 atoms: 0.23 Number of scatterers: 15162 At special positions: 0 Unit cell: (112.2, 126.65, 131.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 111 16.00 P 2 15.00 O 2876 8.00 N 2590 7.00 C 9583 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 658.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3666 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 11 sheets defined 50.8% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'F' and resid 2 through 18 Processing helix chain 'F' and resid 19 through 34 removed outlier: 3.504A pdb=" N MET F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 71 removed outlier: 3.635A pdb=" N TYR F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 112 removed outlier: 3.602A pdb=" N MET F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LYS F 110 " --> pdb=" O ASN F 106 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN F 111 " --> pdb=" O TYR F 107 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 136 Processing helix chain 'F' and resid 140 through 165 removed outlier: 3.755A pdb=" N ILE F 160 " --> pdb=" O GLU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 186 Processing helix chain 'F' and resid 191 through 207 removed outlier: 3.844A pdb=" N GLU F 207 " --> pdb=" O ASP F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 215 through 236 Processing helix chain 'D' and resid 2 through 17 Processing helix chain 'D' and resid 19 through 32 Processing helix chain 'D' and resid 38 through 74 removed outlier: 3.757A pdb=" N ARG D 56 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 107 Processing helix chain 'D' and resid 117 through 137 removed outlier: 3.803A pdb=" N LEU D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL D 137 " --> pdb=" O TYR D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 163 removed outlier: 3.577A pdb=" N ALA D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 186 Processing helix chain 'D' and resid 189 through 207 removed outlier: 3.663A pdb=" N GLU D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 226 Processing helix chain 'D' and resid 227 through 235 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.814A pdb=" N ALA A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 198 Processing helix chain 'A' and resid 203 through 211 removed outlier: 4.146A pdb=" N GLN A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 255 Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.547A pdb=" N LEU A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.706A pdb=" N SER A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 319 Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.659A pdb=" N GLN A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 346 Processing helix chain 'A' and resid 358 through 368 removed outlier: 3.601A pdb=" N THR A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 Processing helix chain 'A' and resid 416 through 424 Processing helix chain 'A' and resid 444 through 458 removed outlier: 3.918A pdb=" N GLN A 448 " --> pdb=" O HIS A 444 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 456 " --> pdb=" O ALA A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.801A pdb=" N GLN A 466 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 476 Processing helix chain 'A' and resid 488 through 498 Processing helix chain 'A' and resid 503 through 512 Processing helix chain 'A' and resid 518 through 532 removed outlier: 3.785A pdb=" N LYS A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.827A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 562 Processing helix chain 'A' and resid 574 through 586 removed outlier: 4.004A pdb=" N LYS A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 639 removed outlier: 3.604A pdb=" N LEU A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 684 through 693 removed outlier: 3.955A pdb=" N PHE A 693 " --> pdb=" O TRP A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 738 through 751 removed outlier: 3.996A pdb=" N TYR A 742 " --> pdb=" O THR A 738 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 744 " --> pdb=" O ILE A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 779 removed outlier: 3.661A pdb=" N SER A 772 " --> pdb=" O LYS A 768 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 807 Processing helix chain 'A' and resid 823 through 836 removed outlier: 3.767A pdb=" N ASN A 836 " --> pdb=" O GLN A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 865 removed outlier: 4.202A pdb=" N ASN A 865 " --> pdb=" O MET A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 892 Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 912 through 923 Processing helix chain 'A' and resid 936 through 949 removed outlier: 3.608A pdb=" N GLU A 946 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 979 removed outlier: 3.748A pdb=" N CYS A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1006 Processing helix chain 'A' and resid 1018 through 1022 removed outlier: 3.859A pdb=" N TYR A1022 " --> pdb=" O LYS A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1037 Processing helix chain 'A' and resid 1045 through 1049 removed outlier: 3.627A pdb=" N SER A1049 " --> pdb=" O TRP A1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 removed outlier: 3.706A pdb=" N LEU B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 171 " --> pdb=" O TRP B 167 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'B' and resid 272 through 278 removed outlier: 3.933A pdb=" N PHE B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'C' and resid 37 through 41 removed outlier: 3.565A pdb=" N GLU C 40 " --> pdb=" O PRO C 37 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 41 " --> pdb=" O ILE C 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 37 through 41' Processing helix chain 'C' and resid 50 through 59 removed outlier: 4.407A pdb=" N ARG C 56 " --> pdb=" O TRP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 73 Processing helix chain 'C' and resid 94 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.615A pdb=" N PHE A 177 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP A 220 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE A 217 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N THR A 267 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE A 219 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 141 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR A 140 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE A 286 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A 142 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL A 288 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR A 285 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG C 28 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 404 through 405 Processing sheet with id=AA3, first strand: chain 'A' and resid 567 through 572 removed outlier: 6.960A pdb=" N LEU A 645 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 674 " --> pdb=" O ASN A 702 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 701 " --> pdb=" O ARG A 731 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU A 730 " --> pdb=" O SER A 759 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU A 815 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU A 844 " --> pdb=" O SER A 873 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU A 958 " --> pdb=" O ASN A 987 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LEU A 986 " --> pdb=" O GLY A1016 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 328 removed outlier: 5.957A pdb=" N LEU B 284 " --> pdb=" O LYS B 580 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS B 580 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS B 286 " --> pdb=" O HIS B 578 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N HIS B 578 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 288 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N CYS B 556 " --> pdb=" O GLY B 569 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 296 through 300 removed outlier: 3.768A pdb=" N GLY B 315 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 346 through 351 removed outlier: 7.010A pdb=" N VAL B 370 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR B 379 " --> pdb=" O ASP B 372 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 394 through 397 removed outlier: 6.593A pdb=" N VAL B 411 " --> pdb=" O ASN B 424 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN B 424 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 413 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 434 through 437 removed outlier: 3.635A pdb=" N GLY B 445 " --> pdb=" O ASN B 434 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 460 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 471 through 476 removed outlier: 4.274A pdb=" N GLN B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N HIS B 492 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 513 through 518 removed outlier: 6.777A pdb=" N VAL B 528 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU B 516 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA B 526 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N PHE B 518 " --> pdb=" O TRP B 524 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TRP B 524 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY B 529 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE B 533 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 534 " --> pdb=" O GLN B 547 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN B 547 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL B 536 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 49 756 hydrogen bonds defined for protein. 2214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 1.85 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: 4989 1.34 - 1.46: 2586 1.46 - 1.58: 7691 1.58 - 1.70: 9 1.70 - 1.82: 161 Bond restraints: 15436 Sorted by residual: bond pdb=" N ASP A 224 " pdb=" CA ASP A 224 " ideal model delta sigma weight residual 1.455 1.482 -0.026 1.09e-02 8.42e+03 5.80e+00 bond pdb=" C GLU B 154 " pdb=" O GLU B 154 " ideal model delta sigma weight residual 1.234 1.245 -0.011 5.00e-03 4.00e+04 4.75e+00 bond pdb=" N PHE B 137 " pdb=" CA PHE B 137 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.40e+00 bond pdb=" CA LEU A 458 " pdb=" CB LEU A 458 " ideal model delta sigma weight residual 1.531 1.578 -0.047 3.28e-02 9.30e+02 2.06e+00 bond pdb=" C ASP A 224 " pdb=" O ASP A 224 " ideal model delta sigma weight residual 1.234 1.248 -0.014 1.00e-02 1.00e+04 1.89e+00 ... (remaining 15431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.05: 20852 5.05 - 10.09: 34 10.09 - 15.14: 2 15.14 - 20.19: 0 20.19 - 25.24: 3 Bond angle restraints: 20891 Sorted by residual: angle pdb=" N ARG B 207 " pdb=" CA ARG B 207 " pdb=" C ARG B 207 " ideal model delta sigma weight residual 108.76 83.52 25.24 1.58e+00 4.01e-01 2.55e+02 angle pdb=" N ASN B 208 " pdb=" CA ASN B 208 " pdb=" C ASN B 208 " ideal model delta sigma weight residual 111.00 87.71 23.29 2.80e+00 1.28e-01 6.92e+01 angle pdb=" N LEU B 138 " pdb=" CA LEU B 138 " pdb=" C LEU B 138 " ideal model delta sigma weight residual 111.00 89.41 21.59 2.80e+00 1.28e-01 5.95e+01 angle pdb=" C SEP B 139 " pdb=" CA SEP B 139 " pdb=" CB SEP B 139 " ideal model delta sigma weight residual 110.10 96.82 13.28 1.90e+00 2.77e-01 4.89e+01 angle pdb=" N MET A 225 " pdb=" CA MET A 225 " pdb=" C MET A 225 " ideal model delta sigma weight residual 113.28 103.40 9.88 1.57e+00 4.06e-01 3.96e+01 ... (remaining 20886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8213 17.91 - 35.83: 939 35.83 - 53.74: 210 53.74 - 71.66: 34 71.66 - 89.57: 15 Dihedral angle restraints: 9411 sinusoidal: 3788 harmonic: 5623 Sorted by residual: dihedral pdb=" C ARG B 207 " pdb=" N ARG B 207 " pdb=" CA ARG B 207 " pdb=" CB ARG B 207 " ideal model delta harmonic sigma weight residual -122.60 -101.09 -21.51 0 2.50e+00 1.60e-01 7.40e+01 dihedral pdb=" C SEP B 139 " pdb=" N SEP B 139 " pdb=" CA SEP B 139 " pdb=" CB SEP B 139 " ideal model delta harmonic sigma weight residual -122.60 -102.84 -19.76 0 2.50e+00 1.60e-01 6.25e+01 dihedral pdb=" N ASN B 208 " pdb=" C ASN B 208 " pdb=" CA ASN B 208 " pdb=" CB ASN B 208 " ideal model delta harmonic sigma weight residual 122.80 104.81 17.99 0 2.50e+00 1.60e-01 5.18e+01 ... (remaining 9408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2373 0.123 - 0.245: 12 0.245 - 0.368: 1 0.368 - 0.490: 1 0.490 - 0.613: 3 Chirality restraints: 2390 Sorted by residual: chirality pdb=" CA ARG B 207 " pdb=" N ARG B 207 " pdb=" C ARG B 207 " pdb=" CB ARG B 207 " both_signs ideal model delta sigma weight residual False 2.51 3.12 -0.61 2.00e-01 2.50e+01 9.38e+00 chirality pdb=" CA ASN B 208 " pdb=" N ASN B 208 " pdb=" C ASN B 208 " pdb=" CB ASN B 208 " both_signs ideal model delta sigma weight residual False 2.51 3.10 -0.59 2.00e-01 2.50e+01 8.80e+00 chirality pdb=" CA LEU B 138 " pdb=" N LEU B 138 " pdb=" C LEU B 138 " pdb=" CB LEU B 138 " both_signs ideal model delta sigma weight residual False 2.51 3.07 -0.56 2.00e-01 2.50e+01 7.85e+00 ... (remaining 2387 not shown) Planarity restraints: 2659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 227 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.91e+00 pdb=" C ARG D 227 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG D 227 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP D 228 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 244 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO A 245 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 795 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 796 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 796 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 796 " -0.025 5.00e-02 4.00e+02 ... (remaining 2656 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 159 2.64 - 3.20: 13539 3.20 - 3.77: 22784 3.77 - 4.33: 30582 4.33 - 4.90: 51975 Nonbonded interactions: 119039 Sorted by model distance: nonbonded pdb=" N ARG B 207 " pdb=" O ARG B 207 " model vdw 2.072 2.496 nonbonded pdb=" OD1 ASN D 212 " pdb=" N GLU D 213 " model vdw 2.161 3.120 nonbonded pdb=" O THR A 206 " pdb=" OG SER A 210 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASP F 129 " pdb=" OH TYR F 154 " model vdw 2.218 3.040 nonbonded pdb=" N GLU C 64 " pdb=" OE1 GLU C 64 " model vdw 2.233 3.120 ... (remaining 119034 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 'D' and (resid 2 through 97 or resid 99 through 235)) selection = (chain 'F' and (resid 2 through 97 or resid 99 through 235)) } 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=0.35 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.520 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.004 0.047 15436 Z= 0.178 Angle : 0.710 25.236 20891 Z= 0.377 Chirality : 0.047 0.613 2390 Planarity : 0.003 0.045 2659 Dihedral : 15.949 89.570 5745 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.35 % Allowed : 13.31 % Favored : 86.34 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.20), residues: 1889 helix: 2.32 (0.18), residues: 910 sheet: -0.71 (0.32), residues: 303 loop : -2.01 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 457 TYR 0.017 0.001 TYR D 179 PHE 0.015 0.001 PHE A 176 TRP 0.017 0.001 TRP B 273 HIS 0.008 0.001 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00394 (15436) covalent geometry : angle 0.70992 (20891) hydrogen bonds : bond 0.08960 ( 756) hydrogen bonds : angle 4.24127 ( 2214) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 240 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: F 5 GLU cc_start: 0.6085 (mp0) cc_final: 0.5800 (tm-30) REVERT: F 87 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6529 (mp0) REVERT: F 165 MET cc_start: 0.6176 (mtt) cc_final: 0.5370 (mtm) REVERT: D 114 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7008 (pm20) REVERT: D 199 THR cc_start: 0.7774 (m) cc_final: 0.7457 (m) REVERT: A 190 LEU cc_start: 0.6976 (tt) cc_final: 0.6528 (mt) REVERT: A 274 GLU cc_start: 0.7677 (tp30) cc_final: 0.6986 (tm-30) REVERT: A 302 GLU cc_start: 0.6272 (mm-30) cc_final: 0.5966 (mt-10) REVERT: A 599 ARG cc_start: 0.7082 (mtt180) cc_final: 0.6345 (mtt180) REVERT: A 644 GLU cc_start: 0.7618 (mt-10) cc_final: 0.6725 (tm-30) REVERT: A 686 LYS cc_start: 0.6955 (mmtp) cc_final: 0.6636 (mptt) REVERT: A 754 ARG cc_start: 0.7187 (mmt-90) cc_final: 0.6770 (mtm-85) REVERT: A 764 ARG cc_start: 0.6749 (mtp-110) cc_final: 0.6467 (mmt-90) REVERT: A 768 LYS cc_start: 0.7273 (mtmm) cc_final: 0.7015 (ptpt) REVERT: A 771 ILE cc_start: 0.7022 (pt) cc_final: 0.6732 (pp) REVERT: A 781 MET cc_start: 0.6691 (mtm) cc_final: 0.6319 (mmt) REVERT: A 876 MET cc_start: 0.7942 (mtt) cc_final: 0.7708 (mtt) REVERT: A 992 ASP cc_start: 0.7231 (t0) cc_final: 0.6959 (t0) REVERT: A 1051 GLU cc_start: 0.6665 (mp0) cc_final: 0.5854 (tt0) REVERT: B 138 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7146 (pp) REVERT: B 328 ASP cc_start: 0.7862 (t0) cc_final: 0.7637 (t0) REVERT: B 332 GLU cc_start: 0.6938 (tt0) cc_final: 0.5904 (tp30) REVERT: B 439 ASP cc_start: 0.7695 (p0) cc_final: 0.7342 (m-30) REVERT: B 440 ASP cc_start: 0.7313 (t0) cc_final: 0.7060 (t0) REVERT: B 458 MET cc_start: 0.7051 (mpp) cc_final: 0.6727 (mtm) REVERT: B 503 VAL cc_start: 0.8371 (m) cc_final: 0.8168 (p) REVERT: B 508 THR cc_start: 0.5055 (p) cc_final: 0.4796 (t) REVERT: C 67 GLU cc_start: 0.7253 (tp30) cc_final: 0.7047 (tp30) REVERT: C 103 ASN cc_start: 0.7595 (m-40) cc_final: 0.7238 (m-40) outliers start: 6 outliers final: 2 residues processed: 245 average time/residue: 0.6111 time to fit residues: 164.1623 Evaluate side-chains 187 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 184 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain B residue 138 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.0370 chunk 149 optimal weight: 1.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 9 GLN F 16 GLN ** F 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN A 775 ASN A 850 ASN A 877 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122027 restraints weight = 19520.044| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.28 r_work: 0.3158 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15436 Z= 0.106 Angle : 0.536 8.271 20891 Z= 0.277 Chirality : 0.038 0.192 2390 Planarity : 0.003 0.045 2659 Dihedral : 4.229 39.499 2055 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.01 % Allowed : 16.03 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.20), residues: 1889 helix: 2.38 (0.17), residues: 910 sheet: -0.49 (0.33), residues: 284 loop : -2.05 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 417 TYR 0.012 0.001 TYR F 130 PHE 0.011 0.001 PHE A 858 TRP 0.015 0.001 TRP B 319 HIS 0.006 0.001 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00216 (15436) covalent geometry : angle 0.53583 (20891) hydrogen bonds : bond 0.03901 ( 756) hydrogen bonds : angle 3.91088 ( 2214) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 68 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.6428 (pt0) REVERT: D 199 THR cc_start: 0.8520 (m) cc_final: 0.8234 (m) REVERT: A 184 TRP cc_start: 0.5597 (OUTLIER) cc_final: 0.4937 (p90) REVERT: A 188 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.7841 (t) REVERT: A 190 LEU cc_start: 0.6957 (tt) cc_final: 0.6475 (mt) REVERT: A 274 GLU cc_start: 0.8265 (tp30) cc_final: 0.7873 (tm-30) REVERT: A 361 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7749 (t80) REVERT: A 599 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7056 (mtt180) REVERT: A 644 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7905 (tm-30) REVERT: A 686 LYS cc_start: 0.7727 (mmtp) cc_final: 0.7460 (mptt) REVERT: A 754 ARG cc_start: 0.8027 (mmt-90) cc_final: 0.7604 (mtm-85) REVERT: A 764 ARG cc_start: 0.7359 (mtp-110) cc_final: 0.7124 (mmt-90) REVERT: A 768 LYS cc_start: 0.7460 (mtmm) cc_final: 0.7088 (ptpt) REVERT: A 781 MET cc_start: 0.7371 (mtm) cc_final: 0.7013 (mmt) REVERT: A 974 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8329 (m) REVERT: A 1051 GLU cc_start: 0.7041 (mp0) cc_final: 0.6396 (tt0) REVERT: B 138 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7766 (pp) REVERT: B 328 ASP cc_start: 0.8331 (t0) cc_final: 0.8108 (t0) REVERT: B 332 GLU cc_start: 0.8149 (tt0) cc_final: 0.7584 (tp30) REVERT: B 439 ASP cc_start: 0.7768 (p0) cc_final: 0.7446 (m-30) REVERT: B 440 ASP cc_start: 0.7960 (t0) cc_final: 0.7566 (t0) REVERT: B 458 MET cc_start: 0.7367 (mpp) cc_final: 0.7065 (mtm) REVERT: B 503 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8266 (p) REVERT: C 103 ASN cc_start: 0.8841 (m-40) cc_final: 0.8526 (m-40) outliers start: 34 outliers final: 10 residues processed: 214 average time/residue: 0.5942 time to fit residues: 140.6516 Evaluate side-chains 186 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 143 optimal weight: 0.0170 chunk 54 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN F 229 ASN D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN A 775 ASN A 850 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118790 restraints weight = 22045.289| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.88 r_work: 0.3085 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15436 Z= 0.133 Angle : 0.556 7.655 20891 Z= 0.287 Chirality : 0.040 0.211 2390 Planarity : 0.003 0.046 2659 Dihedral : 4.153 32.559 2051 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.37 % Allowed : 17.21 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.20), residues: 1889 helix: 2.31 (0.17), residues: 910 sheet: -0.49 (0.33), residues: 289 loop : -2.04 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 417 TYR 0.013 0.001 TYR F 130 PHE 0.012 0.001 PHE A 177 TRP 0.015 0.001 TRP A 162 HIS 0.006 0.001 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00301 (15436) covalent geometry : angle 0.55569 (20891) hydrogen bonds : bond 0.04361 ( 756) hydrogen bonds : angle 3.92936 ( 2214) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: D 68 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.6352 (pt0) REVERT: D 83 ARG cc_start: 0.6779 (mtm110) cc_final: 0.6263 (tmm-80) REVERT: A 188 SER cc_start: 0.8283 (OUTLIER) cc_final: 0.7818 (t) REVERT: A 190 LEU cc_start: 0.6988 (tt) cc_final: 0.6516 (mt) REVERT: A 274 GLU cc_start: 0.8091 (tp30) cc_final: 0.7688 (tm-30) REVERT: A 361 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7758 (t80) REVERT: A 599 ARG cc_start: 0.7587 (mtt180) cc_final: 0.7035 (mtt180) REVERT: A 644 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7903 (tm-30) REVERT: A 686 LYS cc_start: 0.7731 (mmtp) cc_final: 0.7465 (mptt) REVERT: A 754 ARG cc_start: 0.7968 (mmt-90) cc_final: 0.7581 (mtm-85) REVERT: A 764 ARG cc_start: 0.7288 (mtp-110) cc_final: 0.6623 (ttp-170) REVERT: A 768 LYS cc_start: 0.7385 (mtmm) cc_final: 0.6786 (tmtt) REVERT: A 781 MET cc_start: 0.7210 (mtm) cc_final: 0.6941 (mmt) REVERT: A 974 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8280 (m) REVERT: A 975 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8218 (tm) REVERT: A 1051 GLU cc_start: 0.7021 (mp0) cc_final: 0.6472 (tt0) REVERT: B 138 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7785 (pp) REVERT: B 328 ASP cc_start: 0.8250 (t0) cc_final: 0.8031 (t0) REVERT: B 332 GLU cc_start: 0.7846 (tt0) cc_final: 0.7363 (tp30) REVERT: B 439 ASP cc_start: 0.7723 (p0) cc_final: 0.7439 (m-30) REVERT: B 440 ASP cc_start: 0.7819 (t0) cc_final: 0.7432 (t0) REVERT: B 458 MET cc_start: 0.7240 (mpp) cc_final: 0.7021 (mtm) REVERT: B 503 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8208 (p) REVERT: C 103 ASN cc_start: 0.8783 (m-40) cc_final: 0.8490 (m-40) outliers start: 40 outliers final: 9 residues processed: 208 average time/residue: 0.5970 time to fit residues: 137.6168 Evaluate side-chains 186 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 7 optimal weight: 0.2980 chunk 177 optimal weight: 0.0970 chunk 112 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 9 GLN F 16 GLN D 9 GLN D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.150466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119862 restraints weight = 21662.969| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.77 r_work: 0.3132 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15436 Z= 0.106 Angle : 0.522 8.020 20891 Z= 0.268 Chirality : 0.038 0.171 2390 Planarity : 0.003 0.046 2659 Dihedral : 4.065 29.380 2051 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.77 % Favored : 94.18 % Rotamer: Outliers : 2.37 % Allowed : 18.57 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.20), residues: 1889 helix: 2.30 (0.17), residues: 912 sheet: -0.46 (0.32), residues: 307 loop : -1.96 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 417 TYR 0.012 0.001 TYR F 130 PHE 0.010 0.001 PHE B 278 TRP 0.012 0.001 TRP A 162 HIS 0.004 0.001 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00226 (15436) covalent geometry : angle 0.52160 (20891) hydrogen bonds : bond 0.03901 ( 756) hydrogen bonds : angle 3.85941 ( 2214) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: F 27 MET cc_start: 0.7549 (mmt) cc_final: 0.7252 (mmt) REVERT: F 33 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.7008 (tp) REVERT: D 224 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6897 (mm-40) REVERT: A 188 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.7810 (t) REVERT: A 190 LEU cc_start: 0.6970 (tt) cc_final: 0.6512 (mt) REVERT: A 361 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7718 (t80) REVERT: A 599 ARG cc_start: 0.7531 (mtt180) cc_final: 0.6996 (mtt180) REVERT: A 644 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7877 (tm-30) REVERT: A 680 GLU cc_start: 0.7175 (mp0) cc_final: 0.6958 (mt-10) REVERT: A 686 LYS cc_start: 0.7692 (mmtp) cc_final: 0.7421 (mptt) REVERT: A 754 ARG cc_start: 0.7983 (mmt-90) cc_final: 0.7631 (mtm-85) REVERT: A 768 LYS cc_start: 0.7388 (mtmm) cc_final: 0.6777 (tmtt) REVERT: A 781 MET cc_start: 0.7160 (mtm) cc_final: 0.6937 (mmt) REVERT: A 974 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.8262 (m) REVERT: A 1051 GLU cc_start: 0.6959 (mp0) cc_final: 0.6436 (tt0) REVERT: B 138 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7784 (pp) REVERT: B 332 GLU cc_start: 0.7787 (tt0) cc_final: 0.7345 (tp30) REVERT: B 439 ASP cc_start: 0.7711 (p0) cc_final: 0.7429 (m-30) REVERT: B 440 ASP cc_start: 0.7755 (t0) cc_final: 0.7379 (t0) REVERT: B 503 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8196 (p) REVERT: C 103 ASN cc_start: 0.8739 (m-40) cc_final: 0.8531 (m110) outliers start: 40 outliers final: 15 residues processed: 211 average time/residue: 0.5821 time to fit residues: 135.8067 Evaluate side-chains 190 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 135 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 64 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN A 775 ASN A 866 ASN A 877 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120693 restraints weight = 19512.670| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.24 r_work: 0.3140 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15436 Z= 0.105 Angle : 0.526 9.547 20891 Z= 0.269 Chirality : 0.038 0.167 2390 Planarity : 0.003 0.046 2659 Dihedral : 4.000 28.083 2051 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 2.42 % Allowed : 19.46 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.20), residues: 1889 helix: 2.32 (0.17), residues: 909 sheet: -0.45 (0.32), residues: 309 loop : -1.92 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 764 TYR 0.019 0.001 TYR F 117 PHE 0.009 0.001 PHE B 278 TRP 0.017 0.001 TRP B 167 HIS 0.003 0.001 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00226 (15436) covalent geometry : angle 0.52594 (20891) hydrogen bonds : bond 0.03827 ( 756) hydrogen bonds : angle 3.82418 ( 2214) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.574 Fit side-chains REVERT: F 33 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7085 (tp) REVERT: D 224 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7012 (mm-40) REVERT: A 188 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.7825 (t) REVERT: A 190 LEU cc_start: 0.6850 (tt) cc_final: 0.6412 (mt) REVERT: A 274 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8050 (tm-30) REVERT: A 361 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7841 (t80) REVERT: A 599 ARG cc_start: 0.7632 (mtt180) cc_final: 0.7055 (mtt180) REVERT: A 644 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8019 (tm-30) REVERT: A 680 GLU cc_start: 0.7539 (mp0) cc_final: 0.7215 (mt-10) REVERT: A 686 LYS cc_start: 0.7768 (mmtp) cc_final: 0.7469 (mptt) REVERT: A 754 ARG cc_start: 0.8094 (mmt-90) cc_final: 0.7607 (mpt180) REVERT: A 764 ARG cc_start: 0.7956 (mmt-90) cc_final: 0.7279 (ttp-170) REVERT: A 768 LYS cc_start: 0.7464 (mtmm) cc_final: 0.6726 (tmtt) REVERT: A 781 MET cc_start: 0.7353 (mtm) cc_final: 0.7018 (mmp) REVERT: A 866 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8181 (t0) REVERT: A 974 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8324 (m) REVERT: A 1051 GLU cc_start: 0.7105 (mp0) cc_final: 0.6408 (tt0) REVERT: B 138 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7880 (pp) REVERT: B 332 GLU cc_start: 0.8200 (tt0) cc_final: 0.7648 (tp30) REVERT: B 439 ASP cc_start: 0.7923 (p0) cc_final: 0.7539 (m-30) REVERT: B 440 ASP cc_start: 0.8006 (t0) cc_final: 0.7605 (t0) REVERT: B 503 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8127 (p) outliers start: 41 outliers final: 16 residues processed: 205 average time/residue: 0.5866 time to fit residues: 133.0008 Evaluate side-chains 191 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 182 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 129 optimal weight: 0.0000 chunk 163 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN A 866 ASN C 82 ASN C 103 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.150316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.119615 restraints weight = 27746.725| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.50 r_work: 0.3059 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15436 Z= 0.110 Angle : 0.532 9.453 20891 Z= 0.272 Chirality : 0.038 0.160 2390 Planarity : 0.003 0.046 2659 Dihedral : 4.009 28.218 2051 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.91 % Rotamer: Outliers : 2.37 % Allowed : 19.81 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.20), residues: 1889 helix: 2.30 (0.17), residues: 911 sheet: -0.44 (0.32), residues: 309 loop : -1.91 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 764 TYR 0.033 0.001 TYR F 117 PHE 0.012 0.001 PHE B 278 TRP 0.011 0.001 TRP B 167 HIS 0.010 0.001 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00239 (15436) covalent geometry : angle 0.53200 (20891) hydrogen bonds : bond 0.03864 ( 756) hydrogen bonds : angle 3.82014 ( 2214) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.521 Fit side-chains REVERT: F 27 MET cc_start: 0.7624 (mmt) cc_final: 0.7417 (mmt) REVERT: F 33 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.7006 (tp) REVERT: D 224 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6939 (mm-40) REVERT: A 115 LEU cc_start: -0.0151 (OUTLIER) cc_final: -0.0648 (mp) REVERT: A 188 SER cc_start: 0.8232 (OUTLIER) cc_final: 0.7798 (t) REVERT: A 190 LEU cc_start: 0.6827 (tt) cc_final: 0.6399 (mt) REVERT: A 274 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: A 361 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7805 (t80) REVERT: A 599 ARG cc_start: 0.7561 (mtt180) cc_final: 0.7017 (mtt180) REVERT: A 644 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7948 (tm-30) REVERT: A 680 GLU cc_start: 0.7503 (mp0) cc_final: 0.7186 (mt-10) REVERT: A 686 LYS cc_start: 0.7746 (mmtp) cc_final: 0.7456 (mptt) REVERT: A 754 ARG cc_start: 0.8026 (mmt-90) cc_final: 0.7619 (mtm-85) REVERT: A 781 MET cc_start: 0.7267 (mtm) cc_final: 0.6973 (mmp) REVERT: A 974 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8286 (m) REVERT: A 975 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8205 (tm) REVERT: A 1051 GLU cc_start: 0.7075 (mp0) cc_final: 0.6857 (mp0) REVERT: B 138 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7913 (pp) REVERT: B 332 GLU cc_start: 0.8008 (tt0) cc_final: 0.7509 (tp30) REVERT: B 439 ASP cc_start: 0.7858 (p0) cc_final: 0.7509 (m-30) REVERT: B 440 ASP cc_start: 0.7892 (t0) cc_final: 0.7491 (t0) REVERT: B 503 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8151 (p) outliers start: 40 outliers final: 16 residues processed: 199 average time/residue: 0.5778 time to fit residues: 126.6661 Evaluate side-chains 188 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 104 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 165 optimal weight: 5.9990 chunk 100 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.151210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120425 restraints weight = 22061.922| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.01 r_work: 0.3124 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15436 Z= 0.099 Angle : 0.516 8.324 20891 Z= 0.264 Chirality : 0.038 0.157 2390 Planarity : 0.003 0.045 2659 Dihedral : 3.973 27.675 2051 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.77 % Favored : 94.18 % Rotamer: Outliers : 2.13 % Allowed : 19.93 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.20), residues: 1889 helix: 2.36 (0.17), residues: 910 sheet: -0.37 (0.33), residues: 304 loop : -1.91 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 764 TYR 0.023 0.001 TYR F 117 PHE 0.011 0.001 PHE B 278 TRP 0.015 0.001 TRP B 167 HIS 0.005 0.001 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00207 (15436) covalent geometry : angle 0.51592 (20891) hydrogen bonds : bond 0.03593 ( 756) hydrogen bonds : angle 3.77755 ( 2214) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.549 Fit side-chains REVERT: F 33 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6859 (tp) REVERT: D 224 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6840 (mm-40) REVERT: A 115 LEU cc_start: -0.0152 (OUTLIER) cc_final: -0.0637 (mp) REVERT: A 188 SER cc_start: 0.8214 (OUTLIER) cc_final: 0.7698 (t) REVERT: A 190 LEU cc_start: 0.6819 (tt) cc_final: 0.6408 (mt) REVERT: A 274 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: A 361 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7700 (t80) REVERT: A 599 ARG cc_start: 0.7486 (mtt180) cc_final: 0.7017 (mtt180) REVERT: A 644 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7877 (tm-30) REVERT: A 680 GLU cc_start: 0.7458 (mp0) cc_final: 0.7163 (mt-10) REVERT: A 686 LYS cc_start: 0.7726 (mmtp) cc_final: 0.7446 (mptt) REVERT: A 754 ARG cc_start: 0.7988 (mmt-90) cc_final: 0.7656 (mpt180) REVERT: A 764 ARG cc_start: 0.7806 (mmt-90) cc_final: 0.7244 (ttm110) REVERT: A 781 MET cc_start: 0.7175 (mtm) cc_final: 0.6938 (mmp) REVERT: A 974 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8253 (m) REVERT: A 975 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8203 (tm) REVERT: B 138 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7939 (pp) REVERT: B 332 GLU cc_start: 0.7801 (tt0) cc_final: 0.7373 (tp30) REVERT: B 439 ASP cc_start: 0.7771 (p0) cc_final: 0.7455 (m-30) REVERT: B 440 ASP cc_start: 0.7751 (t0) cc_final: 0.7356 (t0) REVERT: B 503 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8114 (p) outliers start: 36 outliers final: 15 residues processed: 195 average time/residue: 0.5914 time to fit residues: 127.7196 Evaluate side-chains 185 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 89 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 186 optimal weight: 0.0670 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN A 800 HIS ** A 866 ASN ** 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 = 0.3723 r_free = 0.3723 target = 0.149623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118987 restraints weight = 21773.522| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.79 r_work: 0.3097 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15436 Z= 0.125 Angle : 0.556 12.118 20891 Z= 0.282 Chirality : 0.039 0.177 2390 Planarity : 0.003 0.050 2659 Dihedral : 4.066 28.756 2051 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.19 % Favored : 93.75 % Rotamer: Outliers : 2.42 % Allowed : 20.22 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.20), residues: 1889 helix: 2.23 (0.17), residues: 914 sheet: -0.43 (0.32), residues: 308 loop : -1.92 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 764 TYR 0.026 0.001 TYR F 117 PHE 0.010 0.001 PHE B 278 TRP 0.025 0.001 TRP A 162 HIS 0.004 0.001 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00280 (15436) covalent geometry : angle 0.55615 (20891) hydrogen bonds : bond 0.04061 ( 756) hydrogen bonds : angle 3.84111 ( 2214) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.631 Fit side-chains REVERT: F 27 MET cc_start: 0.7571 (mmt) cc_final: 0.7125 (mmt) REVERT: F 33 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6858 (tp) REVERT: D 83 ARG cc_start: 0.6733 (mtm110) cc_final: 0.6235 (tmm-80) REVERT: D 224 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6873 (mm-40) REVERT: A 115 LEU cc_start: -0.0144 (OUTLIER) cc_final: -0.0638 (mp) REVERT: A 188 SER cc_start: 0.8189 (OUTLIER) cc_final: 0.7723 (t) REVERT: A 190 LEU cc_start: 0.6817 (tt) cc_final: 0.6399 (mt) REVERT: A 274 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: A 361 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7728 (t80) REVERT: A 599 ARG cc_start: 0.7576 (mtt180) cc_final: 0.7086 (mtt180) REVERT: A 686 LYS cc_start: 0.7771 (mmtp) cc_final: 0.7489 (mptt) REVERT: A 754 ARG cc_start: 0.8006 (mmt-90) cc_final: 0.7666 (mtm-85) REVERT: A 764 ARG cc_start: 0.7809 (mmt-90) cc_final: 0.7285 (ttm110) REVERT: A 781 MET cc_start: 0.7201 (mtm) cc_final: 0.6957 (mmp) REVERT: A 974 SER cc_start: 0.8575 (OUTLIER) cc_final: 0.8291 (m) REVERT: B 138 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8077 (pp) REVERT: B 332 GLU cc_start: 0.7833 (tt0) cc_final: 0.7399 (tp30) REVERT: B 439 ASP cc_start: 0.7781 (p0) cc_final: 0.7490 (m-30) REVERT: B 440 ASP cc_start: 0.7818 (t0) cc_final: 0.7429 (t0) REVERT: B 503 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8152 (p) outliers start: 41 outliers final: 18 residues processed: 199 average time/residue: 0.6002 time to fit residues: 132.6884 Evaluate side-chains 188 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain C residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 33 optimal weight: 0.0470 chunk 155 optimal weight: 0.0170 chunk 122 optimal weight: 6.9990 chunk 48 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN A 775 ASN A 800 HIS ** A 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.152284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120680 restraints weight = 27779.462| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.73 r_work: 0.3092 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15436 Z= 0.096 Angle : 0.518 11.395 20891 Z= 0.265 Chirality : 0.038 0.156 2390 Planarity : 0.003 0.046 2659 Dihedral : 3.960 27.353 2051 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.61 % Favored : 94.34 % Rotamer: Outliers : 1.83 % Allowed : 20.76 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.20), residues: 1889 helix: 2.35 (0.17), residues: 911 sheet: -0.35 (0.32), residues: 304 loop : -1.89 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 764 TYR 0.023 0.001 TYR F 117 PHE 0.011 0.001 PHE B 278 TRP 0.026 0.001 TRP A 162 HIS 0.004 0.001 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00201 (15436) covalent geometry : angle 0.51810 (20891) hydrogen bonds : bond 0.03445 ( 756) hydrogen bonds : angle 3.75848 ( 2214) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.604 Fit side-chains REVERT: F 33 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6765 (tp) REVERT: D 102 SER cc_start: 0.7687 (m) cc_final: 0.7472 (m) REVERT: D 224 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.6889 (mm-40) REVERT: A 115 LEU cc_start: -0.0181 (OUTLIER) cc_final: -0.0676 (mp) REVERT: A 188 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7809 (t) REVERT: A 190 LEU cc_start: 0.6753 (tt) cc_final: 0.6365 (mt) REVERT: A 274 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: A 361 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7748 (t80) REVERT: A 599 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7007 (mtt180) REVERT: A 686 LYS cc_start: 0.7739 (mmtp) cc_final: 0.7450 (mptt) REVERT: A 754 ARG cc_start: 0.8064 (mmt-90) cc_final: 0.7666 (mpt180) REVERT: A 764 ARG cc_start: 0.7866 (mmt-90) cc_final: 0.7252 (ttm110) REVERT: A 781 MET cc_start: 0.7278 (mtm) cc_final: 0.6961 (mmp) REVERT: A 974 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8269 (m) REVERT: B 138 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8005 (pp) REVERT: B 332 GLU cc_start: 0.7949 (tt0) cc_final: 0.7502 (tp30) REVERT: B 439 ASP cc_start: 0.7820 (p0) cc_final: 0.7506 (m-30) REVERT: B 440 ASP cc_start: 0.7795 (t0) cc_final: 0.7396 (t0) REVERT: B 503 VAL cc_start: 0.8460 (OUTLIER) cc_final: 0.8044 (p) REVERT: C 55 GLU cc_start: 0.6906 (tp30) cc_final: 0.6661 (tp30) outliers start: 31 outliers final: 14 residues processed: 192 average time/residue: 0.5790 time to fit residues: 122.8959 Evaluate side-chains 180 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain C residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 188 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 90 optimal weight: 0.0050 chunk 109 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN ** A 866 ASN ** 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 = 0.3756 r_free = 0.3756 target = 0.152290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121894 restraints weight = 19711.869| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.30 r_work: 0.3162 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15436 Z= 0.099 Angle : 0.535 11.505 20891 Z= 0.272 Chirality : 0.038 0.183 2390 Planarity : 0.003 0.044 2659 Dihedral : 3.931 27.301 2051 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 1.77 % Allowed : 21.17 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.20), residues: 1889 helix: 2.31 (0.17), residues: 911 sheet: -0.34 (0.32), residues: 304 loop : -1.87 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 417 TYR 0.026 0.001 TYR F 117 PHE 0.021 0.001 PHE A 858 TRP 0.024 0.001 TRP A 162 HIS 0.007 0.001 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00209 (15436) covalent geometry : angle 0.53544 (20891) hydrogen bonds : bond 0.03441 ( 756) hydrogen bonds : angle 3.78031 ( 2214) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.647 Fit side-chains REVERT: F 27 MET cc_start: 0.7590 (mmt) cc_final: 0.7108 (mmt) REVERT: F 33 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6790 (tp) REVERT: D 102 SER cc_start: 0.7706 (m) cc_final: 0.7500 (m) REVERT: D 224 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7035 (mm-40) REVERT: A 115 LEU cc_start: -0.0149 (OUTLIER) cc_final: -0.0650 (mp) REVERT: A 188 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7826 (t) REVERT: A 190 LEU cc_start: 0.6746 (tt) cc_final: 0.6355 (mt) REVERT: A 274 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: A 361 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7786 (t80) REVERT: A 599 ARG cc_start: 0.7580 (mtt180) cc_final: 0.7024 (mtt180) REVERT: A 644 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8004 (tm-30) REVERT: A 686 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7491 (mptt) REVERT: A 754 ARG cc_start: 0.8107 (mmt-90) cc_final: 0.7545 (mmt-90) REVERT: A 764 ARG cc_start: 0.7875 (mmt-90) cc_final: 0.7222 (ttp-170) REVERT: A 781 MET cc_start: 0.7319 (mtm) cc_final: 0.6979 (mmp) REVERT: A 974 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8313 (m) REVERT: B 138 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8034 (pp) REVERT: B 332 GLU cc_start: 0.8161 (tt0) cc_final: 0.7692 (tp30) REVERT: B 439 ASP cc_start: 0.7899 (p0) cc_final: 0.7545 (m-30) REVERT: B 440 ASP cc_start: 0.7898 (t0) cc_final: 0.7503 (t0) REVERT: B 503 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8009 (p) REVERT: C 55 GLU cc_start: 0.6880 (tp30) cc_final: 0.6627 (tp30) outliers start: 30 outliers final: 15 residues processed: 180 average time/residue: 0.5986 time to fit residues: 119.2681 Evaluate side-chains 180 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain C residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 0.3980 chunk 139 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN F 111 ASN ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN A 800 HIS A 866 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121645 restraints weight = 19476.167| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.32 r_work: 0.3159 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15436 Z= 0.105 Angle : 0.543 11.389 20891 Z= 0.275 Chirality : 0.038 0.158 2390 Planarity : 0.003 0.043 2659 Dihedral : 3.951 28.054 2051 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.72 % Favored : 94.23 % Rotamer: Outliers : 1.83 % Allowed : 21.11 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.20), residues: 1889 helix: 2.30 (0.17), residues: 914 sheet: -0.40 (0.32), residues: 307 loop : -1.87 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 764 TYR 0.026 0.001 TYR F 117 PHE 0.017 0.001 PHE A 858 TRP 0.021 0.001 TRP A 162 HIS 0.007 0.001 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00229 (15436) covalent geometry : angle 0.54281 (20891) hydrogen bonds : bond 0.03655 ( 756) hydrogen bonds : angle 3.77032 ( 2214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5476.07 seconds wall clock time: 94 minutes 5.05 seconds (5645.05 seconds total)