Starting phenix.real_space_refine on Fri Jun 13 15:14:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xi3_38369/06_2025/8xi3_38369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xi3_38369/06_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_38369/06_2025/8xi3_38369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xi3_38369/06_2025/8xi3_38369.map" model { file = "/net/cci-nas-00/data/ceres_data/8xi3_38369/06_2025/8xi3_38369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xi3_38369/06_2025/8xi3_38369.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'HIS: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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP: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: 9.52, per 1000 atoms: 0.63 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: 3.53 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.77 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: 5.29 Time building geometry restraints manager: 4.24 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.800 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.490 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (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 TRP 0.017 0.001 TRP B 273 HIS 0.008 0.001 HIS F 164 PHE 0.015 0.001 PHE A 176 TYR 0.017 0.001 TYR D 179 ARG 0.006 0.000 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.08960 ( 756) hydrogen bonds : angle 4.24127 ( 2214) covalent geometry : bond 0.00394 (15436) covalent geometry : angle 0.70992 (20891) *********************** 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 : 1.558 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: 1.3610 time to fit residues: 369.0285 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 : 1.823 ------------------------------------------------------------------------------- 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 159 optimal weight: 5.9990 chunk 143 optimal weight: 0.5980 chunk 79 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 C 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.149014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117442 restraints weight = 19450.271| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.41 r_work: 0.3105 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15436 Z= 0.132 Angle : 0.577 9.012 20891 Z= 0.296 Chirality : 0.040 0.175 2390 Planarity : 0.004 0.047 2659 Dihedral : 4.374 37.596 2055 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.13 % Allowed : 15.79 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.20), residues: 1889 helix: 2.26 (0.17), residues: 909 sheet: -0.53 (0.33), residues: 284 loop : -2.06 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 319 HIS 0.007 0.001 HIS F 164 PHE 0.012 0.001 PHE A 177 TYR 0.013 0.001 TYR F 130 ARG 0.003 0.000 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 756) hydrogen bonds : angle 3.99134 ( 2214) covalent geometry : bond 0.00292 (15436) covalent geometry : angle 0.57667 (20891) *********************** 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 227 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 1.587 Fit side-chains revert: symmetry clash REVERT: F 33 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.7043 (tp) REVERT: D 68 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.6370 (pt0) REVERT: D 83 ARG cc_start: 0.6909 (mtm110) cc_final: 0.6377 (tmm-80) REVERT: D 114 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7154 (pm20) REVERT: A 190 LEU cc_start: 0.7017 (tt) cc_final: 0.6505 (mt) REVERT: A 274 GLU cc_start: 0.8292 (tp30) cc_final: 0.7845 (tm-30) REVERT: A 361 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7865 (t80) REVERT: A 599 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7077 (mtt180) REVERT: A 644 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8036 (tm-30) REVERT: A 686 LYS cc_start: 0.7792 (mmtp) cc_final: 0.7521 (mptt) REVERT: A 754 ARG cc_start: 0.8088 (mmt-90) cc_final: 0.7602 (mtm-85) REVERT: A 768 LYS cc_start: 0.7479 (mtmm) cc_final: 0.7113 (ptpt) REVERT: A 781 MET cc_start: 0.7375 (mtm) cc_final: 0.7015 (mmt) REVERT: A 974 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8334 (m) REVERT: A 1051 GLU cc_start: 0.7128 (mp0) cc_final: 0.6424 (tt0) REVERT: B 138 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7835 (pp) REVERT: B 328 ASP cc_start: 0.8399 (t0) cc_final: 0.8178 (t0) REVERT: B 332 GLU cc_start: 0.8226 (tt0) cc_final: 0.7649 (tp30) REVERT: B 439 ASP cc_start: 0.7962 (p0) cc_final: 0.7592 (m-30) REVERT: B 440 ASP cc_start: 0.8051 (t0) cc_final: 0.7643 (t0) REVERT: B 458 MET cc_start: 0.7393 (mpp) cc_final: 0.7074 (mtm) REVERT: B 503 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8128 (p) REVERT: C 67 GLU cc_start: 0.8678 (tp30) cc_final: 0.8434 (tp30) REVERT: C 103 ASN cc_start: 0.8867 (m-40) cc_final: 0.8582 (m-40) outliers start: 36 outliers final: 13 residues processed: 209 average time/residue: 1.2640 time to fit residues: 292.1646 Evaluate side-chains 193 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 115 THR 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 Chi-restraints excluded: chain B residue 506 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 27 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 chunk 121 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 775 ASN A 850 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.149066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.118962 restraints weight = 21667.847| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.78 r_work: 0.3098 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15436 Z= 0.119 Angle : 0.546 8.234 20891 Z= 0.282 Chirality : 0.039 0.207 2390 Planarity : 0.003 0.047 2659 Dihedral : 4.202 31.429 2051 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.42 % Allowed : 17.50 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.20), residues: 1889 helix: 2.26 (0.17), residues: 910 sheet: -0.51 (0.32), residues: 307 loop : -2.01 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 167 HIS 0.005 0.001 HIS F 164 PHE 0.010 0.001 PHE B 278 TYR 0.012 0.001 TYR F 130 ARG 0.004 0.000 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 756) hydrogen bonds : angle 3.97871 ( 2214) covalent geometry : bond 0.00259 (15436) covalent geometry : angle 0.54556 (20891) *********************** 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 230 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: D 68 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.6364 (pt0) REVERT: D 83 ARG cc_start: 0.6769 (mtm110) cc_final: 0.6262 (tmm-80) REVERT: A 184 TRP cc_start: 0.5741 (OUTLIER) cc_final: 0.5025 (p90) REVERT: A 188 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.7838 (t) REVERT: A 190 LEU cc_start: 0.6963 (tt) cc_final: 0.6476 (mt) REVERT: A 361 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7748 (t80) REVERT: A 599 ARG cc_start: 0.7589 (mtt180) cc_final: 0.7028 (mtt180) REVERT: A 644 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7902 (tm-30) REVERT: A 680 GLU cc_start: 0.7295 (mp0) cc_final: 0.7022 (mt-10) REVERT: A 686 LYS cc_start: 0.7707 (mmtp) cc_final: 0.7439 (mptt) REVERT: A 754 ARG cc_start: 0.7941 (mmt-90) cc_final: 0.7559 (mtm-85) REVERT: A 764 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6931 (mtp-110) REVERT: A 768 LYS cc_start: 0.7449 (mtmm) cc_final: 0.6875 (tmtt) REVERT: A 781 MET cc_start: 0.7208 (mtm) cc_final: 0.6954 (OUTLIER) REVERT: A 974 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.8258 (m) REVERT: A 1051 GLU cc_start: 0.6993 (mp0) cc_final: 0.6442 (tt0) REVERT: B 138 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7738 (pp) REVERT: B 332 GLU cc_start: 0.7838 (tt0) cc_final: 0.7343 (tp30) REVERT: B 439 ASP cc_start: 0.7753 (p0) cc_final: 0.7470 (m-30) REVERT: B 440 ASP cc_start: 0.7794 (t0) cc_final: 0.7404 (t0) REVERT: B 458 MET cc_start: 0.7268 (mpp) cc_final: 0.7036 (mtm) REVERT: B 503 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8179 (p) REVERT: C 67 GLU cc_start: 0.8427 (tp30) cc_final: 0.8213 (tp30) REVERT: C 103 ASN cc_start: 0.8716 (m-40) cc_final: 0.8429 (m-40) outliers start: 41 outliers final: 14 residues processed: 212 average time/residue: 1.1879 time to fit residues: 279.6413 Evaluate side-chains 188 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 214 ASP 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 244 GLN Chi-restraints excluded: chain A residue 361 TYR 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 764 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 7 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 0.0010 chunk 102 optimal weight: 0.0870 chunk 61 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 39 optimal weight: 0.0980 overall best weight: 0.4766 ------------------------------------------------------------------------------- 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 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN A 775 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 = 0.3751 r_free = 0.3751 target = 0.152041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121506 restraints weight = 27575.123| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.61 r_work: 0.3067 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15436 Z= 0.096 Angle : 0.502 8.194 20891 Z= 0.259 Chirality : 0.038 0.171 2390 Planarity : 0.003 0.047 2659 Dihedral : 4.020 28.427 2051 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.40 % Favored : 94.55 % Rotamer: Outliers : 1.95 % Allowed : 19.34 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.20), residues: 1889 helix: 2.37 (0.17), residues: 909 sheet: -0.39 (0.32), residues: 303 loop : -1.95 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 162 HIS 0.004 0.001 HIS A 467 PHE 0.010 0.001 PHE B 278 TYR 0.011 0.001 TYR F 130 ARG 0.004 0.000 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 756) hydrogen bonds : angle 3.84941 ( 2214) covalent geometry : bond 0.00195 (15436) covalent geometry : angle 0.50244 (20891) *********************** 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 217 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 199 THR cc_start: 0.8507 (m) cc_final: 0.7935 (m) REVERT: D 224 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6911 (mm-40) REVERT: A 184 TRP cc_start: 0.5564 (OUTLIER) cc_final: 0.4919 (p90) REVERT: A 188 SER cc_start: 0.8222 (p) cc_final: 0.7750 (t) REVERT: A 190 LEU cc_start: 0.6940 (tt) cc_final: 0.6464 (mt) REVERT: A 274 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: A 361 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7786 (t80) REVERT: A 599 ARG cc_start: 0.7594 (mtt180) cc_final: 0.7009 (mtt180) REVERT: A 644 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7868 (tm-30) REVERT: A 680 GLU cc_start: 0.7329 (mp0) cc_final: 0.7056 (mt-10) REVERT: A 686 LYS cc_start: 0.7705 (mmtp) cc_final: 0.7407 (mptt) REVERT: A 754 ARG cc_start: 0.8012 (mmt-90) cc_final: 0.7593 (mpt180) REVERT: A 768 LYS cc_start: 0.7378 (mtmm) cc_final: 0.6702 (tmtt) REVERT: A 781 MET cc_start: 0.7244 (mtm) cc_final: 0.6951 (mmt) REVERT: A 974 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.8235 (m) REVERT: A 1051 GLU cc_start: 0.7013 (mp0) cc_final: 0.6379 (tt0) REVERT: B 138 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7722 (pp) REVERT: B 332 GLU cc_start: 0.8026 (tt0) cc_final: 0.7509 (tp30) REVERT: B 420 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7719 (pt0) REVERT: B 439 ASP cc_start: 0.7821 (p0) cc_final: 0.7493 (m-30) REVERT: B 440 ASP cc_start: 0.7879 (t0) cc_final: 0.7488 (t0) REVERT: B 458 MET cc_start: 0.7260 (mpp) cc_final: 0.7039 (mtm) REVERT: B 503 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8166 (p) REVERT: C 67 GLU cc_start: 0.8529 (tp30) cc_final: 0.8284 (tp30) REVERT: C 103 ASN cc_start: 0.8682 (m-40) cc_final: 0.8403 (m-40) outliers start: 33 outliers final: 13 residues processed: 206 average time/residue: 1.2643 time to fit residues: 288.8831 Evaluate side-chains 189 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 1.670 ------------------------------------------------------------------------------- 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 224 GLN Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 244 GLN 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 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 420 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 110 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 58 optimal weight: 0.0270 chunk 39 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 11 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 overall best weight: 2.6642 ------------------------------------------------------------------------------- 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 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN A 775 ASN ** A 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117328 restraints weight = 22179.243| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.91 r_work: 0.3050 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15436 Z= 0.168 Angle : 0.601 10.670 20891 Z= 0.308 Chirality : 0.041 0.173 2390 Planarity : 0.004 0.054 2659 Dihedral : 4.270 30.858 2051 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.41 % Favored : 93.54 % Rotamer: Outliers : 2.72 % Allowed : 19.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1889 helix: 2.07 (0.17), residues: 911 sheet: -0.48 (0.32), residues: 307 loop : -1.97 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 167 HIS 0.007 0.001 HIS B 334 PHE 0.014 0.002 PHE A 177 TYR 0.024 0.002 TYR F 117 ARG 0.004 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.04919 ( 756) hydrogen bonds : angle 4.01324 ( 2214) covalent geometry : bond 0.00391 (15436) covalent geometry : angle 0.60144 (20891) *********************** 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 227 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 2.595 Fit side-chains REVERT: F 33 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7062 (tp) REVERT: D 224 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6948 (mm-40) REVERT: A 115 LEU cc_start: -0.0161 (OUTLIER) cc_final: -0.0653 (mp) REVERT: A 188 SER cc_start: 0.8258 (OUTLIER) cc_final: 0.7784 (t) REVERT: A 190 LEU cc_start: 0.6850 (tt) cc_final: 0.6386 (mt) REVERT: A 274 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: A 361 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7837 (t80) REVERT: A 417 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6685 (tm-30) REVERT: A 599 ARG cc_start: 0.7656 (mtt180) cc_final: 0.7088 (mtt180) REVERT: A 680 GLU cc_start: 0.7520 (mp0) cc_final: 0.7198 (mt-10) REVERT: A 686 LYS cc_start: 0.7751 (mmtp) cc_final: 0.7493 (mptt) REVERT: A 754 ARG cc_start: 0.8019 (mmt-90) cc_final: 0.7523 (mmt-90) REVERT: A 764 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6972 (mtp-110) REVERT: A 781 MET cc_start: 0.7277 (mtm) cc_final: 0.7004 (mmp) REVERT: A 974 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8294 (m) REVERT: A 975 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8211 (tm) REVERT: B 138 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8059 (pp) REVERT: B 277 ARG cc_start: 0.2833 (OUTLIER) cc_final: 0.1122 (tpp-160) REVERT: B 332 GLU cc_start: 0.7865 (tt0) cc_final: 0.7400 (tp30) REVERT: B 439 ASP cc_start: 0.7803 (p0) cc_final: 0.7457 (m-30) REVERT: B 440 ASP cc_start: 0.7886 (t0) cc_final: 0.7501 (t0) REVERT: B 503 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8224 (p) REVERT: C 67 GLU cc_start: 0.8454 (tp30) cc_final: 0.8203 (tp30) REVERT: C 103 ASN cc_start: 0.8678 (m-40) cc_final: 0.8410 (m-40) outliers start: 46 outliers final: 22 residues processed: 211 average time/residue: 1.2186 time to fit residues: 286.4302 Evaluate side-chains 204 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 99 ASP 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 244 GLN Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 568 VAL 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 764 ARG 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 277 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 177 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 64 optimal weight: 0.0050 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN ** 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 775 ASN A 866 ASN A 934 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.148254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118367 restraints weight = 19305.398| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.26 r_work: 0.3083 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15436 Z= 0.128 Angle : 0.559 9.555 20891 Z= 0.286 Chirality : 0.039 0.161 2390 Planarity : 0.004 0.047 2659 Dihedral : 4.255 29.379 2051 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.02 % Rotamer: Outliers : 2.42 % Allowed : 20.76 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1889 helix: 2.14 (0.17), residues: 908 sheet: -0.51 (0.32), residues: 302 loop : -2.03 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 167 HIS 0.009 0.001 HIS F 164 PHE 0.011 0.001 PHE B 278 TYR 0.038 0.001 TYR F 117 ARG 0.005 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 756) hydrogen bonds : angle 3.96189 ( 2214) covalent geometry : bond 0.00289 (15436) covalent geometry : angle 0.55932 (20891) *********************** 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 215 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 1.779 Fit side-chains REVERT: F 115 THR cc_start: 0.6852 (m) cc_final: 0.6597 (p) REVERT: D 83 ARG cc_start: 0.6874 (mtm110) cc_final: 0.6245 (tmm-80) REVERT: D 224 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7098 (mm-40) REVERT: A 115 LEU cc_start: -0.0134 (OUTLIER) cc_final: -0.0631 (mp) REVERT: A 188 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.7787 (t) REVERT: A 190 LEU cc_start: 0.6827 (tt) cc_final: 0.6362 (mt) REVERT: A 274 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: A 361 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7932 (t80) REVERT: A 599 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7072 (mtt180) REVERT: A 680 GLU cc_start: 0.7868 (mp0) cc_final: 0.7566 (tt0) REVERT: A 686 LYS cc_start: 0.7782 (mmtp) cc_final: 0.7498 (mptt) REVERT: A 754 ARG cc_start: 0.8114 (mmt-90) cc_final: 0.7508 (mmt-90) REVERT: A 764 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7031 (mtp-110) REVERT: A 781 MET cc_start: 0.7438 (mtm) cc_final: 0.7060 (mmp) REVERT: A 866 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8259 (t0) REVERT: A 974 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8339 (m) REVERT: A 975 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8241 (tm) REVERT: A 1051 GLU cc_start: 0.7156 (mp0) cc_final: 0.6759 (mp0) REVERT: B 138 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8081 (pp) REVERT: B 330 ASP cc_start: 0.8653 (p0) cc_final: 0.8329 (p0) REVERT: B 332 GLU cc_start: 0.8171 (tt0) cc_final: 0.7570 (tp30) REVERT: B 439 ASP cc_start: 0.7963 (p0) cc_final: 0.7566 (m-30) REVERT: B 440 ASP cc_start: 0.8078 (t0) cc_final: 0.7687 (t0) REVERT: B 503 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8172 (p) REVERT: C 67 GLU cc_start: 0.8680 (tp30) cc_final: 0.8407 (tp30) outliers start: 41 outliers final: 15 residues processed: 200 average time/residue: 1.2283 time to fit residues: 272.1585 Evaluate side-chains 194 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 GLN 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 244 GLN 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 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 764 ARG 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 A residue 975 LEU Chi-restraints excluded: chain B residue 138 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 83 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 178 optimal weight: 8.9990 chunk 62 optimal weight: 0.0870 chunk 125 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- 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 9 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 775 ASN A 866 ASN C 103 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118795 restraints weight = 19507.842| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.32 r_work: 0.3092 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15436 Z= 0.118 Angle : 0.548 8.975 20891 Z= 0.281 Chirality : 0.039 0.176 2390 Planarity : 0.003 0.046 2659 Dihedral : 4.222 28.935 2051 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 2.84 % Allowed : 20.52 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1889 helix: 2.16 (0.17), residues: 908 sheet: -0.54 (0.32), residues: 308 loop : -1.98 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 162 HIS 0.003 0.001 HIS F 164 PHE 0.013 0.001 PHE B 278 TYR 0.028 0.001 TYR F 117 ARG 0.005 0.000 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 756) hydrogen bonds : angle 3.93418 ( 2214) covalent geometry : bond 0.00260 (15436) covalent geometry : angle 0.54756 (20891) *********************** 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 220 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 172 time to evaluate : 1.831 Fit side-chains REVERT: F 33 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6931 (tp) REVERT: F 165 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6028 (mtm) REVERT: D 83 ARG cc_start: 0.6854 (mtm110) cc_final: 0.6255 (tmm-80) REVERT: D 224 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7098 (mm-40) REVERT: A 115 LEU cc_start: -0.0137 (OUTLIER) cc_final: -0.0633 (mp) REVERT: A 188 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.7713 (t) REVERT: A 190 LEU cc_start: 0.6799 (tt) cc_final: 0.6338 (mt) REVERT: A 274 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: A 361 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7904 (t80) REVERT: A 599 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7079 (mtt180) REVERT: A 680 GLU cc_start: 0.7944 (mp0) cc_final: 0.7683 (tt0) REVERT: A 686 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7495 (mptt) REVERT: A 754 ARG cc_start: 0.8118 (mmt-90) cc_final: 0.7509 (mmt-90) REVERT: A 764 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7064 (mtp-110) REVERT: A 781 MET cc_start: 0.7443 (mtm) cc_final: 0.7067 (mmp) REVERT: A 974 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8345 (m) REVERT: A 1051 GLU cc_start: 0.7153 (mp0) cc_final: 0.6739 (mp0) REVERT: B 138 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8071 (pp) REVERT: B 330 ASP cc_start: 0.8618 (p0) cc_final: 0.8285 (p0) REVERT: B 332 GLU cc_start: 0.8187 (tt0) cc_final: 0.7595 (tp30) REVERT: B 439 ASP cc_start: 0.7954 (p0) cc_final: 0.7567 (m-30) REVERT: B 440 ASP cc_start: 0.8080 (t0) cc_final: 0.7696 (t0) REVERT: B 458 MET cc_start: 0.7307 (mpp) cc_final: 0.7041 (mtm) REVERT: B 503 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8156 (p) REVERT: C 67 GLU cc_start: 0.8686 (tp30) cc_final: 0.8414 (tp30) outliers start: 48 outliers final: 22 residues processed: 202 average time/residue: 1.2211 time to fit residues: 273.7180 Evaluate side-chains 193 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain D residue 68 GLN 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 244 GLN Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 261 GLN 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 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 764 ARG 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 392 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 84 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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** D 188 ASN A 144 HIS ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN C 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.146024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116070 restraints weight = 19395.236| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.27 r_work: 0.3057 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15436 Z= 0.182 Angle : 0.624 11.613 20891 Z= 0.319 Chirality : 0.042 0.198 2390 Planarity : 0.004 0.057 2659 Dihedral : 4.420 30.712 2051 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.78 % Favored : 93.17 % Rotamer: Outliers : 2.90 % Allowed : 20.76 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1889 helix: 1.98 (0.17), residues: 905 sheet: -0.49 (0.32), residues: 302 loop : -2.04 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1018 HIS 0.006 0.001 HIS B 334 PHE 0.014 0.002 PHE A 565 TYR 0.034 0.002 TYR F 117 ARG 0.005 0.000 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.05135 ( 756) hydrogen bonds : angle 4.05256 ( 2214) covalent geometry : bond 0.00431 (15436) covalent geometry : angle 0.62440 (20891) *********************** 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 222 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 1.719 Fit side-chains REVERT: F 27 MET cc_start: 0.7697 (mmt) cc_final: 0.7279 (mmt) REVERT: F 115 THR cc_start: 0.6908 (m) cc_final: 0.6706 (p) REVERT: F 165 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6163 (mtm) REVERT: D 214 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7246 (p0) REVERT: D 224 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7132 (mm-40) REVERT: A 115 LEU cc_start: 0.0008 (OUTLIER) cc_final: -0.0530 (mp) REVERT: A 190 LEU cc_start: 0.6790 (tt) cc_final: 0.6352 (mt) REVERT: A 274 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: A 361 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8127 (t80) REVERT: A 599 ARG cc_start: 0.7738 (mtt180) cc_final: 0.7137 (mtt180) REVERT: A 686 LYS cc_start: 0.7818 (mmtp) cc_final: 0.7559 (mptt) REVERT: A 754 ARG cc_start: 0.8153 (mmt-90) cc_final: 0.7533 (mmt-90) REVERT: A 764 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7062 (mtp-110) REVERT: A 781 MET cc_start: 0.7486 (mtm) cc_final: 0.7104 (mmp) REVERT: A 974 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8384 (m) REVERT: B 138 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8199 (pp) REVERT: B 330 ASP cc_start: 0.8678 (p0) cc_final: 0.8328 (p0) REVERT: B 332 GLU cc_start: 0.8187 (tt0) cc_final: 0.7598 (tp30) REVERT: B 439 ASP cc_start: 0.7976 (p0) cc_final: 0.7681 (m-30) REVERT: B 440 ASP cc_start: 0.8156 (t0) cc_final: 0.7749 (t0) REVERT: B 458 MET cc_start: 0.7269 (mpp) cc_final: 0.7028 (mtm) REVERT: B 503 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8134 (p) REVERT: C 67 GLU cc_start: 0.8647 (tp30) cc_final: 0.8378 (tp30) outliers start: 49 outliers final: 26 residues processed: 203 average time/residue: 1.2517 time to fit residues: 282.1350 Evaluate side-chains 204 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 214 ASP 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 244 GLN Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 568 VAL 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 764 ARG 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 392 GLN 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 13 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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** D 9 GLN D 188 ASN ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116784 restraints weight = 19234.841| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.20 r_work: 0.3091 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1972 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= 0.123 Angle : 0.564 11.127 20891 Z= 0.288 Chirality : 0.039 0.182 2390 Planarity : 0.003 0.047 2659 Dihedral : 4.307 28.726 2051 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.88 % Favored : 94.07 % Rotamer: Outliers : 2.60 % Allowed : 21.29 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1889 helix: 2.07 (0.17), residues: 907 sheet: -0.58 (0.32), residues: 308 loop : -2.02 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 162 HIS 0.005 0.001 HIS A 321 PHE 0.012 0.001 PHE B 278 TYR 0.032 0.001 TYR F 117 ARG 0.007 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 756) hydrogen bonds : angle 3.97544 ( 2214) covalent geometry : bond 0.00274 (15436) covalent geometry : angle 0.56413 (20891) *********************** 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 217 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 1.595 Fit side-chains REVERT: D 214 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7224 (p0) REVERT: D 224 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7095 (mm-40) REVERT: A 115 LEU cc_start: 0.0145 (OUTLIER) cc_final: -0.0409 (mp) REVERT: A 188 SER cc_start: 0.8243 (OUTLIER) cc_final: 0.7737 (t) REVERT: A 190 LEU cc_start: 0.6776 (tt) cc_final: 0.6343 (mt) REVERT: A 361 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7958 (t80) REVERT: A 599 ARG cc_start: 0.7709 (mtt180) cc_final: 0.7133 (mtt180) REVERT: A 686 LYS cc_start: 0.7752 (mmtp) cc_final: 0.7474 (mptt) REVERT: A 754 ARG cc_start: 0.8128 (mmt-90) cc_final: 0.7511 (mmt-90) REVERT: A 764 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7003 (mtp-110) REVERT: A 781 MET cc_start: 0.7435 (mtm) cc_final: 0.7068 (mmp) REVERT: A 1051 GLU cc_start: 0.7191 (mp0) cc_final: 0.6784 (mp0) REVERT: B 138 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8109 (pp) REVERT: B 332 GLU cc_start: 0.8148 (tt0) cc_final: 0.7727 (tm-30) REVERT: B 439 ASP cc_start: 0.7996 (p0) cc_final: 0.7695 (m-30) REVERT: B 440 ASP cc_start: 0.8105 (t0) cc_final: 0.7703 (t0) REVERT: B 458 MET cc_start: 0.7271 (mpp) cc_final: 0.7006 (mtm) REVERT: B 503 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8160 (p) REVERT: C 67 GLU cc_start: 0.8633 (tp30) cc_final: 0.8366 (tp30) outliers start: 44 outliers final: 24 residues processed: 201 average time/residue: 1.1879 time to fit residues: 265.0685 Evaluate side-chains 193 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 214 ASP 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 250 MET Chi-restraints excluded: chain A residue 267 THR 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 764 ARG 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 392 GLN 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 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 321 HIS ** 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 = 0.3698 r_free = 0.3698 target = 0.147566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117021 restraints weight = 21470.758| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.82 r_work: 0.3061 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15436 Z= 0.133 Angle : 0.587 11.230 20891 Z= 0.300 Chirality : 0.040 0.178 2390 Planarity : 0.004 0.058 2659 Dihedral : 4.323 29.114 2051 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.14 % Favored : 93.81 % Rotamer: Outliers : 2.31 % Allowed : 21.70 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1889 helix: 2.04 (0.17), residues: 907 sheet: -0.49 (0.33), residues: 296 loop : -2.03 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 414 HIS 0.006 0.001 HIS F 164 PHE 0.012 0.001 PHE B 278 TYR 0.033 0.001 TYR F 117 ARG 0.012 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 756) hydrogen bonds : angle 3.99043 ( 2214) covalent geometry : bond 0.00300 (15436) covalent geometry : angle 0.58718 (20891) ********************** 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 202 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 1.576 Fit side-chains REVERT: F 27 MET cc_start: 0.7502 (mmt) cc_final: 0.7093 (mmt) REVERT: F 166 GLN cc_start: 0.7542 (pt0) cc_final: 0.6822 (pm20) REVERT: D 214 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7244 (p0) REVERT: D 224 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6973 (mm-40) REVERT: A 115 LEU cc_start: 0.0109 (OUTLIER) cc_final: -0.0427 (mp) REVERT: A 190 LEU cc_start: 0.6821 (tt) cc_final: 0.6394 (mt) REVERT: A 274 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7712 (tm-30) REVERT: A 361 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.7939 (t80) REVERT: A 599 ARG cc_start: 0.7612 (mtt180) cc_final: 0.7107 (mtt180) REVERT: A 686 LYS cc_start: 0.7713 (mmtp) cc_final: 0.7447 (mptt) REVERT: A 754 ARG cc_start: 0.8016 (mmt-90) cc_final: 0.7505 (mmt-90) REVERT: A 764 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6886 (mtp-110) REVERT: A 781 MET cc_start: 0.7273 (mtm) cc_final: 0.7004 (mmp) REVERT: A 1051 GLU cc_start: 0.6985 (mp0) cc_final: 0.6582 (mp0) REVERT: B 138 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8113 (pp) REVERT: B 332 GLU cc_start: 0.7811 (tt0) cc_final: 0.7286 (tp30) REVERT: B 439 ASP cc_start: 0.7833 (p0) cc_final: 0.7627 (m-30) REVERT: B 440 ASP cc_start: 0.7952 (t0) cc_final: 0.7560 (t0) REVERT: B 458 MET cc_start: 0.7222 (mpp) cc_final: 0.6971 (mtm) REVERT: B 503 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8210 (p) REVERT: C 67 GLU cc_start: 0.8412 (tp30) cc_final: 0.8160 (tp30) outliers start: 39 outliers final: 23 residues processed: 191 average time/residue: 1.2136 time to fit residues: 257.2474 Evaluate side-chains 190 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 214 ASP 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 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 764 ARG 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 392 GLN 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 84 optimal weight: 0.0970 chunk 173 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 47 optimal weight: 0.0050 chunk 83 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 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 ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.150806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120711 restraints weight = 21981.595| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.74 r_work: 0.3139 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2050 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= 0.100 Angle : 0.541 10.797 20891 Z= 0.275 Chirality : 0.038 0.157 2390 Planarity : 0.003 0.055 2659 Dihedral : 4.104 27.570 2051 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.40 % Favored : 94.55 % Rotamer: Outliers : 1.48 % Allowed : 22.65 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1889 helix: 2.19 (0.17), residues: 911 sheet: -0.35 (0.33), residues: 292 loop : -1.94 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 162 HIS 0.007 0.001 HIS F 164 PHE 0.012 0.001 PHE B 278 TYR 0.029 0.001 TYR F 117 ARG 0.011 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 756) hydrogen bonds : angle 3.85759 ( 2214) covalent geometry : bond 0.00210 (15436) covalent geometry : angle 0.54094 (20891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11272.58 seconds wall clock time: 193 minutes 32.41 seconds (11612.41 seconds total)