Starting phenix.real_space_refine on Mon Jan 20 11:11:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xi3_38369/01_2025/8xi3_38369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xi3_38369/01_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_38369/01_2025/8xi3_38369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xi3_38369/01_2025/8xi3_38369.map" model { file = "/net/cci-nas-00/data/ceres_data/8xi3_38369/01_2025/8xi3_38369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xi3_38369/01_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 9.40, per 1000 atoms: 0.62 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: 3.67 Conformation dependent library (CDL) restraints added in 2.0 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: 1.80 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: 5.92 Time building geometry restraints manager: 4.29 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 35.780 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.380 ------------------------------------------------------------------------------- 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= 0.257 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 *********************** 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 : 1.566 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: 1.3537 time to fit residues: 365.7790 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 : 1.627 ------------------------------------------------------------------------------- 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 = 0.149013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117441 restraints weight = 19450.234| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.41 r_work: 0.3103 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 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 = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- 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= 0.192 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 *********************** 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 : 1.659 Fit side-chains revert: symmetry clash REVERT: F 33 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7040 (tp) REVERT: D 68 GLN cc_start: 0.6733 (OUTLIER) cc_final: 0.6365 (pt0) REVERT: D 83 ARG cc_start: 0.6912 (mtm110) cc_final: 0.6377 (tmm-80) REVERT: D 114 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7153 (pm20) REVERT: A 190 LEU cc_start: 0.7003 (tt) cc_final: 0.6492 (mt) REVERT: A 274 GLU cc_start: 0.8291 (tp30) cc_final: 0.7844 (tm-30) REVERT: A 361 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.7865 (t80) REVERT: A 599 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7075 (mtt180) REVERT: A 644 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8033 (tm-30) REVERT: A 686 LYS cc_start: 0.7790 (mmtp) cc_final: 0.7518 (mptt) REVERT: A 754 ARG cc_start: 0.8084 (mmt-90) cc_final: 0.7601 (mtm-85) REVERT: A 768 LYS cc_start: 0.7476 (mtmm) cc_final: 0.7110 (ptpt) REVERT: A 781 MET cc_start: 0.7377 (mtm) cc_final: 0.7015 (mmt) REVERT: A 974 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.8333 (m) REVERT: A 1051 GLU cc_start: 0.7122 (mp0) cc_final: 0.6429 (tt0) REVERT: B 138 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7834 (pp) REVERT: B 328 ASP cc_start: 0.8399 (t0) cc_final: 0.8178 (t0) REVERT: B 332 GLU cc_start: 0.8229 (tt0) cc_final: 0.7653 (tp30) REVERT: B 439 ASP cc_start: 0.7955 (p0) cc_final: 0.7589 (m-30) REVERT: B 440 ASP cc_start: 0.8052 (t0) cc_final: 0.7645 (t0) REVERT: B 458 MET cc_start: 0.7398 (mpp) cc_final: 0.7079 (mtm) REVERT: B 503 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8129 (p) REVERT: C 67 GLU cc_start: 0.8681 (tp30) cc_final: 0.8439 (tp30) REVERT: C 103 ASN cc_start: 0.8861 (m-40) cc_final: 0.8576 (m-40) outliers start: 36 outliers final: 13 residues processed: 209 average time/residue: 1.2823 time to fit residues: 296.7584 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 : 1.622 ------------------------------------------------------------------------------- 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: 0.0570 chunk 103 optimal weight: 0.5980 chunk 187 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.150577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120474 restraints weight = 21672.680| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.76 r_work: 0.3119 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15436 Z= 0.140 Angle : 0.527 8.047 20891 Z= 0.273 Chirality : 0.038 0.200 2390 Planarity : 0.003 0.048 2659 Dihedral : 4.130 31.822 2051 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.31 % Allowed : 17.56 % Favored : 80.13 % 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: 0.59 (0.20), residues: 1889 helix: 2.32 (0.17), residues: 910 sheet: -0.50 (0.32), residues: 307 loop : -1.99 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.005 0.000 ARG A 764 *********************** 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: 39 poor density : 191 time to evaluate : 1.795 Fit side-chains revert: symmetry clash REVERT: A 184 TRP cc_start: 0.5659 (OUTLIER) cc_final: 0.4935 (p90) REVERT: A 188 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.7794 (t) REVERT: A 190 LEU cc_start: 0.6984 (tt) cc_final: 0.6513 (mt) REVERT: A 361 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7708 (t80) REVERT: A 599 ARG cc_start: 0.7574 (mtt180) cc_final: 0.7017 (mtt180) REVERT: A 644 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7874 (tm-30) REVERT: A 680 GLU cc_start: 0.7215 (mp0) cc_final: 0.6961 (mt-10) REVERT: A 686 LYS cc_start: 0.7679 (mmtp) cc_final: 0.7404 (mptt) REVERT: A 754 ARG cc_start: 0.7915 (mmt-90) cc_final: 0.7553 (mtm-85) REVERT: A 764 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6916 (mtp-110) REVERT: A 768 LYS cc_start: 0.7388 (mtmm) cc_final: 0.6782 (tmtt) REVERT: A 781 MET cc_start: 0.7193 (mtm) cc_final: 0.6948 (mmt) REVERT: A 974 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8251 (m) REVERT: A 1051 GLU cc_start: 0.6965 (mp0) cc_final: 0.6428 (tt0) REVERT: B 138 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7698 (pp) REVERT: B 332 GLU cc_start: 0.7858 (tt0) cc_final: 0.7336 (tp30) REVERT: B 420 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7575 (pt0) REVERT: B 439 ASP cc_start: 0.7729 (p0) cc_final: 0.7442 (m-30) REVERT: B 440 ASP cc_start: 0.7777 (t0) cc_final: 0.7398 (t0) REVERT: B 458 MET cc_start: 0.7253 (mpp) cc_final: 0.7047 (mtm) REVERT: B 503 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8185 (p) REVERT: C 67 GLU cc_start: 0.8397 (tp30) cc_final: 0.8187 (tp30) REVERT: C 103 ASN cc_start: 0.8699 (m-40) cc_final: 0.8392 (m-40) outliers start: 39 outliers final: 10 residues processed: 214 average time/residue: 1.2784 time to fit residues: 304.2720 Evaluate side-chains 184 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 214 ASP 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 613 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 764 ARG 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 7 optimal weight: 0.0170 chunk 88 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 102 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- 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 775 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.149972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118738 restraints weight = 27574.326| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.76 r_work: 0.3043 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 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 = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15436 Z= 0.156 Angle : 0.531 8.890 20891 Z= 0.273 Chirality : 0.039 0.169 2390 Planarity : 0.003 0.047 2659 Dihedral : 4.106 28.881 2051 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.77 % Favored : 94.18 % Rotamer: Outliers : 2.19 % Allowed : 19.04 % Favored : 78.77 % 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: 0.61 (0.20), residues: 1889 helix: 2.31 (0.17), residues: 910 sheet: -0.47 (0.32), residues: 308 loop : -1.96 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 162 HIS 0.006 0.001 HIS A 467 PHE 0.010 0.001 PHE A 177 TYR 0.020 0.001 TYR F 117 ARG 0.004 0.000 ARG B 417 *********************** 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 219 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 1.762 Fit side-chains revert: symmetry clash REVERT: D 83 ARG cc_start: 0.6786 (mtm110) cc_final: 0.6264 (tmm-80) REVERT: D 224 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.6979 (mm-40) REVERT: A 184 TRP cc_start: 0.5602 (OUTLIER) cc_final: 0.4912 (p90) REVERT: A 188 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7779 (t) REVERT: A 190 LEU cc_start: 0.6991 (tt) cc_final: 0.6506 (mt) REVERT: A 274 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: A 361 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.7792 (t80) REVERT: A 417 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: A 599 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7012 (mtt180) REVERT: A 644 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7947 (tm-30) REVERT: A 680 GLU cc_start: 0.7398 (mp0) cc_final: 0.7101 (mt-10) REVERT: A 686 LYS cc_start: 0.7741 (mmtp) cc_final: 0.7459 (mptt) REVERT: A 754 ARG cc_start: 0.8052 (mmt-90) cc_final: 0.7615 (mtm-85) REVERT: A 768 LYS cc_start: 0.7400 (mtmm) cc_final: 0.6738 (tmtt) REVERT: A 781 MET cc_start: 0.7289 (mtm) cc_final: 0.6984 (mmt) REVERT: A 974 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.8291 (m) REVERT: A 1051 GLU cc_start: 0.7037 (mp0) cc_final: 0.6400 (tt0) REVERT: B 138 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7831 (pp) REVERT: B 332 GLU cc_start: 0.7980 (tt0) cc_final: 0.7370 (tp30) REVERT: B 439 ASP cc_start: 0.7844 (p0) cc_final: 0.7521 (m-30) REVERT: B 440 ASP cc_start: 0.7897 (t0) cc_final: 0.7501 (t0) REVERT: B 458 MET cc_start: 0.7254 (mpp) cc_final: 0.6997 (mtm) REVERT: B 503 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8181 (p) REVERT: C 67 GLU cc_start: 0.8521 (tp30) cc_final: 0.8292 (tp30) REVERT: C 103 ASN cc_start: 0.8719 (m-40) cc_final: 0.8510 (m110) outliers start: 37 outliers final: 14 residues processed: 206 average time/residue: 1.2736 time to fit residues: 290.9679 Evaluate side-chains 189 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain A residue 184 TRP 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 274 GLU 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 573 ASN 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 503 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 110 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 58 optimal weight: 0.2980 chunk 39 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 11 optimal weight: 0.0000 chunk 71 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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 A 877 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120091 restraints weight = 22234.350| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.86 r_work: 0.3134 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15436 Z= 0.134 Angle : 0.516 8.502 20891 Z= 0.266 Chirality : 0.038 0.165 2390 Planarity : 0.003 0.047 2659 Dihedral : 4.025 27.932 2051 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.56 % Favored : 94.39 % Rotamer: Outliers : 2.13 % Allowed : 19.40 % Favored : 78.47 % 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: 0.62 (0.20), residues: 1889 helix: 2.31 (0.17), residues: 909 sheet: -0.43 (0.32), residues: 305 loop : -1.94 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 162 HIS 0.009 0.001 HIS F 164 PHE 0.009 0.001 PHE B 278 TYR 0.030 0.001 TYR F 117 ARG 0.005 0.000 ARG B 417 *********************** 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 214 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 1.746 Fit side-chains revert: symmetry clash REVERT: D 224 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6901 (mm-40) REVERT: A 115 LEU cc_start: -0.0129 (OUTLIER) cc_final: -0.0600 (mp) REVERT: A 184 TRP cc_start: 0.5574 (OUTLIER) cc_final: 0.4920 (p90) REVERT: A 188 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7792 (t) REVERT: A 190 LEU cc_start: 0.6889 (tt) cc_final: 0.6430 (mt) REVERT: A 274 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: A 361 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7748 (t80) REVERT: A 417 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6511 (tm-30) REVERT: A 599 ARG cc_start: 0.7562 (mtt180) cc_final: 0.7019 (mtt180) REVERT: A 644 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7886 (tm-30) REVERT: A 680 GLU cc_start: 0.7280 (mp0) cc_final: 0.7042 (mt-10) REVERT: A 686 LYS cc_start: 0.7715 (mmtp) cc_final: 0.7430 (mptt) REVERT: A 754 ARG cc_start: 0.8001 (mmt-90) cc_final: 0.7646 (mpt180) REVERT: A 768 LYS cc_start: 0.7432 (mtmm) cc_final: 0.6743 (tmtt) REVERT: A 781 MET cc_start: 0.7190 (mtm) cc_final: 0.6953 (mmt) REVERT: A 866 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8218 (t0) REVERT: A 974 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8255 (m) REVERT: B 138 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7825 (pp) REVERT: B 332 GLU cc_start: 0.7797 (tt0) cc_final: 0.7335 (tp30) REVERT: B 439 ASP cc_start: 0.7728 (p0) cc_final: 0.7457 (m-30) REVERT: B 440 ASP cc_start: 0.7775 (t0) cc_final: 0.7393 (t0) REVERT: B 503 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8182 (p) REVERT: C 55 GLU cc_start: 0.6827 (tp30) cc_final: 0.6622 (tp30) REVERT: C 67 GLU cc_start: 0.8418 (tp30) cc_final: 0.8195 (tp30) outliers start: 36 outliers final: 15 residues processed: 205 average time/residue: 1.2792 time to fit residues: 289.9929 Evaluate side-chains 184 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 184 TRP 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 417 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 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: 0.8980 chunk 60 optimal weight: 20.0000 chunk 150 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN A 866 ASN A 877 ASN C 82 ASN C 103 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.117503 restraints weight = 19285.147| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.21 r_work: 0.3096 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 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 = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15436 Z= 0.269 Angle : 0.620 10.441 20891 Z= 0.317 Chirality : 0.041 0.164 2390 Planarity : 0.004 0.060 2659 Dihedral : 4.352 31.260 2051 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.46 % Favored : 93.49 % Rotamer: Outliers : 2.84 % Allowed : 19.99 % Favored : 77.17 % 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: 0.39 (0.20), residues: 1889 helix: 2.10 (0.17), residues: 905 sheet: -0.45 (0.32), residues: 302 loop : -2.04 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 167 HIS 0.007 0.001 HIS B 334 PHE 0.015 0.002 PHE B 278 TYR 0.022 0.002 TYR F 117 ARG 0.006 0.000 ARG B 417 *********************** 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 227 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 1.719 Fit side-chains REVERT: F 33 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7058 (tp) REVERT: D 224 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7103 (mm-40) REVERT: A 115 LEU cc_start: -0.0021 (OUTLIER) cc_final: -0.0553 (mp) REVERT: A 190 LEU cc_start: 0.6905 (tt) cc_final: 0.6440 (mt) REVERT: A 274 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: A 361 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7937 (t80) REVERT: A 409 ASP cc_start: 0.7315 (m-30) cc_final: 0.6686 (m-30) REVERT: A 599 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7101 (mtt180) REVERT: A 680 GLU cc_start: 0.8022 (mp0) cc_final: 0.7677 (tt0) REVERT: A 686 LYS cc_start: 0.7884 (mmtp) cc_final: 0.7645 (mptt) REVERT: A 754 ARG cc_start: 0.8180 (mmt-90) cc_final: 0.7588 (mmt-90) REVERT: A 764 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7100 (mtp-110) REVERT: A 781 MET cc_start: 0.7440 (mtm) cc_final: 0.7099 (mmp) REVERT: A 974 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.8437 (m) REVERT: B 138 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8256 (pp) REVERT: B 332 GLU cc_start: 0.8217 (tt0) cc_final: 0.7661 (tp30) REVERT: B 439 ASP cc_start: 0.8021 (p0) cc_final: 0.7628 (m-30) REVERT: B 440 ASP cc_start: 0.8129 (t0) cc_final: 0.7716 (t0) REVERT: B 503 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8139 (p) REVERT: C 67 GLU cc_start: 0.8683 (tp30) cc_final: 0.8437 (tp30) outliers start: 48 outliers final: 23 residues processed: 211 average time/residue: 1.2221 time to fit residues: 287.5517 Evaluate side-chains 199 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 33 LEU 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 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 355 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 83 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 HIS A 368 GLN ** 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 = 0.3713 r_free = 0.3713 target = 0.148369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.118614 restraints weight = 19495.334| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.26 r_work: 0.3115 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15436 Z= 0.234 Angle : 0.591 9.884 20891 Z= 0.303 Chirality : 0.041 0.181 2390 Planarity : 0.004 0.050 2659 Dihedral : 4.395 29.645 2051 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.19 % Favored : 93.75 % Rotamer: Outliers : 2.78 % Allowed : 20.52 % Favored : 76.70 % 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: 0.25 (0.20), residues: 1889 helix: 1.96 (0.17), residues: 910 sheet: -0.56 (0.32), residues: 302 loop : -2.08 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 414 HIS 0.005 0.001 HIS B 334 PHE 0.012 0.002 PHE A 693 TYR 0.023 0.001 TYR F 117 ARG 0.007 0.000 ARG D 83 *********************** 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 224 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 1.773 Fit side-chains REVERT: F 27 MET cc_start: 0.7663 (mmt) cc_final: 0.7205 (mmt) REVERT: F 33 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6908 (tp) REVERT: D 83 ARG cc_start: 0.6948 (mtm110) cc_final: 0.6338 (tmm-80) REVERT: D 224 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7037 (mm-40) REVERT: A 115 LEU cc_start: 0.0087 (OUTLIER) cc_final: -0.0463 (mp) REVERT: A 188 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7770 (t) REVERT: A 190 LEU cc_start: 0.6845 (tt) cc_final: 0.6405 (mt) REVERT: A 274 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: A 361 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8072 (t80) REVERT: A 599 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7063 (mtt180) REVERT: A 680 GLU cc_start: 0.8139 (mp0) cc_final: 0.7937 (tt0) REVERT: A 686 LYS cc_start: 0.7834 (mmtp) cc_final: 0.7584 (mptt) REVERT: A 754 ARG cc_start: 0.8156 (mmt-90) cc_final: 0.7551 (mmt-90) REVERT: A 764 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7049 (mtp-110) REVERT: A 781 MET cc_start: 0.7428 (mtm) cc_final: 0.7091 (mmp) REVERT: A 974 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8395 (m) REVERT: B 138 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8198 (pp) REVERT: B 332 GLU cc_start: 0.8177 (tt0) cc_final: 0.7613 (tp30) REVERT: B 440 ASP cc_start: 0.8118 (t0) cc_final: 0.7742 (t0) REVERT: B 503 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8154 (p) REVERT: C 67 GLU cc_start: 0.8610 (tp30) cc_final: 0.8364 (tp30) outliers start: 47 outliers final: 23 residues processed: 207 average time/residue: 1.2445 time to fit residues: 286.4821 Evaluate side-chains 200 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 D residue 68 GLN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 199 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 355 GLN 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 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: 0.5980 chunk 56 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.114709 restraints weight = 19502.271| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.48 r_work: 0.3057 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15436 Z= 0.262 Angle : 0.619 9.916 20891 Z= 0.317 Chirality : 0.041 0.169 2390 Planarity : 0.004 0.052 2659 Dihedral : 4.483 29.922 2051 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.67 % Favored : 93.28 % Rotamer: Outliers : 2.84 % Allowed : 20.88 % Favored : 76.29 % 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: 0.16 (0.20), residues: 1889 helix: 1.87 (0.17), residues: 910 sheet: -0.58 (0.32), residues: 303 loop : -2.11 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 167 HIS 0.006 0.001 HIS B 334 PHE 0.014 0.002 PHE B 278 TYR 0.027 0.002 TYR F 117 ARG 0.006 0.000 ARG B 417 *********************** 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 219 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 1.595 Fit side-chains REVERT: D 214 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7272 (p0) REVERT: A 115 LEU cc_start: 0.0223 (OUTLIER) cc_final: -0.0364 (mp) REVERT: A 190 LEU cc_start: 0.6755 (tt) cc_final: 0.6356 (mt) REVERT: A 274 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: A 361 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.8060 (t80) REVERT: A 599 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7175 (mtt180) REVERT: A 686 LYS cc_start: 0.7827 (mmtp) cc_final: 0.7572 (mptt) REVERT: A 754 ARG cc_start: 0.8169 (mmt-90) cc_final: 0.7546 (mmt-90) REVERT: A 764 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7065 (mtp180) REVERT: A 781 MET cc_start: 0.7489 (mtm) cc_final: 0.7129 (mmp) REVERT: B 332 GLU cc_start: 0.8220 (tt0) cc_final: 0.7749 (tm-30) REVERT: B 439 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7536 (m-30) REVERT: B 440 ASP cc_start: 0.8139 (t0) cc_final: 0.7725 (t0) REVERT: B 503 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8117 (p) REVERT: C 67 GLU cc_start: 0.8625 (tp30) cc_final: 0.8380 (tp30) outliers start: 48 outliers final: 28 residues processed: 202 average time/residue: 1.2425 time to fit residues: 277.8456 Evaluate side-chains 196 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 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 199 THR Chi-restraints excluded: chain D residue 214 ASP 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 355 GLN 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 763 ASN Chi-restraints excluded: chain A residue 764 ARG Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 974 SER 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 439 ASP 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: 0.9990 chunk 179 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.146994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116472 restraints weight = 19339.953| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.17 r_work: 0.3102 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15436 Z= 0.195 Angle : 0.578 9.408 20891 Z= 0.297 Chirality : 0.040 0.185 2390 Planarity : 0.004 0.053 2659 Dihedral : 4.346 22.487 2049 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 2.25 % Allowed : 22.00 % Favored : 75.75 % 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: 0.24 (0.20), residues: 1889 helix: 1.97 (0.17), residues: 910 sheet: -0.56 (0.32), residues: 301 loop : -2.12 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 414 HIS 0.004 0.001 HIS B 334 PHE 0.013 0.001 PHE B 278 TYR 0.025 0.001 TYR F 117 ARG 0.009 0.000 ARG B 174 *********************** 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 209 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 1.882 Fit side-chains REVERT: D 214 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7274 (p0) REVERT: D 224 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7075 (mm-40) REVERT: A 115 LEU cc_start: 0.0298 (OUTLIER) cc_final: -0.0246 (mp) REVERT: A 190 LEU cc_start: 0.6743 (tt) cc_final: 0.6376 (mt) REVERT: A 274 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: A 361 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.8051 (t80) REVERT: A 599 ARG cc_start: 0.7699 (mtt180) cc_final: 0.7151 (mtt180) REVERT: A 686 LYS cc_start: 0.7773 (mmtp) cc_final: 0.7514 (mptt) REVERT: A 754 ARG cc_start: 0.8148 (mmt-90) cc_final: 0.7533 (mmt-90) REVERT: A 764 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7047 (mtp-110) REVERT: A 781 MET cc_start: 0.7447 (mtm) cc_final: 0.7083 (mmp) REVERT: B 332 GLU cc_start: 0.8156 (tt0) cc_final: 0.7726 (tm-30) REVERT: B 439 ASP cc_start: 0.7797 (p0) cc_final: 0.7558 (m-30) REVERT: B 440 ASP cc_start: 0.8093 (t0) cc_final: 0.7678 (t0) REVERT: B 503 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8146 (p) REVERT: C 67 GLU cc_start: 0.8566 (tp30) cc_final: 0.8266 (tp30) outliers start: 38 outliers final: 24 residues processed: 195 average time/residue: 1.2652 time to fit residues: 274.0113 Evaluate side-chains 197 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain D residue 234 THR 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 355 GLN 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 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: 5.9990 chunk 36 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 137 optimal weight: 0.0970 overall best weight: 1.1380 ------------------------------------------------------------------------------- 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** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117568 restraints weight = 21635.547| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.87 r_work: 0.3085 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2111 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= 0.158 Angle : 0.554 9.231 20891 Z= 0.284 Chirality : 0.039 0.158 2390 Planarity : 0.003 0.053 2659 Dihedral : 4.191 21.842 2049 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 2.19 % Allowed : 22.18 % Favored : 75.64 % 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: 0.39 (0.20), residues: 1889 helix: 2.07 (0.17), residues: 910 sheet: -0.53 (0.32), residues: 303 loop : -1.98 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 162 HIS 0.003 0.001 HIS A 104 PHE 0.012 0.001 PHE B 278 TYR 0.023 0.001 TYR F 117 ARG 0.007 0.000 ARG B 174 ********************** 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 203 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 1.777 Fit side-chains REVERT: D 214 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7172 (p0) REVERT: D 224 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6949 (mm-40) REVERT: A 115 LEU cc_start: 0.0275 (OUTLIER) cc_final: -0.0282 (mp) REVERT: A 181 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.5081 (mp0) REVERT: A 188 SER cc_start: 0.8246 (OUTLIER) cc_final: 0.7722 (t) REVERT: A 190 LEU cc_start: 0.6750 (tt) cc_final: 0.6414 (mt) REVERT: A 274 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: A 361 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7910 (t80) REVERT: A 599 ARG cc_start: 0.7601 (mtt180) cc_final: 0.7117 (mtt180) REVERT: A 686 LYS cc_start: 0.7704 (mmtp) cc_final: 0.7442 (mptt) REVERT: A 754 ARG cc_start: 0.8039 (mmt-90) cc_final: 0.7552 (mmt-90) REVERT: A 764 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6896 (mtp-110) REVERT: A 781 MET cc_start: 0.7281 (mtm) cc_final: 0.7014 (mmp) REVERT: B 332 GLU cc_start: 0.7779 (tt0) cc_final: 0.7531 (tm-30) REVERT: B 440 ASP cc_start: 0.7884 (t0) cc_final: 0.7495 (t0) REVERT: B 503 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8193 (p) REVERT: C 67 GLU cc_start: 0.8404 (tp30) cc_final: 0.8171 (tp30) outliers start: 37 outliers final: 23 residues processed: 193 average time/residue: 1.2964 time to fit residues: 276.8555 Evaluate side-chains 194 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 214 ASP 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 181 GLU 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 355 GLN 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 953 SER Chi-restraints excluded: chain A residue 974 SER 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: 10.0000 chunk 173 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.149074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.118694 restraints weight = 21992.198| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.90 r_work: 0.3099 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 15436 Z= 0.156 Angle : 0.556 12.373 20891 Z= 0.284 Chirality : 0.039 0.154 2390 Planarity : 0.004 0.055 2659 Dihedral : 4.110 21.974 2049 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 2.07 % Allowed : 22.35 % Favored : 75.58 % 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: 2.15 (0.17), residues: 904 sheet: -0.43 (0.33), residues: 296 loop : -1.94 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 167 HIS 0.003 0.001 HIS A 104 PHE 0.011 0.001 PHE B 278 TYR 0.022 0.001 TYR F 117 ARG 0.012 0.000 ARG D 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11003.91 seconds wall clock time: 194 minutes 39.49 seconds (11679.49 seconds total)