Starting phenix.real_space_refine on Sun Oct 13 14:29:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xi3_38369/10_2024/8xi3_38369.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xi3_38369/10_2024/8xi3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xi3_38369/10_2024/8xi3_38369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xi3_38369/10_2024/8xi3_38369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xi3_38369/10_2024/8xi3_38369.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xi3_38369/10_2024/8xi3_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 9.97, per 1000 atoms: 0.66 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: 3.96 Conformation dependent library (CDL) restraints added in 2.1 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: 2.18 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: 5.49 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4989 1.34 - 1.46: 2586 1.46 - 1.58: 7691 1.58 - 1.70: 9 1.70 - 1.82: 161 Bond restraints: 15436 Sorted by residual: bond pdb=" N ASP A 224 " pdb=" CA ASP A 224 " ideal model delta sigma weight residual 1.455 1.482 -0.026 1.09e-02 8.42e+03 5.80e+00 bond pdb=" C GLU B 154 " pdb=" O GLU B 154 " ideal model delta sigma weight residual 1.234 1.245 -0.011 5.00e-03 4.00e+04 4.75e+00 bond pdb=" N PHE B 137 " pdb=" CA PHE B 137 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.40e+00 bond pdb=" CA LEU A 458 " pdb=" CB LEU A 458 " ideal model delta sigma weight residual 1.531 1.578 -0.047 3.28e-02 9.30e+02 2.06e+00 bond pdb=" C ASP A 224 " pdb=" O ASP A 224 " ideal model delta sigma weight residual 1.234 1.248 -0.014 1.00e-02 1.00e+04 1.89e+00 ... (remaining 15431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.05: 20852 5.05 - 10.09: 34 10.09 - 15.14: 2 15.14 - 20.19: 0 20.19 - 25.24: 3 Bond angle restraints: 20891 Sorted by residual: angle pdb=" N ARG B 207 " pdb=" CA ARG B 207 " pdb=" C ARG B 207 " ideal model delta sigma weight residual 108.76 83.52 25.24 1.58e+00 4.01e-01 2.55e+02 angle pdb=" N ASN B 208 " pdb=" CA ASN B 208 " pdb=" C ASN B 208 " ideal model delta sigma weight residual 111.00 87.71 23.29 2.80e+00 1.28e-01 6.92e+01 angle pdb=" N LEU B 138 " pdb=" CA LEU B 138 " pdb=" C LEU B 138 " ideal model delta sigma weight residual 111.00 89.41 21.59 2.80e+00 1.28e-01 5.95e+01 angle pdb=" C SEP B 139 " pdb=" CA SEP B 139 " pdb=" CB SEP B 139 " ideal model delta sigma weight residual 110.10 96.82 13.28 1.90e+00 2.77e-01 4.89e+01 angle pdb=" N MET A 225 " pdb=" CA MET A 225 " pdb=" C MET A 225 " ideal model delta sigma weight residual 113.28 103.40 9.88 1.57e+00 4.06e-01 3.96e+01 ... (remaining 20886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8213 17.91 - 35.83: 939 35.83 - 53.74: 210 53.74 - 71.66: 34 71.66 - 89.57: 15 Dihedral angle restraints: 9411 sinusoidal: 3788 harmonic: 5623 Sorted by residual: dihedral pdb=" C ARG B 207 " pdb=" N ARG B 207 " pdb=" CA ARG B 207 " pdb=" CB ARG B 207 " ideal model delta harmonic sigma weight residual -122.60 -101.09 -21.51 0 2.50e+00 1.60e-01 7.40e+01 dihedral pdb=" C SEP B 139 " pdb=" N SEP B 139 " pdb=" CA SEP B 139 " pdb=" CB SEP B 139 " ideal model delta harmonic sigma weight residual -122.60 -102.84 -19.76 0 2.50e+00 1.60e-01 6.25e+01 dihedral pdb=" N ASN B 208 " pdb=" C ASN B 208 " pdb=" CA ASN B 208 " pdb=" CB ASN B 208 " ideal model delta harmonic sigma weight residual 122.80 104.81 17.99 0 2.50e+00 1.60e-01 5.18e+01 ... (remaining 9408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2373 0.123 - 0.245: 12 0.245 - 0.368: 1 0.368 - 0.490: 1 0.490 - 0.613: 3 Chirality restraints: 2390 Sorted by residual: chirality pdb=" CA ARG B 207 " pdb=" N ARG B 207 " pdb=" C ARG B 207 " pdb=" CB ARG B 207 " both_signs ideal model delta sigma weight residual False 2.51 3.12 -0.61 2.00e-01 2.50e+01 9.38e+00 chirality pdb=" CA ASN B 208 " pdb=" N ASN B 208 " pdb=" C ASN B 208 " pdb=" CB ASN B 208 " both_signs ideal model delta sigma weight residual False 2.51 3.10 -0.59 2.00e-01 2.50e+01 8.80e+00 chirality pdb=" CA LEU B 138 " pdb=" N LEU B 138 " pdb=" C LEU B 138 " pdb=" CB LEU B 138 " both_signs ideal model delta sigma weight residual False 2.51 3.07 -0.56 2.00e-01 2.50e+01 7.85e+00 ... (remaining 2387 not shown) Planarity restraints: 2659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 227 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.91e+00 pdb=" C ARG D 227 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG D 227 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP D 228 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 244 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO A 245 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 795 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 796 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 796 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 796 " -0.025 5.00e-02 4.00e+02 ... (remaining 2656 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 159 2.64 - 3.20: 13539 3.20 - 3.77: 22784 3.77 - 4.33: 30582 4.33 - 4.90: 51975 Nonbonded interactions: 119039 Sorted by model distance: nonbonded pdb=" N ARG B 207 " pdb=" O ARG B 207 " model vdw 2.072 2.496 nonbonded pdb=" OD1 ASN D 212 " pdb=" N GLU D 213 " model vdw 2.161 3.120 nonbonded pdb=" O THR A 206 " pdb=" OG SER A 210 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASP F 129 " pdb=" OH TYR F 154 " model vdw 2.218 3.040 nonbonded pdb=" N GLU C 64 " pdb=" OE1 GLU C 64 " model vdw 2.233 3.120 ... (remaining 119034 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 2 through 97 or resid 99 through 235)) selection = (chain 'F' and (resid 2 through 97 or resid 99 through 235)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.35 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.980 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.140 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 6 poor density : 240 time to evaluate : 1.961 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: 1.4733 time to fit residues: 397.2444 Evaluate side-chains 187 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 1.900 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 1.706 Fit side-chains revert: symmetry clash REVERT: D 68 GLN cc_start: 0.6423 (OUTLIER) cc_final: 0.6090 (pt0) REVERT: D 83 ARG cc_start: 0.6425 (mtm110) cc_final: 0.5941 (tmm-80) REVERT: D 114 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6991 (pm20) REVERT: A 190 LEU cc_start: 0.6792 (tt) cc_final: 0.6354 (mt) REVERT: A 274 GLU cc_start: 0.7694 (tp30) cc_final: 0.6915 (tm-30) REVERT: A 302 GLU cc_start: 0.6362 (mm-30) cc_final: 0.6129 (mt-10) REVERT: A 361 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7561 (t80) REVERT: A 368 GLN cc_start: 0.7630 (tp40) cc_final: 0.7372 (tp40) REVERT: A 599 ARG cc_start: 0.7071 (mtt180) cc_final: 0.6371 (mtt180) REVERT: A 644 GLU cc_start: 0.7805 (mt-10) cc_final: 0.6806 (tm-30) REVERT: A 686 LYS cc_start: 0.7034 (mmtp) cc_final: 0.6642 (mptt) REVERT: A 754 ARG cc_start: 0.7248 (mmt-90) cc_final: 0.6825 (mtm-85) REVERT: A 768 LYS cc_start: 0.7288 (mtmm) cc_final: 0.6891 (ptpt) REVERT: A 781 MET cc_start: 0.6654 (mtm) cc_final: 0.6341 (mmt) REVERT: A 825 GLU cc_start: 0.8057 (pm20) cc_final: 0.7851 (pm20) REVERT: A 876 MET cc_start: 0.7959 (mtt) cc_final: 0.7730 (mtt) REVERT: A 974 SER cc_start: 0.7765 (OUTLIER) cc_final: 0.7396 (m) REVERT: A 992 ASP cc_start: 0.7413 (t0) cc_final: 0.7186 (t0) REVERT: A 1051 GLU cc_start: 0.6779 (mp0) cc_final: 0.5914 (tt0) REVERT: B 138 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7448 (pp) REVERT: B 328 ASP cc_start: 0.7862 (t0) cc_final: 0.7626 (t0) REVERT: B 332 GLU cc_start: 0.7069 (tt0) cc_final: 0.6077 (tp30) REVERT: B 439 ASP cc_start: 0.7799 (p0) cc_final: 0.7475 (m-30) REVERT: B 440 ASP cc_start: 0.7621 (t0) cc_final: 0.7136 (t0) REVERT: B 458 MET cc_start: 0.7223 (mpp) cc_final: 0.6955 (mtm) REVERT: B 503 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8028 (p) REVERT: C 67 GLU cc_start: 0.7480 (tp30) cc_final: 0.7166 (tp30) REVERT: C 103 ASN cc_start: 0.7701 (m-40) cc_final: 0.7391 (m-40) outliers start: 36 outliers final: 13 residues processed: 209 average time/residue: 1.4245 time to fit residues: 328.3473 Evaluate side-chains 195 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 THR 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 95 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 47 optimal weight: 0.1980 chunk 171 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 137 optimal weight: 3.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 321 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN A 850 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15436 Z= 0.362 Angle : 0.692 10.190 20891 Z= 0.356 Chirality : 0.044 0.189 2390 Planarity : 0.005 0.074 2659 Dihedral : 4.716 33.703 2051 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.96 % Allowed : 17.92 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.07 (0.20), residues: 1889 helix: 1.79 (0.17), residues: 908 sheet: -0.55 (0.32), residues: 301 loop : -2.18 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 167 HIS 0.011 0.001 HIS B 334 PHE 0.018 0.002 PHE A 177 TYR 0.023 0.002 TYR F 117 ARG 0.010 0.001 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 235 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 185 time to evaluate : 2.140 Fit side-chains REVERT: F 5 GLU cc_start: 0.6277 (tm-30) cc_final: 0.5935 (pt0) REVERT: F 115 THR cc_start: 0.6716 (m) cc_final: 0.6437 (p) REVERT: F 165 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6023 (mtm) REVERT: D 68 GLN cc_start: 0.6479 (OUTLIER) cc_final: 0.6095 (pt0) REVERT: D 114 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7064 (pm20) REVERT: A 190 LEU cc_start: 0.6643 (tt) cc_final: 0.6206 (mt) REVERT: A 274 GLU cc_start: 0.7721 (tp30) cc_final: 0.7189 (tm-30) REVERT: A 361 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7844 (t80) REVERT: A 368 GLN cc_start: 0.7776 (tp40) cc_final: 0.7339 (tp40) REVERT: A 462 GLU cc_start: 0.6446 (mt-10) cc_final: 0.6221 (mp0) REVERT: A 599 ARG cc_start: 0.7252 (mtt180) cc_final: 0.6473 (mtt180) REVERT: A 680 GLU cc_start: 0.7100 (mp0) cc_final: 0.6532 (mt-10) REVERT: A 686 LYS cc_start: 0.7133 (mmtp) cc_final: 0.6804 (mptt) REVERT: A 754 ARG cc_start: 0.7274 (mmt-90) cc_final: 0.6700 (mmt-90) REVERT: A 764 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6347 (mtp-110) REVERT: A 768 LYS cc_start: 0.7384 (mtmm) cc_final: 0.6631 (tmtt) REVERT: A 781 MET cc_start: 0.6797 (mtm) cc_final: 0.6483 (mmp) REVERT: A 876 MET cc_start: 0.7995 (mtt) cc_final: 0.7752 (mtt) REVERT: A 974 SER cc_start: 0.7937 (OUTLIER) cc_final: 0.7533 (m) REVERT: B 138 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7735 (pp) REVERT: B 332 GLU cc_start: 0.7176 (tt0) cc_final: 0.6016 (tp30) REVERT: B 416 LEU cc_start: 0.8389 (mt) cc_final: 0.8107 (mt) REVERT: B 440 ASP cc_start: 0.7712 (t0) cc_final: 0.7231 (t0) REVERT: B 503 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8032 (p) REVERT: C 67 GLU cc_start: 0.7464 (tp30) cc_final: 0.7113 (tp30) REVERT: C 103 ASN cc_start: 0.7555 (m-40) cc_final: 0.7309 (m-40) outliers start: 50 outliers final: 22 residues processed: 213 average time/residue: 1.4409 time to fit residues: 339.3941 Evaluate side-chains 201 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 764 ARG Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain C residue 53 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 0.0470 chunk 129 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 182 optimal weight: 0.2980 chunk 90 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 321 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15436 Z= 0.134 Angle : 0.523 8.836 20891 Z= 0.271 Chirality : 0.038 0.168 2390 Planarity : 0.003 0.049 2659 Dihedral : 4.294 28.343 2051 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.40 % Favored : 94.55 % Rotamer: Outliers : 2.84 % Allowed : 19.40 % Favored : 77.76 % 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: 0.41 (0.20), residues: 1889 helix: 2.16 (0.17), residues: 906 sheet: -0.50 (0.32), residues: 298 loop : -2.08 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 319 HIS 0.005 0.001 HIS F 164 PHE 0.012 0.001 PHE B 278 TYR 0.014 0.001 TYR F 117 ARG 0.005 0.000 ARG D 83 *********************** 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 234 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 186 time to evaluate : 2.256 Fit side-chains REVERT: F 5 GLU cc_start: 0.6267 (tm-30) cc_final: 0.5935 (pt0) REVERT: D 83 ARG cc_start: 0.6296 (mtm110) cc_final: 0.5772 (tmm-80) REVERT: D 114 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7026 (pm20) REVERT: D 199 THR cc_start: 0.7672 (m) cc_final: 0.7131 (m) REVERT: D 224 GLN cc_start: 0.6732 (OUTLIER) cc_final: 0.6325 (mm-40) REVERT: A 115 LEU cc_start: -0.0466 (OUTLIER) cc_final: -0.0889 (mp) REVERT: A 188 SER cc_start: 0.8084 (OUTLIER) cc_final: 0.7649 (t) REVERT: A 190 LEU cc_start: 0.6608 (tt) cc_final: 0.6222 (mt) REVERT: A 344 LYS cc_start: 0.6850 (OUTLIER) cc_final: 0.6607 (tppp) REVERT: A 361 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7707 (t80) REVERT: A 368 GLN cc_start: 0.7675 (tp40) cc_final: 0.7243 (tp40) REVERT: A 599 ARG cc_start: 0.7122 (mtt180) cc_final: 0.6393 (mtt180) REVERT: A 680 GLU cc_start: 0.7021 (mp0) cc_final: 0.6585 (tt0) REVERT: A 686 LYS cc_start: 0.6990 (mmtp) cc_final: 0.6591 (mptt) REVERT: A 754 ARG cc_start: 0.7265 (mmt-90) cc_final: 0.6732 (mmt-90) REVERT: A 764 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6376 (mtp-110) REVERT: A 768 LYS cc_start: 0.7344 (mtmm) cc_final: 0.6493 (tmtt) REVERT: A 781 MET cc_start: 0.6770 (mtm) cc_final: 0.6441 (mmp) REVERT: A 825 GLU cc_start: 0.8091 (pm20) cc_final: 0.7891 (pm20) REVERT: A 876 MET cc_start: 0.7904 (mtt) cc_final: 0.7646 (mtt) REVERT: A 974 SER cc_start: 0.7788 (OUTLIER) cc_final: 0.7405 (m) REVERT: A 1051 GLU cc_start: 0.6852 (mp0) cc_final: 0.5935 (tt0) REVERT: B 138 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7500 (pp) REVERT: B 332 GLU cc_start: 0.7078 (tt0) cc_final: 0.5991 (tp30) REVERT: B 439 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7375 (m-30) REVERT: B 440 ASP cc_start: 0.7649 (t0) cc_final: 0.7166 (t0) REVERT: B 503 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.8042 (p) REVERT: C 67 GLU cc_start: 0.7417 (tp30) cc_final: 0.7060 (tp30) outliers start: 48 outliers final: 15 residues processed: 216 average time/residue: 1.4563 time to fit residues: 347.8850 Evaluate side-chains 198 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 344 LYS 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 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 418 THR 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 57 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 321 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN ** A 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN C 82 ASN C 103 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15436 Z= 0.303 Angle : 0.638 10.220 20891 Z= 0.326 Chirality : 0.042 0.175 2390 Planarity : 0.004 0.059 2659 Dihedral : 4.566 31.761 2051 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.72 % Favored : 93.22 % Rotamer: Outliers : 3.25 % Allowed : 19.93 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1889 helix: 1.85 (0.17), residues: 913 sheet: -0.53 (0.32), residues: 301 loop : -2.17 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 167 HIS 0.007 0.001 HIS B 334 PHE 0.016 0.002 PHE A 177 TYR 0.029 0.002 TYR F 117 ARG 0.004 0.000 ARG A 310 *********************** 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 236 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 181 time to evaluate : 1.797 Fit side-chains REVERT: F 5 GLU cc_start: 0.6504 (tm-30) cc_final: 0.6032 (pt0) REVERT: F 115 THR cc_start: 0.6719 (m) cc_final: 0.6456 (p) REVERT: D 114 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7025 (pm20) REVERT: D 224 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.6282 (mm-40) REVERT: A 115 LEU cc_start: -0.0128 (OUTLIER) cc_final: -0.0609 (mp) REVERT: A 190 LEU cc_start: 0.6597 (tt) cc_final: 0.6214 (mt) REVERT: A 274 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6914 (tm-30) REVERT: A 322 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: A 361 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7751 (t80) REVERT: A 368 GLN cc_start: 0.7690 (tp40) cc_final: 0.7250 (tp40) REVERT: A 599 ARG cc_start: 0.7200 (mtt180) cc_final: 0.6415 (mtt180) REVERT: A 680 GLU cc_start: 0.7320 (mp0) cc_final: 0.6964 (tt0) REVERT: A 686 LYS cc_start: 0.7067 (mmtp) cc_final: 0.6740 (mptt) REVERT: A 754 ARG cc_start: 0.7309 (mmt-90) cc_final: 0.6741 (mmt-90) REVERT: A 764 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6426 (mtp-110) REVERT: A 781 MET cc_start: 0.6759 (mtm) cc_final: 0.6454 (mmp) REVERT: A 825 GLU cc_start: 0.8071 (pm20) cc_final: 0.7706 (pm20) REVERT: A 876 MET cc_start: 0.7942 (mtt) cc_final: 0.7694 (mtt) REVERT: A 974 SER cc_start: 0.7875 (OUTLIER) cc_final: 0.7470 (m) REVERT: B 332 GLU cc_start: 0.7189 (tt0) cc_final: 0.6060 (tp30) REVERT: B 416 LEU cc_start: 0.8393 (mt) cc_final: 0.8129 (mt) REVERT: B 439 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7428 (m-30) REVERT: B 440 ASP cc_start: 0.7744 (t0) cc_final: 0.7216 (t0) REVERT: B 503 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8038 (p) REVERT: C 67 GLU cc_start: 0.7446 (tp30) cc_final: 0.7036 (tp30) outliers start: 55 outliers final: 24 residues processed: 215 average time/residue: 1.4760 time to fit residues: 348.5526 Evaluate side-chains 205 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 172 time to evaluate : 1.806 ------------------------------------------------------------------------------- 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 115 THR Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 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 974 SER Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 418 THR 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 57 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 84 optimal weight: 0.0030 chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 0.0010 chunk 96 optimal weight: 3.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 GLN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 GLN D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN A 866 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15436 Z= 0.130 Angle : 0.522 9.232 20891 Z= 0.270 Chirality : 0.038 0.172 2390 Planarity : 0.003 0.049 2659 Dihedral : 4.237 23.761 2049 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.65 % Rotamer: Outliers : 2.78 % Allowed : 21.11 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1889 helix: 2.14 (0.17), residues: 907 sheet: -0.48 (0.32), residues: 298 loop : -2.10 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 414 HIS 0.005 0.001 HIS F 164 PHE 0.011 0.001 PHE B 278 TYR 0.024 0.001 TYR F 117 ARG 0.006 0.000 ARG D 83 *********************** 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 224 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 177 time to evaluate : 1.769 Fit side-chains REVERT: F 5 GLU cc_start: 0.6428 (tm-30) cc_final: 0.6038 (pt0) REVERT: D 83 ARG cc_start: 0.6328 (mtm110) cc_final: 0.5803 (tmm-80) REVERT: D 114 GLU cc_start: 0.7421 (mm-30) cc_final: 0.6990 (pm20) REVERT: D 224 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6254 (mm-40) REVERT: A 115 LEU cc_start: -0.0127 (OUTLIER) cc_final: -0.0598 (mp) REVERT: A 181 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.4595 (mp0) REVERT: A 188 SER cc_start: 0.7927 (p) cc_final: 0.7500 (t) REVERT: A 190 LEU cc_start: 0.6598 (tt) cc_final: 0.6205 (mt) REVERT: A 274 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6724 (tm-30) REVERT: A 344 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6562 (tppp) REVERT: A 361 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7607 (t80) REVERT: A 368 GLN cc_start: 0.7743 (tp40) cc_final: 0.7222 (tp40) REVERT: A 599 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6414 (mtt180) REVERT: A 680 GLU cc_start: 0.7267 (mp0) cc_final: 0.6933 (tt0) REVERT: A 686 LYS cc_start: 0.6945 (mmtp) cc_final: 0.6601 (mptt) REVERT: A 754 ARG cc_start: 0.7269 (mmt-90) cc_final: 0.6735 (mmt-90) REVERT: A 764 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6398 (mtp180) REVERT: A 781 MET cc_start: 0.6751 (mtm) cc_final: 0.6435 (mmp) REVERT: A 866 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7966 (t0) REVERT: A 876 MET cc_start: 0.7829 (mtt) cc_final: 0.7571 (mtt) REVERT: A 1051 GLU cc_start: 0.6764 (mp0) cc_final: 0.6270 (mp0) REVERT: B 330 ASP cc_start: 0.7935 (p0) cc_final: 0.7451 (p0) REVERT: B 332 GLU cc_start: 0.7119 (tt0) cc_final: 0.6266 (tm-30) REVERT: B 439 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7480 (m-30) REVERT: B 440 ASP cc_start: 0.7680 (t0) cc_final: 0.7178 (t0) REVERT: B 503 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8043 (p) REVERT: C 67 GLU cc_start: 0.7408 (tp30) cc_final: 0.7058 (tp30) outliers start: 47 outliers final: 21 residues processed: 209 average time/residue: 1.4409 time to fit residues: 332.2047 Evaluate side-chains 199 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 168 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F 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 223 ASP Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 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 800 HIS Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain A residue 879 VAL 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 418 THR 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 57 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 GLN F 111 ASN ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15436 Z= 0.189 Angle : 0.554 9.157 20891 Z= 0.285 Chirality : 0.039 0.177 2390 Planarity : 0.004 0.049 2659 Dihedral : 4.229 23.435 2049 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.88 % Favored : 94.07 % Rotamer: Outliers : 2.90 % Allowed : 21.35 % 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: 0.40 (0.20), residues: 1889 helix: 2.11 (0.17), residues: 904 sheet: -0.50 (0.32), residues: 303 loop : -2.02 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 162 HIS 0.006 0.001 HIS F 164 PHE 0.014 0.001 PHE B 278 TYR 0.023 0.001 TYR F 117 ARG 0.004 0.000 ARG B 417 *********************** 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 222 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 173 time to evaluate : 2.161 Fit side-chains REVERT: F 5 GLU cc_start: 0.6465 (tm-30) cc_final: 0.6057 (pt0) REVERT: F 115 THR cc_start: 0.6795 (m) cc_final: 0.6543 (p) REVERT: D 83 ARG cc_start: 0.6487 (mtm110) cc_final: 0.5949 (tmm-80) REVERT: D 114 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6989 (pm20) REVERT: D 224 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6309 (mm-40) REVERT: A 115 LEU cc_start: -0.0234 (OUTLIER) cc_final: -0.0664 (mp) REVERT: A 181 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.4669 (mp0) REVERT: A 188 SER cc_start: 0.7952 (OUTLIER) cc_final: 0.7511 (t) REVERT: A 190 LEU cc_start: 0.6514 (tt) cc_final: 0.6131 (mt) REVERT: A 274 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6673 (tm-30) REVERT: A 322 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: A 344 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6486 (tppp) REVERT: A 361 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7775 (t80) REVERT: A 368 GLN cc_start: 0.7665 (tp40) cc_final: 0.7176 (tp-100) REVERT: A 599 ARG cc_start: 0.7168 (mtt180) cc_final: 0.6472 (mtt180) REVERT: A 680 GLU cc_start: 0.7381 (mp0) cc_final: 0.7029 (tt0) REVERT: A 686 LYS cc_start: 0.7032 (mmtp) cc_final: 0.6694 (mptt) REVERT: A 754 ARG cc_start: 0.7279 (mmt-90) cc_final: 0.6735 (mmt-90) REVERT: A 764 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6421 (mtp-110) REVERT: A 781 MET cc_start: 0.6745 (mtm) cc_final: 0.6430 (mmp) REVERT: A 876 MET cc_start: 0.7856 (mtt) cc_final: 0.7603 (mtt) REVERT: A 974 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7439 (m) REVERT: A 1051 GLU cc_start: 0.6797 (mp0) cc_final: 0.6291 (mp0) REVERT: B 330 ASP cc_start: 0.7970 (p0) cc_final: 0.7425 (p0) REVERT: B 332 GLU cc_start: 0.7147 (tt0) cc_final: 0.6241 (tm-30) REVERT: B 440 ASP cc_start: 0.7741 (t0) cc_final: 0.7227 (t0) REVERT: B 503 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8056 (p) REVERT: C 67 GLU cc_start: 0.7416 (tp30) cc_final: 0.7064 (tp30) outliers start: 49 outliers final: 22 residues processed: 207 average time/residue: 1.4876 time to fit residues: 340.8326 Evaluate side-chains 201 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F 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 261 GLN Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 344 LYS 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 418 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 568 THR 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 112 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 143 optimal weight: 0.0470 chunk 165 optimal weight: 0.7980 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 GLN F 111 ASN D 9 GLN D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15436 Z= 0.150 Angle : 0.531 11.240 20891 Z= 0.273 Chirality : 0.039 0.157 2390 Planarity : 0.003 0.050 2659 Dihedral : 4.135 23.214 2049 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.61 % Favored : 94.34 % Rotamer: Outliers : 2.72 % Allowed : 21.58 % Favored : 75.69 % 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: 0.46 (0.20), residues: 1889 helix: 2.19 (0.17), residues: 904 sheet: -0.42 (0.33), residues: 298 loop : -2.04 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 162 HIS 0.005 0.001 HIS F 164 PHE 0.012 0.001 PHE B 278 TYR 0.022 0.001 TYR F 117 ARG 0.005 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 216 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 170 time to evaluate : 1.877 Fit side-chains REVERT: F 5 GLU cc_start: 0.6518 (tm-30) cc_final: 0.6043 (pt0) REVERT: F 111 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7392 (m-40) REVERT: F 115 THR cc_start: 0.6756 (m) cc_final: 0.6512 (p) REVERT: F 163 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7768 (pp20) REVERT: D 83 ARG cc_start: 0.6457 (mtm110) cc_final: 0.5929 (tmm-80) REVERT: D 114 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6994 (pm20) REVERT: D 224 GLN cc_start: 0.6663 (OUTLIER) cc_final: 0.6300 (mm-40) REVERT: A 115 LEU cc_start: -0.0197 (OUTLIER) cc_final: -0.0626 (mp) REVERT: A 181 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.4734 (mp0) REVERT: A 188 SER cc_start: 0.7999 (OUTLIER) cc_final: 0.7581 (t) REVERT: A 190 LEU cc_start: 0.6495 (tt) cc_final: 0.6162 (mt) REVERT: A 274 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6628 (tm-30) REVERT: A 322 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: A 344 LYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6573 (tppp) REVERT: A 361 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7685 (t80) REVERT: A 599 ARG cc_start: 0.7132 (mtt180) cc_final: 0.6444 (mtt180) REVERT: A 680 GLU cc_start: 0.7369 (mp0) cc_final: 0.7050 (tt0) REVERT: A 686 LYS cc_start: 0.6983 (mmtp) cc_final: 0.6644 (mptt) REVERT: A 754 ARG cc_start: 0.7281 (mmt-90) cc_final: 0.6733 (mmt-90) REVERT: A 764 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6397 (mtp180) REVERT: A 781 MET cc_start: 0.6697 (mtm) cc_final: 0.6390 (mmp) REVERT: A 876 MET cc_start: 0.7849 (mtt) cc_final: 0.7603 (mtt) REVERT: A 974 SER cc_start: 0.7790 (OUTLIER) cc_final: 0.7403 (m) REVERT: A 1051 GLU cc_start: 0.6822 (mp0) cc_final: 0.6331 (mp0) REVERT: B 330 ASP cc_start: 0.7929 (p0) cc_final: 0.7361 (p0) REVERT: B 332 GLU cc_start: 0.7146 (tt0) cc_final: 0.6332 (tm-30) REVERT: B 420 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7502 (pt0) REVERT: B 440 ASP cc_start: 0.7650 (t0) cc_final: 0.7106 (t0) REVERT: B 503 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8057 (p) REVERT: C 67 GLU cc_start: 0.7417 (tp30) cc_final: 0.7070 (tp30) outliers start: 46 outliers final: 20 residues processed: 201 average time/residue: 1.4534 time to fit residues: 322.2472 Evaluate side-chains 200 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 166 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 111 ASN Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F 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 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 322 GLN Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 764 ARG Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 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 420 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain C residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 52 optimal weight: 0.0870 chunk 153 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 15436 Z= 0.198 Angle : 0.743 59.174 20891 Z= 0.424 Chirality : 0.040 0.398 2390 Planarity : 0.004 0.070 2659 Dihedral : 4.135 23.184 2049 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.77 % Favored : 94.18 % Rotamer: Outliers : 2.42 % Allowed : 22.06 % Favored : 75.52 % Cbeta Deviations : 0.05 % 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: 0.44 (0.20), residues: 1889 helix: 2.18 (0.17), residues: 904 sheet: -0.41 (0.33), residues: 298 loop : -2.07 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 162 HIS 0.006 0.001 HIS A 467 PHE 0.012 0.001 PHE B 278 TYR 0.020 0.001 TYR F 117 ARG 0.004 0.000 ARG B 417 *********************** 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 fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 1.739 Fit side-chains REVERT: F 5 GLU cc_start: 0.6519 (tm-30) cc_final: 0.6041 (pt0) REVERT: F 115 THR cc_start: 0.6756 (m) cc_final: 0.6512 (p) REVERT: F 163 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7769 (pp20) REVERT: D 83 ARG cc_start: 0.6456 (mtm110) cc_final: 0.5933 (tmm-80) REVERT: D 114 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6994 (pm20) REVERT: D 224 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6302 (mm-40) REVERT: A 115 LEU cc_start: -0.0196 (OUTLIER) cc_final: -0.0626 (mp) REVERT: A 181 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.4737 (mp0) REVERT: A 188 SER cc_start: 0.8000 (OUTLIER) cc_final: 0.7582 (t) REVERT: A 190 LEU cc_start: 0.6495 (tt) cc_final: 0.6162 (mt) REVERT: A 274 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: A 322 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: A 344 LYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6575 (tppp) REVERT: A 361 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7672 (t80) REVERT: A 599 ARG cc_start: 0.7134 (mtt180) cc_final: 0.6446 (mtt180) REVERT: A 680 GLU cc_start: 0.7371 (mp0) cc_final: 0.7051 (tt0) REVERT: A 686 LYS cc_start: 0.6986 (mmtp) cc_final: 0.6647 (mptt) REVERT: A 754 ARG cc_start: 0.7282 (mmt-90) cc_final: 0.6733 (mmt-90) REVERT: A 764 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6438 (mtp180) REVERT: A 781 MET cc_start: 0.6699 (mtm) cc_final: 0.6391 (mmp) REVERT: A 876 MET cc_start: 0.7851 (mtt) cc_final: 0.7604 (mtt) REVERT: A 974 SER cc_start: 0.7793 (OUTLIER) cc_final: 0.7405 (m) REVERT: A 1051 GLU cc_start: 0.6823 (mp0) cc_final: 0.6331 (mp0) REVERT: B 330 ASP cc_start: 0.7930 (p0) cc_final: 0.7361 (p0) REVERT: B 332 GLU cc_start: 0.7149 (tt0) cc_final: 0.6332 (tm-30) REVERT: B 440 ASP cc_start: 0.7652 (t0) cc_final: 0.7107 (t0) REVERT: B 503 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8058 (p) REVERT: C 67 GLU cc_start: 0.7418 (tp30) cc_final: 0.7070 (tp30) outliers start: 41 outliers final: 23 residues processed: 196 average time/residue: 1.3124 time to fit residues: 286.6483 Evaluate side-chains 202 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain D residue 81 MET 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 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 322 GLN Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 764 ARG Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 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 Chi-restraints excluded: chain C residue 112 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 173 optimal weight: 0.0980 chunk 149 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 15436 Z= 0.198 Angle : 0.743 59.174 20891 Z= 0.424 Chirality : 0.040 0.398 2390 Planarity : 0.004 0.070 2659 Dihedral : 4.135 23.184 2049 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.77 % Favored : 94.18 % Rotamer: Outliers : 2.19 % Allowed : 22.24 % Favored : 75.58 % Cbeta Deviations : 0.05 % 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: 0.44 (0.20), residues: 1889 helix: 2.18 (0.17), residues: 904 sheet: -0.41 (0.33), residues: 298 loop : -2.07 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 162 HIS 0.006 0.001 HIS A 467 PHE 0.012 0.001 PHE B 278 TYR 0.020 0.001 TYR F 117 ARG 0.004 0.000 ARG B 417 ********************** 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 204 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 167 time to evaluate : 1.773 Fit side-chains REVERT: F 5 GLU cc_start: 0.6519 (tm-30) cc_final: 0.6041 (pt0) REVERT: F 115 THR cc_start: 0.6755 (m) cc_final: 0.6512 (p) REVERT: F 163 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7769 (pp20) REVERT: D 83 ARG cc_start: 0.6456 (mtm110) cc_final: 0.5933 (tmm-80) REVERT: D 114 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6994 (pm20) REVERT: D 224 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6302 (mm-40) REVERT: A 115 LEU cc_start: -0.0196 (OUTLIER) cc_final: -0.0626 (mp) REVERT: A 181 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.4737 (mp0) REVERT: A 188 SER cc_start: 0.7999 (OUTLIER) cc_final: 0.7582 (t) REVERT: A 190 LEU cc_start: 0.6495 (tt) cc_final: 0.6162 (mt) REVERT: A 274 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: A 322 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: A 344 LYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6575 (tppp) REVERT: A 361 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7672 (t80) REVERT: A 599 ARG cc_start: 0.7135 (mtt180) cc_final: 0.6446 (mtt180) REVERT: A 680 GLU cc_start: 0.7371 (mp0) cc_final: 0.7051 (tt0) REVERT: A 686 LYS cc_start: 0.6987 (mmtp) cc_final: 0.6647 (mptt) REVERT: A 754 ARG cc_start: 0.7282 (mmt-90) cc_final: 0.6733 (mmt-90) REVERT: A 764 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6438 (mtp180) REVERT: A 781 MET cc_start: 0.6699 (mtm) cc_final: 0.6390 (mmp) REVERT: A 876 MET cc_start: 0.7851 (mtt) cc_final: 0.7604 (mtt) REVERT: A 974 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.7405 (m) REVERT: A 1051 GLU cc_start: 0.6823 (mp0) cc_final: 0.6331 (mp0) REVERT: B 330 ASP cc_start: 0.7930 (p0) cc_final: 0.7361 (p0) REVERT: B 332 GLU cc_start: 0.7148 (tt0) cc_final: 0.6332 (tm-30) REVERT: B 440 ASP cc_start: 0.7650 (t0) cc_final: 0.7109 (t0) REVERT: B 503 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8058 (p) REVERT: C 67 GLU cc_start: 0.7418 (tp30) cc_final: 0.7070 (tp30) outliers start: 37 outliers final: 23 residues processed: 193 average time/residue: 1.4824 time to fit residues: 315.6713 Evaluate side-chains 202 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain D residue 81 MET 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 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 322 GLN Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 764 ARG Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 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 Chi-restraints excluded: chain C residue 112 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 150 optimal weight: 0.2980 chunk 62 optimal weight: 7.9990 chunk 154 optimal weight: 0.0270 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119644 restraints weight = 27484.371| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.43 r_work: 0.3074 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 15436 Z= 0.198 Angle : 0.743 59.173 20891 Z= 0.424 Chirality : 0.040 0.398 2390 Planarity : 0.004 0.070 2659 Dihedral : 4.135 23.184 2049 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.77 % Favored : 94.18 % Rotamer: Outliers : 2.19 % Allowed : 22.24 % Favored : 75.58 % Cbeta Deviations : 0.05 % 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: 0.44 (0.20), residues: 1889 helix: 2.18 (0.17), residues: 904 sheet: -0.41 (0.33), residues: 298 loop : -2.07 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 162 HIS 0.006 0.001 HIS A 467 PHE 0.012 0.001 PHE B 278 TYR 0.020 0.001 TYR F 117 ARG 0.004 0.000 ARG B 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5463.93 seconds wall clock time: 106 minutes 35.01 seconds (6395.01 seconds total)