Starting phenix.real_space_refine on Wed Feb 4 15:27:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l4j_62813/02_2026/9l4j_62813.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l4j_62813/02_2026/9l4j_62813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l4j_62813/02_2026/9l4j_62813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l4j_62813/02_2026/9l4j_62813.map" model { file = "/net/cci-nas-00/data/ceres_data/9l4j_62813/02_2026/9l4j_62813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l4j_62813/02_2026/9l4j_62813.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 Zn 1 6.06 5 S 96 5.16 5 C 7191 2.51 5 N 1941 2.21 5 O 2064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11293 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7303 Classifications: {'peptide': 927} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 25, 'TRANS': 901} Chain breaks: 3 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2817 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 719 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "E" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 453 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11063 SG CYS E 60 78.980 55.819 57.335 1.00 32.86 S ATOM 11088 SG CYS E 63 80.919 53.552 54.929 1.00 26.47 S Time building chain proxies: 2.33, per 1000 atoms: 0.21 Number of scatterers: 11293 At special positions: 0 Unit cell: (97.75, 107.95, 114.75, 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) Zn 1 29.99 S 96 16.00 O 2064 8.00 N 1941 7.00 C 7191 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: 0.89 Conformation dependent library (CDL) restraints added in 466.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 101 " pdb="ZN ZN E 101 " - pdb=" NE2 HIS E 88 " pdb="ZN ZN E 101 " - pdb=" NE2 HIS E 83 " pdb="ZN ZN E 101 " - pdb=" SG CYS E 63 " pdb="ZN ZN E 101 " - pdb=" SG CYS E 60 " Number of angles added : 2 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 14 sheets defined 42.0% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.726A pdb=" N LYS A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 165 removed outlier: 3.616A pdb=" N LEU A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 198 removed outlier: 3.826A pdb=" N GLU A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 209 removed outlier: 3.508A pdb=" N MET A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 213 removed outlier: 6.397A pdb=" N GLU A 213 " --> pdb=" O SER A 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 210 through 213' Processing helix chain 'A' and resid 221 through 228 removed outlier: 3.658A pdb=" N ASP A 224 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER A 227 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 272 through 277 removed outlier: 4.117A pdb=" N LEU A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 302 removed outlier: 3.578A pdb=" N GLU A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.890A pdb=" N VAL A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.558A 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 347 through 350 removed outlier: 3.698A pdb=" N CYS A 350 " --> pdb=" O GLY A 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 350' Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.515A pdb=" N GLN A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 407 through 413 removed outlier: 3.503A pdb=" N TYR A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 424 Processing helix chain 'A' and resid 444 through 454 removed outlier: 3.588A pdb=" N GLN A 448 " --> pdb=" O HIS A 444 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 488 through 498 Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.883A pdb=" N THR A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 532 removed outlier: 3.992A pdb=" N LYS A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.691A pdb=" N GLU A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 Processing helix chain 'A' and resid 575 through 586 removed outlier: 3.589A pdb=" N LYS A 579 " --> pdb=" O LYS A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'A' and resid 685 through 695 removed outlier: 3.727A pdb=" N LYS A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 691 " --> pdb=" O HIS A 687 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 693 " --> pdb=" O TRP A 689 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 738 through 751 removed outlier: 3.697A pdb=" N ILE A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 778 Processing helix chain 'A' and resid 795 through 807 removed outlier: 3.533A pdb=" N PHE A 807 " --> pdb=" O VAL A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 836 removed outlier: 3.760A pdb=" N GLY A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 836 " --> pdb=" O GLN A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 864 removed outlier: 3.637A pdb=" N PHE A 858 " --> pdb=" O ASP A 854 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 892 removed outlier: 3.957A pdb=" N ALA A 883 " --> pdb=" O VAL A 879 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 886 " --> pdb=" O GLY A 882 " (cutoff:3.500A) 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 945 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 969 through 980 Processing helix chain 'A' and resid 994 through 1006 Processing helix chain 'A' and resid 1018 through 1022 removed outlier: 3.934A 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: 3.705A pdb=" N SER A1049 " --> pdb=" O TRP A1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 174 removed outlier: 3.536A pdb=" N ARG B 174 " --> pdb=" O PHE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'D' and resid 37 through 41 removed outlier: 3.519A pdb=" N GLU D 40 " --> pdb=" O PRO D 37 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 41 " --> pdb=" O ILE D 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 37 through 41' Processing helix chain 'D' and resid 51 through 59 Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 94 through 114 Processing helix chain 'E' and resid 35 through 40 removed outlier: 4.046A pdb=" N TRP E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 55 removed outlier: 3.992A pdb=" N SER E 55 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 88 Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 178 removed outlier: 3.507A pdb=" N GLY A 145 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR A 285 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AA3, first strand: chain 'A' and resid 405 through 406 Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 571 removed outlier: 6.338A pdb=" N ILE A 594 " --> pdb=" O ASP A 646 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU A 674 " --> pdb=" O ASN A 702 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU A 701 " --> pdb=" O ARG A 731 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 730 " --> pdb=" O SER A 759 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU A 758 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU A 787 " --> pdb=" O CYS A 816 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 815 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU A 901 " --> pdb=" O ASP A 930 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU A 929 " --> pdb=" O GLY A 959 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU A 958 " --> pdb=" O ASN A 987 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU A 986 " --> pdb=" O GLY A1016 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 283 through 290 removed outlier: 5.850A pdb=" N LEU B 284 " --> pdb=" O LYS B 580 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS B 580 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LYS B 286 " --> pdb=" O HIS B 578 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS B 578 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 288 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS B 556 " --> pdb=" O GLY B 569 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 298 through 302 removed outlier: 3.525A pdb=" N HIS B 307 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 318 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 333 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 348 through 351 removed outlier: 5.837A pdb=" N VAL B 368 " --> pdb=" O GLN B 383 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN B 383 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 370 " --> pdb=" O LYS B 381 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 391 through 396 removed outlier: 6.474A pdb=" N GLY B 405 " --> pdb=" O GLN B 392 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU B 394 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU B 403 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASN B 396 " --> pdb=" O MET B 401 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N MET B 401 " --> pdb=" O ASN B 396 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 412 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE B 413 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 434 through 438 removed outlier: 3.648A pdb=" N CYS B 453 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 463 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP B 455 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 461 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 471 through 476 removed outlier: 4.010A pdb=" N HIS B 492 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 513 through 518 removed outlier: 6.511A pdb=" N VAL B 528 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU B 516 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA B 526 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N PHE B 518 " --> pdb=" O TRP B 524 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N TRP B 524 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY B 529 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE B 533 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 534 " --> pdb=" O GLN B 547 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN B 547 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 536 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 45 through 50 removed outlier: 3.597A pdb=" N MET D 49 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 50 removed outlier: 3.597A pdb=" N MET D 49 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 42 through 43 472 hydrogen bonds defined for protein. 1338 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: 1.91 Time building geometry restraints manager: 1.21 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: 3675 1.34 - 1.46: 2034 1.46 - 1.58: 5671 1.58 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 11516 Sorted by residual: bond pdb=" N SER D 26 " pdb=" CA SER D 26 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N ASP A 97 " pdb=" CA ASP A 97 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N SER E 34 " pdb=" CA SER E 34 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" N GLY B 446 " pdb=" CA GLY B 446 " ideal model delta sigma weight residual 1.450 1.440 0.009 9.10e-03 1.21e+04 1.03e+00 bond pdb=" CB GLN D 94 " pdb=" CG GLN D 94 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.72e-01 ... (remaining 11511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 14630 0.95 - 1.90: 828 1.90 - 2.85: 84 2.85 - 3.80: 41 3.80 - 4.75: 8 Bond angle restraints: 15591 Sorted by residual: angle pdb=" C ARG A 599 " pdb=" N ASP A 600 " pdb=" CA ASP A 600 " ideal model delta sigma weight residual 121.54 126.29 -4.75 1.91e+00 2.74e-01 6.18e+00 angle pdb=" C GLU B 399 " pdb=" N ASN B 400 " pdb=" CA ASN B 400 " ideal model delta sigma weight residual 123.93 127.57 -3.64 1.54e+00 4.22e-01 5.58e+00 angle pdb=" CA GLY A 536 " pdb=" C GLY A 536 " pdb=" O GLY A 536 " ideal model delta sigma weight residual 122.59 120.29 2.30 1.04e+00 9.25e-01 4.90e+00 angle pdb=" CA ASP A 600 " pdb=" C ASP A 600 " pdb=" N LEU A 601 " ideal model delta sigma weight residual 116.84 120.17 -3.33 1.71e+00 3.42e-01 3.78e+00 angle pdb=" C PHE A 693 " pdb=" CA PHE A 693 " pdb=" CB PHE A 693 " ideal model delta sigma weight residual 110.88 107.86 3.02 1.57e+00 4.06e-01 3.69e+00 ... (remaining 15586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6127 17.87 - 35.73: 601 35.73 - 53.59: 162 53.59 - 71.46: 39 71.46 - 89.32: 15 Dihedral angle restraints: 6944 sinusoidal: 2779 harmonic: 4165 Sorted by residual: dihedral pdb=" CA CYS A 849 " pdb=" C CYS A 849 " pdb=" N ASN A 850 " pdb=" CA ASN A 850 " ideal model delta harmonic sigma weight residual -180.00 -157.05 -22.95 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA LYS B 291 " pdb=" C LYS B 291 " pdb=" N HIS B 292 " pdb=" CA HIS B 292 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PHE A 693 " pdb=" C PHE A 693 " pdb=" N SER A 694 " pdb=" CA SER A 694 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 6941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1102 0.030 - 0.059: 500 0.059 - 0.089: 96 0.089 - 0.119: 72 0.119 - 0.148: 19 Chirality restraints: 1789 Sorted by residual: chirality pdb=" CA ILE B 534 " pdb=" N ILE B 534 " pdb=" C ILE B 534 " pdb=" CB ILE B 534 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ILE A 851 " pdb=" N ILE A 851 " pdb=" C ILE A 851 " pdb=" CB ILE A 851 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE D 89 " pdb=" N ILE D 89 " pdb=" C ILE D 89 " pdb=" CB ILE D 89 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 1786 not shown) Planarity restraints: 1965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 82 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.26e+00 pdb=" C ASN D 82 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN D 82 " 0.012 2.00e-02 2.50e+03 pdb=" N SER D 83 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 211 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.47e+00 pdb=" N PRO A 212 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 32 " -0.108 9.50e-02 1.11e+02 4.83e-02 1.45e+00 pdb=" NE ARG D 32 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG D 32 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 32 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 32 " -0.005 2.00e-02 2.50e+03 ... (remaining 1962 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 136 2.66 - 3.22: 10062 3.22 - 3.78: 15947 3.78 - 4.34: 23610 4.34 - 4.90: 40060 Nonbonded interactions: 89815 Sorted by model distance: nonbonded pdb=" NH1 ARG D 100 " pdb=" O ASP E 45 " model vdw 2.103 3.120 nonbonded pdb=" OG SER B 519 " pdb=" OD1 ASN B 521 " model vdw 2.121 3.040 nonbonded pdb=" OE1 GLU A 396 " pdb=" OH TYR A 413 " model vdw 2.124 3.040 nonbonded pdb=" NH1 ARG D 32 " pdb=" O PHE D 36 " model vdw 2.136 3.120 nonbonded pdb=" OE2 GLU B 327 " pdb=" NH1 ARG B 329 " model vdw 2.151 3.120 ... (remaining 89810 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.850 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 0.033 11520 Z= 0.187 Angle : 0.507 4.749 15593 Z= 0.274 Chirality : 0.039 0.148 1789 Planarity : 0.004 0.048 1965 Dihedral : 16.119 89.323 4230 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.16 % Allowed : 13.15 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.22), residues: 1414 helix: 0.78 (0.23), residues: 540 sheet: -0.96 (0.29), residues: 310 loop : -0.68 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 764 TYR 0.015 0.001 TYR A 247 PHE 0.014 0.001 PHE A1035 TRP 0.010 0.002 TRP B 319 HIS 0.005 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00442 (11516) covalent geometry : angle 0.50606 (15591) hydrogen bonds : bond 0.17865 ( 467) hydrogen bonds : angle 6.58290 ( 1338) metal coordination : bond 0.00619 ( 4) metal coordination : angle 2.68324 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 TRP cc_start: 0.6002 (m-10) cc_final: 0.5589 (m-10) outliers start: 2 outliers final: 2 residues processed: 174 average time/residue: 0.6676 time to fit residues: 124.5967 Evaluate side-chains 112 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain D residue 58 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 ASN A 666 ASN A 866 ASN B 292 HIS D 82 ASN D 94 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.083174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.059797 restraints weight = 22109.477| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.41 r_work: 0.2673 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11520 Z= 0.151 Angle : 0.552 10.289 15593 Z= 0.289 Chirality : 0.041 0.153 1789 Planarity : 0.004 0.039 1965 Dihedral : 4.183 20.766 1516 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.46 % Allowed : 15.37 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.23), residues: 1414 helix: 1.25 (0.23), residues: 561 sheet: -0.44 (0.30), residues: 311 loop : -0.59 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 498 TYR 0.015 0.001 TYR A 251 PHE 0.012 0.001 PHE A 557 TRP 0.024 0.002 TRP A 240 HIS 0.003 0.001 HIS D 112 Details of bonding type rmsd covalent geometry : bond 0.00351 (11516) covalent geometry : angle 0.55146 (15591) hydrogen bonds : bond 0.04381 ( 467) hydrogen bonds : angle 4.65268 ( 1338) metal coordination : bond 0.01038 ( 4) metal coordination : angle 2.76494 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 184 TRP cc_start: 0.6991 (m-10) cc_final: 0.5853 (m-10) REVERT: A 1032 GLU cc_start: 0.7636 (tm-30) cc_final: 0.6914 (tm-30) REVERT: B 458 MET cc_start: 0.8860 (ttt) cc_final: 0.8544 (tmm) REVERT: D 55 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8341 (pp20) REVERT: D 56 ARG cc_start: 0.8531 (tpp80) cc_final: 0.8114 (tpp80) REVERT: D 67 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8429 (mm-30) REVERT: E 35 TYR cc_start: 0.7162 (t80) cc_final: 0.6742 (t80) REVERT: E 37 GLU cc_start: 0.7156 (pt0) cc_final: 0.6783 (pt0) REVERT: E 75 MET cc_start: 0.8354 (mmm) cc_final: 0.8083 (mmm) outliers start: 31 outliers final: 6 residues processed: 141 average time/residue: 0.6106 time to fit residues: 93.3685 Evaluate side-chains 110 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain E residue 85 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 24 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 64 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 137 optimal weight: 0.0270 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN D 82 ASN D 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.084009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.061053 restraints weight = 22417.503| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.39 r_work: 0.2680 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11520 Z= 0.108 Angle : 0.492 10.366 15593 Z= 0.255 Chirality : 0.039 0.156 1789 Planarity : 0.003 0.041 1965 Dihedral : 3.884 19.396 1513 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.38 % Allowed : 16.96 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1414 helix: 1.55 (0.23), residues: 561 sheet: -0.36 (0.30), residues: 313 loop : -0.27 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 498 TYR 0.016 0.001 TYR A 251 PHE 0.010 0.001 PHE A 366 TRP 0.015 0.001 TRP B 167 HIS 0.002 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00247 (11516) covalent geometry : angle 0.49176 (15591) hydrogen bonds : bond 0.03491 ( 467) hydrogen bonds : angle 4.26933 ( 1338) metal coordination : bond 0.00606 ( 4) metal coordination : angle 2.04104 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 184 TRP cc_start: 0.7117 (m-10) cc_final: 0.6326 (m-10) REVERT: A 224 ASP cc_start: 0.8202 (p0) cc_final: 0.7847 (p0) REVERT: A 713 MET cc_start: 0.8998 (mmm) cc_final: 0.8797 (mmm) REVERT: A 1032 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7603 (tm-30) REVERT: D 55 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8457 (pp20) REVERT: D 62 GLN cc_start: 0.8308 (tm-30) cc_final: 0.8078 (tm-30) REVERT: D 67 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8354 (mm-30) REVERT: E 35 TYR cc_start: 0.7162 (t80) cc_final: 0.6826 (t80) REVERT: E 37 GLU cc_start: 0.7219 (pt0) cc_final: 0.6768 (pt0) REVERT: E 61 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8692 (mtt-85) REVERT: E 65 LEU cc_start: 0.8673 (tp) cc_final: 0.8436 (tt) outliers start: 30 outliers final: 9 residues processed: 131 average time/residue: 0.5890 time to fit residues: 83.7219 Evaluate side-chains 117 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain E residue 61 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 82 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 0.0070 chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN D 43 ASN D 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.083086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.059257 restraints weight = 21877.777| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.41 r_work: 0.2681 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11520 Z= 0.137 Angle : 0.485 10.058 15593 Z= 0.251 Chirality : 0.039 0.163 1789 Planarity : 0.003 0.042 1965 Dihedral : 3.855 19.245 1513 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.54 % Allowed : 17.51 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1414 helix: 1.67 (0.23), residues: 563 sheet: -0.29 (0.31), residues: 301 loop : -0.33 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 78 TYR 0.016 0.001 TYR B 363 PHE 0.010 0.001 PHE A 557 TRP 0.020 0.001 TRP B 167 HIS 0.003 0.001 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00326 (11516) covalent geometry : angle 0.48457 (15591) hydrogen bonds : bond 0.03554 ( 467) hydrogen bonds : angle 4.13754 ( 1338) metal coordination : bond 0.00360 ( 4) metal coordination : angle 1.95354 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8536 (mmm) REVERT: A 184 TRP cc_start: 0.7237 (m-10) cc_final: 0.6396 (m-10) REVERT: A 186 GLU cc_start: 0.8952 (mp0) cc_final: 0.8699 (mp0) REVERT: A 224 ASP cc_start: 0.8352 (p0) cc_final: 0.7974 (p0) REVERT: A 713 MET cc_start: 0.9034 (mmm) cc_final: 0.8811 (mmm) REVERT: B 456 LEU cc_start: 0.9134 (mt) cc_final: 0.8931 (mt) REVERT: D 55 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8471 (pp20) REVERT: D 62 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8213 (tm-30) REVERT: D 67 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8482 (mm-30) REVERT: E 35 TYR cc_start: 0.7177 (t80) cc_final: 0.6834 (t80) REVERT: E 37 GLU cc_start: 0.7205 (pt0) cc_final: 0.6788 (pt0) REVERT: E 50 ARG cc_start: 0.8907 (mtt90) cc_final: 0.8618 (mtp85) REVERT: E 65 LEU cc_start: 0.8939 (tp) cc_final: 0.8715 (tt) outliers start: 32 outliers final: 14 residues processed: 129 average time/residue: 0.5775 time to fit residues: 81.1475 Evaluate side-chains 122 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain E residue 85 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 67 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 87 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN D 43 ASN D 82 ASN D 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.083610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.059668 restraints weight = 21614.425| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.42 r_work: 0.2692 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11520 Z= 0.119 Angle : 0.475 9.978 15593 Z= 0.246 Chirality : 0.039 0.186 1789 Planarity : 0.003 0.041 1965 Dihedral : 3.779 21.087 1513 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.46 % Allowed : 17.99 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1414 helix: 1.72 (0.23), residues: 565 sheet: -0.37 (0.30), residues: 317 loop : -0.20 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 78 TYR 0.016 0.001 TYR A 251 PHE 0.008 0.001 PHE A 557 TRP 0.023 0.001 TRP B 167 HIS 0.002 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00283 (11516) covalent geometry : angle 0.47430 (15591) hydrogen bonds : bond 0.03282 ( 467) hydrogen bonds : angle 4.04265 ( 1338) metal coordination : bond 0.00370 ( 4) metal coordination : angle 1.91993 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TRP cc_start: 0.7311 (m-10) cc_final: 0.6405 (m-10) REVERT: A 186 GLU cc_start: 0.8950 (mp0) cc_final: 0.8691 (mp0) REVERT: A 224 ASP cc_start: 0.8326 (p0) cc_final: 0.7975 (p0) REVERT: A 250 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8462 (mmm) REVERT: A 462 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: A 513 TYR cc_start: 0.7884 (t80) cc_final: 0.7365 (m-10) REVERT: A 713 MET cc_start: 0.9050 (mmm) cc_final: 0.8816 (mmm) REVERT: A 1032 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7674 (tm-30) REVERT: B 332 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: B 456 LEU cc_start: 0.9172 (mt) cc_final: 0.8962 (mt) REVERT: B 458 MET cc_start: 0.8260 (tmt) cc_final: 0.8009 (tmm) REVERT: D 55 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8450 (pp20) REVERT: D 62 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8236 (tm-30) REVERT: D 67 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8498 (mm-30) REVERT: E 35 TYR cc_start: 0.7169 (t80) cc_final: 0.6809 (t80) REVERT: E 37 GLU cc_start: 0.7251 (pt0) cc_final: 0.6806 (pt0) REVERT: E 50 ARG cc_start: 0.8877 (mtt90) cc_final: 0.8576 (mtp85) REVERT: E 61 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8674 (mtp85) REVERT: E 65 LEU cc_start: 0.8953 (tp) cc_final: 0.8734 (tt) outliers start: 31 outliers final: 15 residues processed: 128 average time/residue: 0.6175 time to fit residues: 85.7354 Evaluate side-chains 123 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 67 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 67 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN D 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.082931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.059117 restraints weight = 21827.017| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.39 r_work: 0.2682 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11520 Z= 0.146 Angle : 0.486 9.718 15593 Z= 0.249 Chirality : 0.040 0.186 1789 Planarity : 0.003 0.041 1965 Dihedral : 3.771 20.541 1513 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.46 % Allowed : 18.86 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1414 helix: 1.75 (0.23), residues: 563 sheet: -0.38 (0.30), residues: 317 loop : -0.23 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 349 TYR 0.016 0.001 TYR B 363 PHE 0.009 0.001 PHE A 557 TRP 0.028 0.001 TRP A 202 HIS 0.003 0.001 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00347 (11516) covalent geometry : angle 0.48525 (15591) hydrogen bonds : bond 0.03431 ( 467) hydrogen bonds : angle 4.03528 ( 1338) metal coordination : bond 0.00343 ( 4) metal coordination : angle 1.93459 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TRP cc_start: 0.7380 (m-10) cc_final: 0.6419 (m-10) REVERT: A 186 GLU cc_start: 0.8963 (mp0) cc_final: 0.8712 (mp0) REVERT: A 224 ASP cc_start: 0.8385 (p0) cc_final: 0.8028 (p0) REVERT: A 250 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8417 (mmm) REVERT: A 462 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: A 513 TYR cc_start: 0.7911 (t80) cc_final: 0.7404 (m-10) REVERT: A 713 MET cc_start: 0.9061 (mmm) cc_final: 0.8819 (mmm) REVERT: B 460 LYS cc_start: 0.9033 (mmmm) cc_final: 0.8797 (mmmm) REVERT: B 472 MET cc_start: 0.8827 (mtp) cc_final: 0.8599 (mtt) REVERT: D 55 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8449 (pp20) REVERT: D 62 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8167 (tm-30) REVERT: D 67 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8558 (mm-30) REVERT: E 35 TYR cc_start: 0.7166 (t80) cc_final: 0.6804 (t80) REVERT: E 37 GLU cc_start: 0.7148 (pt0) cc_final: 0.6696 (pt0) REVERT: E 50 ARG cc_start: 0.8886 (mtt90) cc_final: 0.8586 (mtp85) REVERT: E 61 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8651 (mtp85) REVERT: E 65 LEU cc_start: 0.8961 (tp) cc_final: 0.8740 (tt) outliers start: 31 outliers final: 16 residues processed: 126 average time/residue: 0.5910 time to fit residues: 80.9449 Evaluate side-chains 122 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 85 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 5 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 108 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN D 43 ASN D 82 ASN D 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.061384 restraints weight = 21558.206| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.33 r_work: 0.2718 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11520 Z= 0.097 Angle : 0.462 9.903 15593 Z= 0.238 Chirality : 0.039 0.180 1789 Planarity : 0.003 0.039 1965 Dihedral : 3.622 23.911 1513 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.98 % Allowed : 19.89 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.23), residues: 1414 helix: 2.00 (0.23), residues: 552 sheet: -0.35 (0.30), residues: 317 loop : -0.08 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 78 TYR 0.019 0.001 TYR B 363 PHE 0.007 0.001 PHE A 557 TRP 0.035 0.001 TRP A 202 HIS 0.002 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00224 (11516) covalent geometry : angle 0.46117 (15591) hydrogen bonds : bond 0.02948 ( 467) hydrogen bonds : angle 3.88593 ( 1338) metal coordination : bond 0.00404 ( 4) metal coordination : angle 1.99586 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: 0.9086 (mmm) cc_final: 0.8636 (mtp) REVERT: A 184 TRP cc_start: 0.7372 (m-10) cc_final: 0.6383 (m-10) REVERT: A 186 GLU cc_start: 0.8960 (mp0) cc_final: 0.8751 (mp0) REVERT: A 224 ASP cc_start: 0.8301 (p0) cc_final: 0.7977 (p0) REVERT: A 250 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8432 (mmm) REVERT: A 462 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: A 513 TYR cc_start: 0.7866 (t80) cc_final: 0.7530 (OUTLIER) REVERT: A 713 MET cc_start: 0.9044 (mmm) cc_final: 0.8804 (mmm) REVERT: B 171 MET cc_start: 0.8566 (tpp) cc_final: 0.8261 (mpp) REVERT: B 332 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: B 458 MET cc_start: 0.8329 (tmt) cc_final: 0.7700 (tmm) REVERT: D 40 GLU cc_start: 0.8580 (mm-30) cc_final: 0.7932 (tt0) REVERT: D 55 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8382 (pp20) REVERT: D 62 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8231 (tm-30) REVERT: D 67 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8514 (mm-30) REVERT: E 35 TYR cc_start: 0.7108 (t80) cc_final: 0.6781 (t80) REVERT: E 37 GLU cc_start: 0.7153 (pt0) cc_final: 0.6685 (pt0) REVERT: E 50 ARG cc_start: 0.8867 (mtt90) cc_final: 0.8562 (mtp85) REVERT: E 61 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8633 (mtp85) REVERT: E 65 LEU cc_start: 0.8898 (tp) cc_final: 0.8678 (tt) outliers start: 25 outliers final: 13 residues processed: 128 average time/residue: 0.5747 time to fit residues: 79.6301 Evaluate side-chains 123 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 67 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 15 optimal weight: 0.0030 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN D 39 GLN D 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.083532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.059728 restraints weight = 21566.578| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.38 r_work: 0.2695 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11520 Z= 0.121 Angle : 0.492 10.947 15593 Z= 0.251 Chirality : 0.040 0.183 1789 Planarity : 0.003 0.039 1965 Dihedral : 3.691 31.524 1513 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.82 % Allowed : 20.44 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.24), residues: 1414 helix: 2.04 (0.24), residues: 552 sheet: -0.35 (0.30), residues: 317 loop : -0.07 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 349 TYR 0.016 0.001 TYR B 363 PHE 0.008 0.001 PHE A 557 TRP 0.038 0.001 TRP A 202 HIS 0.002 0.000 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00288 (11516) covalent geometry : angle 0.49187 (15591) hydrogen bonds : bond 0.03123 ( 467) hydrogen bonds : angle 3.90275 ( 1338) metal coordination : bond 0.00300 ( 4) metal coordination : angle 1.76702 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: 0.9096 (mmm) cc_final: 0.8603 (mtp) REVERT: A 184 TRP cc_start: 0.7383 (m-10) cc_final: 0.6724 (m-10) REVERT: A 250 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8458 (mmm) REVERT: A 462 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: A 513 TYR cc_start: 0.7876 (t80) cc_final: 0.7591 (m-80) REVERT: A 713 MET cc_start: 0.9068 (mmm) cc_final: 0.8816 (mmm) REVERT: B 171 MET cc_start: 0.8561 (tpp) cc_final: 0.8210 (mpp) REVERT: B 458 MET cc_start: 0.8416 (tmt) cc_final: 0.8085 (tmm) REVERT: D 40 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7887 (tt0) REVERT: D 55 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8375 (pp20) REVERT: D 62 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8256 (tm-30) REVERT: D 67 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8578 (mm-30) REVERT: E 35 TYR cc_start: 0.7152 (t80) cc_final: 0.6801 (t80) REVERT: E 37 GLU cc_start: 0.7150 (pt0) cc_final: 0.6677 (pt0) REVERT: E 50 ARG cc_start: 0.8864 (mtt90) cc_final: 0.8546 (mtp85) REVERT: E 61 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8613 (mtp85) REVERT: E 65 LEU cc_start: 0.8943 (tp) cc_final: 0.8720 (tt) outliers start: 23 outliers final: 14 residues processed: 123 average time/residue: 0.6283 time to fit residues: 83.3326 Evaluate side-chains 119 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 85 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 1 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 83 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 ASN D 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.083843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.060142 restraints weight = 21295.230| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.36 r_work: 0.2705 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11520 Z= 0.105 Angle : 0.492 11.495 15593 Z= 0.251 Chirality : 0.040 0.252 1789 Planarity : 0.003 0.038 1965 Dihedral : 3.695 35.270 1513 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.58 % Allowed : 20.68 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.24), residues: 1414 helix: 2.06 (0.23), residues: 552 sheet: -0.31 (0.30), residues: 316 loop : -0.07 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 349 TYR 0.017 0.001 TYR B 363 PHE 0.007 0.001 PHE A 557 TRP 0.045 0.001 TRP A 202 HIS 0.002 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00246 (11516) covalent geometry : angle 0.49126 (15591) hydrogen bonds : bond 0.03017 ( 467) hydrogen bonds : angle 3.86817 ( 1338) metal coordination : bond 0.00349 ( 4) metal coordination : angle 1.85530 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: 0.9097 (mmm) cc_final: 0.8608 (mtp) REVERT: A 250 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8478 (mmm) REVERT: A 462 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: A 513 TYR cc_start: 0.7873 (t80) cc_final: 0.7577 (m-80) REVERT: A 713 MET cc_start: 0.9126 (mmm) cc_final: 0.8899 (mmm) REVERT: B 171 MET cc_start: 0.8520 (tpp) cc_final: 0.8284 (mpp) REVERT: D 40 GLU cc_start: 0.8514 (mm-30) cc_final: 0.7886 (tt0) REVERT: D 55 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8391 (pp20) REVERT: D 62 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8266 (tm-30) REVERT: D 67 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8545 (mm-30) REVERT: E 35 TYR cc_start: 0.7145 (t80) cc_final: 0.6790 (t80) REVERT: E 37 GLU cc_start: 0.7178 (pt0) cc_final: 0.6691 (pt0) REVERT: E 50 ARG cc_start: 0.8860 (mtt90) cc_final: 0.8548 (mtp85) REVERT: E 61 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8599 (mtp85) REVERT: E 65 LEU cc_start: 0.8941 (tp) cc_final: 0.8719 (tt) outliers start: 20 outliers final: 13 residues processed: 120 average time/residue: 0.6078 time to fit residues: 78.9612 Evaluate side-chains 120 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 3 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.084010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.060342 restraints weight = 21572.944| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.39 r_work: 0.2709 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11520 Z= 0.098 Angle : 0.505 12.030 15593 Z= 0.254 Chirality : 0.040 0.282 1789 Planarity : 0.003 0.038 1965 Dihedral : 3.605 28.264 1513 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.35 % Allowed : 21.32 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.24), residues: 1414 helix: 2.06 (0.23), residues: 554 sheet: -0.29 (0.30), residues: 326 loop : -0.02 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 349 TYR 0.017 0.001 TYR B 363 PHE 0.007 0.001 PHE A 557 TRP 0.045 0.002 TRP A 202 HIS 0.002 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00228 (11516) covalent geometry : angle 0.50423 (15591) hydrogen bonds : bond 0.02904 ( 467) hydrogen bonds : angle 3.84390 ( 1338) metal coordination : bond 0.00399 ( 4) metal coordination : angle 1.86199 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: 0.9082 (mmm) cc_final: 0.8643 (mtp) REVERT: A 202 TRP cc_start: 0.8344 (t60) cc_final: 0.7989 (t-100) REVERT: A 224 ASP cc_start: 0.8527 (p0) cc_final: 0.8201 (p0) REVERT: A 250 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8477 (mmm) REVERT: A 462 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: A 513 TYR cc_start: 0.7885 (t80) cc_final: 0.7592 (m-80) REVERT: A 713 MET cc_start: 0.9153 (mmm) cc_final: 0.8929 (mmm) REVERT: B 171 MET cc_start: 0.8530 (tpp) cc_final: 0.8274 (mpp) REVERT: D 40 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7913 (tt0) REVERT: D 55 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8456 (pp20) REVERT: D 62 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8266 (tm-30) REVERT: D 67 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8464 (mm-30) REVERT: E 35 TYR cc_start: 0.7142 (t80) cc_final: 0.6814 (t80) REVERT: E 37 GLU cc_start: 0.7151 (pt0) cc_final: 0.6675 (pt0) REVERT: E 61 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8506 (mtp85) REVERT: E 65 LEU cc_start: 0.8970 (tp) cc_final: 0.8750 (tt) outliers start: 17 outliers final: 12 residues processed: 119 average time/residue: 0.6155 time to fit residues: 79.4849 Evaluate side-chains 117 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 0.0870 chunk 79 optimal weight: 4.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 ASN D 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.082795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.059242 restraints weight = 21654.871| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.38 r_work: 0.2685 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11520 Z= 0.136 Angle : 0.518 11.631 15593 Z= 0.262 Chirality : 0.040 0.288 1789 Planarity : 0.003 0.038 1965 Dihedral : 3.693 26.853 1513 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.98 % Allowed : 20.84 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.24), residues: 1414 helix: 1.96 (0.23), residues: 560 sheet: -0.32 (0.30), residues: 317 loop : -0.12 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 349 TYR 0.018 0.001 TYR B 363 PHE 0.008 0.001 PHE A 557 TRP 0.040 0.002 TRP A 202 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00322 (11516) covalent geometry : angle 0.51744 (15591) hydrogen bonds : bond 0.03243 ( 467) hydrogen bonds : angle 3.88047 ( 1338) metal coordination : bond 0.00369 ( 4) metal coordination : angle 1.76700 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3550.82 seconds wall clock time: 61 minutes 27.69 seconds (3687.69 seconds total)