Starting phenix.real_space_refine on Thu May 22 13:19:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qh5_18398/05_2025/8qh5_18398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qh5_18398/05_2025/8qh5_18398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qh5_18398/05_2025/8qh5_18398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qh5_18398/05_2025/8qh5_18398.map" model { file = "/net/cci-nas-00/data/ceres_data/8qh5_18398/05_2025/8qh5_18398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qh5_18398/05_2025/8qh5_18398.cif" } resolution = 3.4 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= 0.001 sd= 0.948 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 156 atoms to isotropic. 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 S 72 5.16 5 C 8411 2.51 5 N 2286 2.21 5 O 2540 1.98 5 H 9435 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22744 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1230 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 142} Chain: "A" Number of atoms: 5546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 5546 Classifications: {'peptide': 359} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 349} Chain breaks: 1 Chain: "B" Number of atoms: 15083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1126, 15083 Classifications: {'peptide': 1126} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 1084} Chain breaks: 3 Chain: "C" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 885 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain breaks: 1 Time building chain proxies: 11.70, per 1000 atoms: 0.51 Number of scatterers: 22744 At special positions: 0 Unit cell: (107.814, 139.524, 119.441, 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 72 16.00 O 2540 8.00 N 2286 7.00 C 8411 6.00 H 9435 1.00 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: 6.42 Conformation dependent library (CDL) restraints added in 2.2 seconds 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3142 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 32 sheets defined 14.6% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'D' and resid 1 through 14 Processing helix chain 'D' and resid 21 through 35 removed outlier: 3.614A pdb=" N SER D 35 " --> pdb=" O ILE D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 51 Processing helix chain 'D' and resid 54 through 72 Processing helix chain 'D' and resid 72 through 82 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 102 through 125 Processing helix chain 'D' and resid 128 through 140 Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 14 through 29 removed outlier: 3.639A pdb=" N LEU A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.871A pdb=" N LYS B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN B 255 " --> pdb=" O PRO B 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 255' Processing helix chain 'B' and resid 381 through 384 Processing helix chain 'B' and resid 985 through 991 Processing helix chain 'B' and resid 1044 through 1062 Processing helix chain 'B' and resid 1064 through 1068 removed outlier: 4.223A pdb=" N ILE B1068 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1075 Processing helix chain 'B' and resid 1091 through 1096 Processing helix chain 'B' and resid 1097 through 1100 removed outlier: 3.553A pdb=" N ILE B1100 " --> pdb=" O PHE B1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1097 through 1100' Processing helix chain 'B' and resid 1101 through 1109 Processing helix chain 'B' and resid 1125 through 1139 removed outlier: 3.522A pdb=" N ILE B1130 " --> pdb=" O ALA B1126 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B1139 " --> pdb=" O GLU B1135 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1140 No H-bonds generated for 'chain 'B' and resid 1140 through 1140' Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 53 through 61 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 38 removed outlier: 7.190A pdb=" N ASP A 37 " --> pdb=" O CYS A 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 51 removed outlier: 3.506A pdb=" N THR A 48 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS A 88 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP A 72 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA A 86 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 107 removed outlier: 3.552A pdb=" N THR A 104 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 144 through 149 removed outlier: 6.652A pdb=" N VAL A 168 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE A 181 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU A 170 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 179 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 189 through 194 removed outlier: 6.638A pdb=" N ASP A 215 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N CYS A 222 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 248 through 253 removed outlier: 3.781A pdb=" N ARG A 268 " --> pdb=" O GLY A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 299 removed outlier: 3.536A pdb=" N VAL A 308 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1004 through 1009 removed outlier: 6.721A pdb=" N GLY B1031 " --> pdb=" O ASN B1005 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B1007 " --> pdb=" O LEU B1029 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B1029 " --> pdb=" O PHE B1007 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 17 through 21 removed outlier: 6.430A pdb=" N VAL B 43 " --> pdb=" O PRO B 51 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR C 35 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU B 54 " --> pdb=" O TYR C 35 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 67 removed outlier: 3.898A pdb=" N ASN B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU B 90 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR B 102 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS B 92 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE B 100 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N SER B 94 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N GLN C 45 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG B 103 " --> pdb=" O GLN C 45 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE C 47 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N HIS B 105 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N THR C 49 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N ASN B 107 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LYS B 153 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 163 through 169 removed outlier: 4.363A pdb=" N HIS B 163 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 163 through 169 removed outlier: 4.363A pdb=" N HIS B 163 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 218 through 221 Processing sheet with id=AB6, first strand: chain 'B' and resid 258 through 263 removed outlier: 3.588A pdb=" N CYS B 260 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 280 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP B 299 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLU B 288 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU B 297 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 311 through 318 removed outlier: 7.141A pdb=" N GLY B 325 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B 314 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE B 323 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR B 316 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 321 " --> pdb=" O TYR B 316 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS B 335 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ALA B 349 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 359 through 365 removed outlier: 4.118A pdb=" N ASP B 361 " --> pdb=" O CYS B 378 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 396 through 402 removed outlier: 6.390A pdb=" N ILE B 701 " --> pdb=" O HIS B 399 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER B 401 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU B 699 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 409 through 413 removed outlier: 4.062A pdb=" N GLY B 409 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL B 435 " --> pdb=" O THR B 446 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 444 " --> pdb=" O MET B 437 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 457 through 463 removed outlier: 6.620A pdb=" N VAL B 476 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU B 489 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU B 478 " --> pdb=" O VAL B 487 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 500 through 503 removed outlier: 3.559A pdb=" N VAL B 500 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 516 " --> pdb=" O HIS B 531 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N HIS B 531 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR B 518 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.487A pdb=" N GLY B 559 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU B 541 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 557 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 565 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS B 570 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 576 " --> pdb=" O LYS B 570 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 588 through 596 removed outlier: 4.604A pdb=" N HIS B 600 " --> pdb=" O LEU B 616 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B 611 " --> pdb=" O LYS B 628 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS B 628 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR B 613 " --> pdb=" O ARG B 626 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG B 626 " --> pdb=" O TYR B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 637 through 643 removed outlier: 8.746A pdb=" N THR B 647 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER B 661 " --> pdb=" O THR B 647 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 720 through 727 removed outlier: 6.545A pdb=" N LEU B 736 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 724 " --> pdb=" O GLY B 734 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 734 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR B 726 " --> pdb=" O CYS B 732 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N CYS B 732 " --> pdb=" O TYR B 726 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 720 through 727 removed outlier: 6.545A pdb=" N LEU B 736 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 724 " --> pdb=" O GLY B 734 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 734 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR B 726 " --> pdb=" O CYS B 732 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N CYS B 732 " --> pdb=" O TYR B 726 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP B 795 " --> pdb=" O VAL B 801 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 801 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER B 762 " --> pdb=" O ALA B 804 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLN B 806 " --> pdb=" O SER B 762 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER B 764 " --> pdb=" O GLN B 806 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 812 through 819 removed outlier: 5.333A pdb=" N ALA B 813 " --> pdb=" O ALA B 834 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA B 834 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY B 846 " --> pdb=" O GLU B 865 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLU B 865 " --> pdb=" O GLY B 846 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 848 " --> pdb=" O GLU B 863 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU B 863 " --> pdb=" O ILE B 848 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 850 " --> pdb=" O VAL B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 870 through 876 removed outlier: 3.966A pdb=" N SER B 872 " --> pdb=" O SER B 883 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL B 888 " --> pdb=" O ASN B 904 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN B 904 " --> pdb=" O VAL B 888 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU B 890 " --> pdb=" O GLU B 902 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 911 through 917 removed outlier: 6.465A pdb=" N ALA B 934 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU B 944 " --> pdb=" O ALA B 934 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 954 through 959 removed outlier: 4.685A pdb=" N ALA B 956 " --> pdb=" O ALA B 968 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN B 978 " --> pdb=" O GLU B 994 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLU B 994 " --> pdb=" O GLN B 978 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1076 through 1077 Processing sheet with id=AD5, first strand: chain 'B' and resid 1112 through 1115 removed outlier: 4.535A pdb=" N LEU B1112 " --> pdb=" O ALA B1124 " (cutoff:3.500A) 541 hydrogen bonds defined for protein. 1467 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: 10.81 Time building geometry restraints manager: 7.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9407 1.03 - 1.23: 570 1.23 - 1.43: 5130 1.43 - 1.63: 7784 1.63 - 1.82: 108 Bond restraints: 22999 Sorted by residual: bond pdb=" CA SER A 314 " pdb=" C SER A 314 " ideal model delta sigma weight residual 1.523 1.448 0.075 1.34e-02 5.57e+03 3.16e+01 bond pdb=" CA TRP A 272 " pdb=" C TRP A 272 " ideal model delta sigma weight residual 1.522 1.468 0.054 1.23e-02 6.61e+03 1.91e+01 bond pdb=" CA ARG B 391 " pdb=" C ARG B 391 " ideal model delta sigma weight residual 1.525 1.476 0.048 1.28e-02 6.10e+03 1.44e+01 bond pdb=" CA VAL B 476 " pdb=" CB VAL B 476 " ideal model delta sigma weight residual 1.539 1.583 -0.044 1.18e-02 7.18e+03 1.41e+01 bond pdb=" CA VAL B 365 " pdb=" C VAL B 365 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.24e-02 6.50e+03 1.40e+01 ... (remaining 22994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.30: 39732 5.30 - 10.60: 26 10.60 - 15.90: 1 15.90 - 21.20: 1 21.20 - 26.50: 1 Bond angle restraints: 39761 Sorted by residual: angle pdb=" H1 MET A 1 " pdb=" N MET A 1 " pdb=" H2 MET A 1 " ideal model delta sigma weight residual 109.47 82.97 26.50 3.00e+00 1.11e-01 7.80e+01 angle pdb=" N ASP A 128 " pdb=" CA ASP A 128 " pdb=" C ASP A 128 " ideal model delta sigma weight residual 109.95 100.93 9.02 1.44e+00 4.82e-01 3.92e+01 angle pdb=" N ARG B 369 " pdb=" CA ARG B 369 " pdb=" C ARG B 369 " ideal model delta sigma weight residual 113.23 105.85 7.38 1.22e+00 6.72e-01 3.65e+01 angle pdb=" H1 MET A 1 " pdb=" N MET A 1 " pdb=" H3 MET A 1 " ideal model delta sigma weight residual 109.47 127.17 -17.70 3.00e+00 1.11e-01 3.48e+01 angle pdb=" N ASN A 273 " pdb=" CA ASN A 273 " pdb=" C ASN A 273 " ideal model delta sigma weight residual 110.20 101.06 9.14 1.58e+00 4.01e-01 3.34e+01 ... (remaining 39756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 10113 17.53 - 35.05: 899 35.05 - 52.58: 238 52.58 - 70.11: 76 70.11 - 87.64: 19 Dihedral angle restraints: 11345 sinusoidal: 5869 harmonic: 5476 Sorted by residual: dihedral pdb=" CD ARG B 639 " pdb=" NE ARG B 639 " pdb=" CZ ARG B 639 " pdb=" NH1 ARG B 639 " ideal model delta sinusoidal sigma weight residual 0.00 83.53 -83.53 1 1.00e+01 1.00e-02 8.52e+01 dihedral pdb=" CD ARG B 369 " pdb=" NE ARG B 369 " pdb=" CZ ARG B 369 " pdb=" NH1 ARG B 369 " ideal model delta sinusoidal sigma weight residual 0.00 -80.63 80.63 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CD ARG B1080 " pdb=" NE ARG B1080 " pdb=" CZ ARG B1080 " pdb=" NH1 ARG B1080 " ideal model delta sinusoidal sigma weight residual 0.00 74.22 -74.22 1 1.00e+01 1.00e-02 6.99e+01 ... (remaining 11342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1728 0.061 - 0.122: 301 0.122 - 0.184: 46 0.184 - 0.245: 4 0.245 - 0.306: 3 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CA TYR B 613 " pdb=" N TYR B 613 " pdb=" C TYR B 613 " pdb=" CB TYR B 613 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA SER B 598 " pdb=" N SER B 598 " pdb=" C SER B 598 " pdb=" CB SER B 598 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA VAL B 508 " pdb=" N VAL B 508 " pdb=" C VAL B 508 " pdb=" CB VAL B 508 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2079 not shown) Planarity restraints: 3530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 18 " 0.405 9.50e-02 1.11e+02 2.22e-01 7.18e+02 pdb=" NE ARG C 18 " 0.096 2.00e-02 2.50e+03 pdb=" CZ ARG C 18 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG C 18 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG C 18 " -0.043 2.00e-02 2.50e+03 pdb="HH11 ARG C 18 " -0.339 2.00e-02 2.50e+03 pdb="HH12 ARG C 18 " 0.356 2.00e-02 2.50e+03 pdb="HH21 ARG C 18 " 0.028 2.00e-02 2.50e+03 pdb="HH22 ARG C 18 " -0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 273 " -0.192 2.00e-02 2.50e+03 2.16e-01 6.99e+02 pdb=" CG ASN A 273 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN A 273 " 0.187 2.00e-02 2.50e+03 pdb=" ND2 ASN A 273 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN A 273 " 0.321 2.00e-02 2.50e+03 pdb="HD22 ASN A 273 " -0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 796 " -0.130 2.00e-02 2.50e+03 1.41e-01 2.98e+02 pdb=" CD GLN B 796 " 0.003 2.00e-02 2.50e+03 pdb=" OE1 GLN B 796 " 0.129 2.00e-02 2.50e+03 pdb=" NE2 GLN B 796 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 796 " 0.207 2.00e-02 2.50e+03 pdb="HE22 GLN B 796 " -0.206 2.00e-02 2.50e+03 ... (remaining 3527 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.12: 489 2.12 - 2.74: 35434 2.74 - 3.36: 59836 3.36 - 3.98: 81934 3.98 - 4.60: 124353 Nonbonded interactions: 302046 Sorted by model distance: nonbonded pdb=" OE1 GLU B 117 " pdb=" H GLU B 117 " model vdw 1.505 2.450 nonbonded pdb=" H ASP B 744 " pdb=" O GLY B 748 " model vdw 1.543 2.450 nonbonded pdb=" H LYS A 247 " pdb=" OG1 THR A 265 " model vdw 1.579 2.450 nonbonded pdb=" H ALA B 869 " pdb=" OD1 ASN B 885 " model vdw 1.587 2.450 nonbonded pdb=" OE1 GLN B 759 " pdb=" H GLN B 759 " model vdw 1.597 2.450 ... (remaining 302041 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=0.00 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.450 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 53.710 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 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 : 0.005 0.121 13564 Z= 0.333 Angle : 0.830 9.135 18357 Z= 0.533 Chirality : 0.050 0.306 2082 Planarity : 0.023 0.486 2368 Dihedral : 14.694 83.529 5027 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.34 % Allowed : 14.13 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.33 (0.20), residues: 1669 helix: 0.95 (0.36), residues: 214 sheet: -0.82 (0.20), residues: 600 loop : -1.38 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 272 HIS 0.008 0.001 HIS B1070 PHE 0.018 0.002 PHE C 19 TYR 0.019 0.002 TYR B 613 ARG 0.009 0.001 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.16307 ( 528) hydrogen bonds : angle 7.36287 ( 1467) covalent geometry : bond 0.00536 (13564) covalent geometry : angle 0.82975 (18357) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 365 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8021 (mtp85) cc_final: 0.7785 (mtm180) REVERT: A 31 GLU cc_start: 0.7603 (pp20) cc_final: 0.7273 (pp20) REVERT: A 32 LEU cc_start: 0.8444 (tp) cc_final: 0.7892 (tp) REVERT: A 39 GLU cc_start: 0.6423 (tm-30) cc_final: 0.6197 (tm-30) REVERT: A 46 ILE cc_start: 0.8496 (mm) cc_final: 0.7935 (mm) REVERT: A 50 ASP cc_start: 0.7720 (t0) cc_final: 0.7292 (t0) REVERT: A 136 ASP cc_start: 0.7781 (t0) cc_final: 0.7338 (t0) REVERT: A 138 PHE cc_start: 0.8124 (m-80) cc_final: 0.7524 (m-80) REVERT: A 195 SER cc_start: 0.8675 (t) cc_final: 0.8451 (t) REVERT: A 210 ARG cc_start: 0.7027 (mtp180) cc_final: 0.6715 (ttm-80) REVERT: A 256 ASP cc_start: 0.8205 (p0) cc_final: 0.7920 (p0) REVERT: A 281 LEU cc_start: 0.8454 (tp) cc_final: 0.8198 (tp) REVERT: A 338 ASP cc_start: 0.7145 (t0) cc_final: 0.6844 (t0) REVERT: B 11 LYS cc_start: 0.8342 (mmmm) cc_final: 0.8129 (mmtp) REVERT: B 28 ASP cc_start: 0.7057 (t0) cc_final: 0.6594 (t70) REVERT: B 30 ASN cc_start: 0.7398 (m110) cc_final: 0.7006 (m-40) REVERT: B 40 GLU cc_start: 0.6553 (mp0) cc_final: 0.6223 (mp0) REVERT: B 54 GLU cc_start: 0.6323 (tp30) cc_final: 0.5308 (tp30) REVERT: B 92 LYS cc_start: 0.7972 (ttpp) cc_final: 0.7743 (ttmm) REVERT: B 158 ARG cc_start: 0.8305 (mmm160) cc_final: 0.7892 (tpp80) REVERT: B 185 PRO cc_start: 0.8833 (Cg_exo) cc_final: 0.8629 (Cg_endo) REVERT: B 196 SER cc_start: 0.7572 (t) cc_final: 0.7054 (p) REVERT: B 204 LYS cc_start: 0.8397 (tttt) cc_final: 0.8091 (tttp) REVERT: B 259 VAL cc_start: 0.8550 (m) cc_final: 0.8298 (p) REVERT: B 276 MET cc_start: 0.7847 (mmm) cc_final: 0.7510 (mmm) REVERT: B 277 GLU cc_start: 0.7332 (tt0) cc_final: 0.6956 (tp30) REVERT: B 374 GLN cc_start: 0.7959 (mt0) cc_final: 0.7740 (mt0) REVERT: B 719 GLU cc_start: 0.7335 (pt0) cc_final: 0.7042 (pt0) REVERT: B 730 SER cc_start: 0.8580 (m) cc_final: 0.7588 (p) REVERT: B 732 CYS cc_start: 0.7007 (p) cc_final: 0.6564 (p) REVERT: B 801 VAL cc_start: 0.8731 (t) cc_final: 0.8528 (m) REVERT: B 857 LYS cc_start: 0.8202 (tppt) cc_final: 0.7775 (tppt) REVERT: B 864 LYS cc_start: 0.8552 (tptt) cc_final: 0.7779 (tptm) REVERT: B 879 LYS cc_start: 0.8064 (mttt) cc_final: 0.7843 (mttm) REVERT: B 897 LYS cc_start: 0.7792 (mmtp) cc_final: 0.7490 (mmtp) REVERT: B 927 MET cc_start: 0.7744 (ptp) cc_final: 0.7428 (ptm) REVERT: B 944 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6849 (tm-30) REVERT: B 1014 MET cc_start: 0.6501 (mmm) cc_final: 0.6088 (mmm) REVERT: B 1086 THR cc_start: 0.8381 (t) cc_final: 0.8158 (p) REVERT: B 1134 GLU cc_start: 0.7215 (tp30) cc_final: 0.6999 (tp30) REVERT: C 14 SER cc_start: 0.8312 (t) cc_final: 0.8038 (t) outliers start: 5 outliers final: 3 residues processed: 369 average time/residue: 0.7022 time to fit residues: 347.4106 Evaluate side-chains 313 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 310 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain B residue 639 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 ASN B 30 ASN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN B 497 ASN B 507 GLN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.177764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130216 restraints weight = 48430.026| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.05 r_work: 0.3404 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 13564 Z= 0.217 Angle : 0.563 5.957 18357 Z= 0.303 Chirality : 0.044 0.171 2082 Planarity : 0.007 0.245 2368 Dihedral : 4.997 64.321 1830 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.35 % Allowed : 15.34 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.10 (0.20), residues: 1669 helix: 1.83 (0.36), residues: 213 sheet: -0.86 (0.20), residues: 633 loop : -1.26 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 561 HIS 0.007 0.001 HIS B 711 PHE 0.014 0.001 PHE B 829 TYR 0.024 0.001 TYR A 71 ARG 0.011 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 528) hydrogen bonds : angle 5.58581 ( 1467) covalent geometry : bond 0.00461 (13564) covalent geometry : angle 0.56311 (18357) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 333 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7969 (pp20) cc_final: 0.7711 (pp20) REVERT: A 32 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8140 (tt) REVERT: A 39 GLU cc_start: 0.6648 (tm-30) cc_final: 0.6131 (tm-30) REVERT: A 46 ILE cc_start: 0.8614 (mm) cc_final: 0.8032 (mm) REVERT: A 50 ASP cc_start: 0.8096 (t0) cc_final: 0.7733 (t0) REVERT: A 69 VAL cc_start: 0.8777 (t) cc_final: 0.8539 (m) REVERT: A 114 MET cc_start: 0.8013 (mpp) cc_final: 0.7521 (mpp) REVERT: A 122 LYS cc_start: 0.8664 (mmtp) cc_final: 0.8287 (mmtp) REVERT: A 136 ASP cc_start: 0.8157 (t0) cc_final: 0.7842 (t0) REVERT: A 138 PHE cc_start: 0.8581 (m-80) cc_final: 0.7978 (m-80) REVERT: A 210 ARG cc_start: 0.7538 (mtp180) cc_final: 0.7043 (ttm-80) REVERT: A 265 THR cc_start: 0.8332 (p) cc_final: 0.8123 (p) REVERT: A 266 ASP cc_start: 0.8139 (p0) cc_final: 0.7842 (p0) REVERT: A 281 LEU cc_start: 0.8898 (tp) cc_final: 0.8639 (tp) REVERT: A 306 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7413 (mm-30) REVERT: A 338 ASP cc_start: 0.7578 (t0) cc_final: 0.7295 (t0) REVERT: B 28 ASP cc_start: 0.7508 (t0) cc_final: 0.7195 (t0) REVERT: B 30 ASN cc_start: 0.8320 (m-40) cc_final: 0.8086 (m-40) REVERT: B 40 GLU cc_start: 0.7109 (mp0) cc_final: 0.6704 (mp0) REVERT: B 54 GLU cc_start: 0.6992 (tp30) cc_final: 0.6032 (tp30) REVERT: B 92 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8189 (ttmm) REVERT: B 117 GLU cc_start: 0.7472 (pm20) cc_final: 0.7184 (pm20) REVERT: B 127 GLU cc_start: 0.8332 (mp0) cc_final: 0.8034 (mp0) REVERT: B 151 GLU cc_start: 0.8192 (mp0) cc_final: 0.7961 (tp30) REVERT: B 196 SER cc_start: 0.8064 (t) cc_final: 0.7549 (p) REVERT: B 204 LYS cc_start: 0.8901 (tttt) cc_final: 0.8654 (tttp) REVERT: B 213 GLU cc_start: 0.7528 (tt0) cc_final: 0.6493 (tt0) REVERT: B 244 LYS cc_start: 0.8596 (tptm) cc_final: 0.8395 (tppp) REVERT: B 245 TYR cc_start: 0.8145 (t80) cc_final: 0.7924 (t80) REVERT: B 259 VAL cc_start: 0.8791 (m) cc_final: 0.8542 (p) REVERT: B 260 CYS cc_start: 0.7662 (p) cc_final: 0.7438 (p) REVERT: B 277 GLU cc_start: 0.8020 (tt0) cc_final: 0.7092 (tp30) REVERT: B 679 MET cc_start: 0.5745 (tmt) cc_final: 0.5360 (tmt) REVERT: B 730 SER cc_start: 0.8780 (m) cc_final: 0.7958 (p) REVERT: B 732 CYS cc_start: 0.8151 (p) cc_final: 0.7843 (p) REVERT: B 857 LYS cc_start: 0.8379 (tppt) cc_final: 0.8065 (ttmm) REVERT: B 889 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7921 (mtp85) REVERT: B 898 GLU cc_start: 0.7673 (mp0) cc_final: 0.7322 (mp0) REVERT: B 927 MET cc_start: 0.8300 (ptp) cc_final: 0.8058 (ptm) REVERT: B 1014 MET cc_start: 0.6880 (mmm) cc_final: 0.6628 (mmm) REVERT: B 1036 MET cc_start: 0.8744 (tmt) cc_final: 0.8309 (tmt) REVERT: B 1083 GLU cc_start: 0.7986 (mp0) cc_final: 0.7713 (mp0) REVERT: B 1131 LYS cc_start: 0.8658 (tttp) cc_final: 0.8364 (tptt) REVERT: B 1135 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7862 (tp30) REVERT: C 14 SER cc_start: 0.8479 (t) cc_final: 0.8166 (p) outliers start: 20 outliers final: 9 residues processed: 343 average time/residue: 0.7036 time to fit residues: 317.6676 Evaluate side-chains 326 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 315 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 1135 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 55 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 118 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 134 optimal weight: 0.6980 chunk 52 optimal weight: 0.0770 chunk 139 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.172946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124784 restraints weight = 48268.922| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.03 r_work: 0.3352 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13564 Z= 0.170 Angle : 0.517 6.130 18357 Z= 0.275 Chirality : 0.043 0.164 2082 Planarity : 0.004 0.095 2368 Dihedral : 4.268 14.906 1822 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.62 % Allowed : 15.88 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.95 (0.20), residues: 1669 helix: 2.06 (0.36), residues: 216 sheet: -0.81 (0.20), residues: 636 loop : -1.18 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.010 0.001 HIS A 333 PHE 0.012 0.001 PHE B 829 TYR 0.021 0.001 TYR A 71 ARG 0.005 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 528) hydrogen bonds : angle 5.22235 ( 1467) covalent geometry : bond 0.00367 (13564) covalent geometry : angle 0.51687 (18357) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 327 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7913 (pp20) cc_final: 0.7711 (pp20) REVERT: A 39 GLU cc_start: 0.6617 (tm-30) cc_final: 0.6015 (tm-30) REVERT: A 46 ILE cc_start: 0.8652 (mm) cc_final: 0.8338 (mm) REVERT: A 50 ASP cc_start: 0.8115 (t0) cc_final: 0.7682 (t0) REVERT: A 51 ILE cc_start: 0.8622 (pt) cc_final: 0.8168 (mt) REVERT: A 114 MET cc_start: 0.8021 (mpp) cc_final: 0.7495 (mpp) REVERT: A 122 LYS cc_start: 0.8616 (mmtp) cc_final: 0.8302 (mmtp) REVERT: A 210 ARG cc_start: 0.7630 (mtp180) cc_final: 0.7121 (ttm-80) REVERT: A 266 ASP cc_start: 0.8212 (p0) cc_final: 0.7920 (p0) REVERT: A 281 LEU cc_start: 0.8884 (tp) cc_final: 0.8626 (tp) REVERT: A 322 TYR cc_start: 0.8284 (m-80) cc_final: 0.7963 (m-80) REVERT: A 338 ASP cc_start: 0.7541 (t0) cc_final: 0.7292 (t0) REVERT: A 350 TYR cc_start: 0.8212 (m-80) cc_final: 0.8010 (m-80) REVERT: B 40 GLU cc_start: 0.7141 (mp0) cc_final: 0.6763 (mp0) REVERT: B 54 GLU cc_start: 0.6990 (tp30) cc_final: 0.6096 (tp30) REVERT: B 92 LYS cc_start: 0.8466 (ttpp) cc_final: 0.8171 (ttmm) REVERT: B 117 GLU cc_start: 0.7481 (pm20) cc_final: 0.7228 (pm20) REVERT: B 127 GLU cc_start: 0.8309 (mp0) cc_final: 0.8032 (mp0) REVERT: B 191 LYS cc_start: 0.8693 (tttt) cc_final: 0.8345 (ttmt) REVERT: B 196 SER cc_start: 0.8089 (t) cc_final: 0.7541 (p) REVERT: B 204 LYS cc_start: 0.8906 (tttt) cc_final: 0.8610 (tttp) REVERT: B 213 GLU cc_start: 0.7358 (tt0) cc_final: 0.6963 (tm-30) REVERT: B 215 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7847 (mm-30) REVERT: B 259 VAL cc_start: 0.8804 (m) cc_final: 0.8597 (p) REVERT: B 277 GLU cc_start: 0.7953 (tt0) cc_final: 0.7021 (tp30) REVERT: B 291 MET cc_start: 0.7277 (mmm) cc_final: 0.7046 (mmm) REVERT: B 679 MET cc_start: 0.5940 (tmt) cc_final: 0.5728 (tmt) REVERT: B 719 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7771 (pt0) REVERT: B 739 ARG cc_start: 0.7703 (ptt-90) cc_final: 0.7468 (ptt90) REVERT: B 801 VAL cc_start: 0.9094 (t) cc_final: 0.8780 (m) REVERT: B 857 LYS cc_start: 0.8347 (tppt) cc_final: 0.8039 (ttmm) REVERT: B 898 GLU cc_start: 0.7756 (mp0) cc_final: 0.7530 (mp0) REVERT: B 927 MET cc_start: 0.8266 (ptp) cc_final: 0.8062 (ptm) REVERT: B 980 ASP cc_start: 0.6841 (t0) cc_final: 0.6321 (t0) REVERT: B 989 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7481 (mtt90) REVERT: B 1014 MET cc_start: 0.6939 (mmm) cc_final: 0.6565 (mmm) REVERT: B 1083 GLU cc_start: 0.8085 (mp0) cc_final: 0.7746 (mp0) REVERT: B 1131 LYS cc_start: 0.8653 (tttp) cc_final: 0.8214 (tptp) REVERT: C 14 SER cc_start: 0.8562 (t) cc_final: 0.8222 (p) outliers start: 24 outliers final: 17 residues processed: 337 average time/residue: 0.6727 time to fit residues: 298.7116 Evaluate side-chains 336 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 318 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain B residue 1135 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 97 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 11 optimal weight: 40.0000 chunk 42 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.170743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124123 restraints weight = 48937.536| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.93 r_work: 0.3365 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 13564 Z= 0.240 Angle : 0.523 5.573 18357 Z= 0.280 Chirality : 0.043 0.142 2082 Planarity : 0.003 0.060 2368 Dihedral : 4.319 16.189 1822 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.75 % Allowed : 16.29 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.96 (0.20), residues: 1669 helix: 2.28 (0.36), residues: 216 sheet: -0.83 (0.20), residues: 640 loop : -1.24 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 561 HIS 0.006 0.001 HIS A 333 PHE 0.017 0.002 PHE B 733 TYR 0.014 0.001 TYR B 171 ARG 0.007 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 528) hydrogen bonds : angle 5.12880 ( 1467) covalent geometry : bond 0.00512 (13564) covalent geometry : angle 0.52327 (18357) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 336 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.6730 (tm-30) cc_final: 0.5889 (tm-30) REVERT: A 46 ILE cc_start: 0.8720 (mm) cc_final: 0.8282 (mm) REVERT: A 50 ASP cc_start: 0.8085 (t0) cc_final: 0.7690 (t0) REVERT: A 51 ILE cc_start: 0.8587 (pt) cc_final: 0.8234 (mt) REVERT: A 71 TYR cc_start: 0.8455 (m-10) cc_final: 0.8086 (m-10) REVERT: A 114 MET cc_start: 0.8111 (mpp) cc_final: 0.7536 (mpp) REVERT: A 167 LYS cc_start: 0.8452 (mttt) cc_final: 0.8154 (mttp) REVERT: A 210 ARG cc_start: 0.7619 (mtp180) cc_final: 0.7122 (ttm-80) REVERT: A 266 ASP cc_start: 0.8136 (p0) cc_final: 0.7829 (p0) REVERT: A 281 LEU cc_start: 0.8811 (tp) cc_final: 0.8544 (tp) REVERT: A 322 TYR cc_start: 0.8403 (m-80) cc_final: 0.8059 (m-80) REVERT: A 335 LYS cc_start: 0.7435 (mttt) cc_final: 0.7216 (mttt) REVERT: A 338 ASP cc_start: 0.7542 (t0) cc_final: 0.7270 (t0) REVERT: B 54 GLU cc_start: 0.7014 (tp30) cc_final: 0.6658 (tp30) REVERT: B 92 LYS cc_start: 0.8481 (ttpp) cc_final: 0.8188 (ttmm) REVERT: B 127 GLU cc_start: 0.8274 (mp0) cc_final: 0.7960 (mp0) REVERT: B 204 LYS cc_start: 0.8832 (tttt) cc_final: 0.8566 (tttm) REVERT: B 215 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7918 (mm-30) REVERT: B 277 GLU cc_start: 0.7989 (tt0) cc_final: 0.7147 (tp30) REVERT: B 291 MET cc_start: 0.7294 (mmm) cc_final: 0.7076 (mmm) REVERT: B 739 ARG cc_start: 0.7909 (ptt-90) cc_final: 0.7672 (ptt90) REVERT: B 801 VAL cc_start: 0.9176 (t) cc_final: 0.8866 (m) REVERT: B 854 SER cc_start: 0.7640 (t) cc_final: 0.7347 (p) REVERT: B 857 LYS cc_start: 0.8353 (tppt) cc_final: 0.8098 (ttmm) REVERT: B 875 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7401 (tm-30) REVERT: B 898 GLU cc_start: 0.7720 (mp0) cc_final: 0.7149 (mm-30) REVERT: B 980 ASP cc_start: 0.6822 (t0) cc_final: 0.6228 (t0) REVERT: B 989 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7739 (mtt180) REVERT: B 1014 MET cc_start: 0.6853 (mmm) cc_final: 0.6527 (mmm) REVERT: B 1069 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8145 (mm-30) REVERT: B 1083 GLU cc_start: 0.8161 (mp0) cc_final: 0.7764 (mp0) REVERT: B 1131 LYS cc_start: 0.8712 (tttp) cc_final: 0.8291 (tptp) REVERT: B 1134 GLU cc_start: 0.8643 (tp30) cc_final: 0.8103 (tp30) outliers start: 26 outliers final: 19 residues processed: 347 average time/residue: 0.6852 time to fit residues: 315.5261 Evaluate side-chains 343 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 324 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 805 HIS Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1105 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 29 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 8 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 600 HIS ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.171492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.123508 restraints weight = 48195.464| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.06 r_work: 0.3352 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13564 Z= 0.176 Angle : 0.500 5.637 18357 Z= 0.265 Chirality : 0.043 0.144 2082 Planarity : 0.003 0.066 2368 Dihedral : 4.221 15.554 1822 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.22 % Allowed : 16.29 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.86 (0.20), residues: 1669 helix: 2.38 (0.35), residues: 222 sheet: -0.85 (0.19), residues: 647 loop : -1.12 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 561 HIS 0.004 0.001 HIS B1070 PHE 0.013 0.001 PHE B 733 TYR 0.011 0.001 TYR B 171 ARG 0.008 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 528) hydrogen bonds : angle 5.04434 ( 1467) covalent geometry : bond 0.00378 (13564) covalent geometry : angle 0.49962 (18357) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 324 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7754 (pp20) cc_final: 0.7553 (pp20) REVERT: A 39 GLU cc_start: 0.6767 (tm-30) cc_final: 0.5862 (tm-30) REVERT: A 46 ILE cc_start: 0.8744 (mm) cc_final: 0.8299 (mm) REVERT: A 50 ASP cc_start: 0.8136 (t0) cc_final: 0.7692 (t0) REVERT: A 51 ILE cc_start: 0.8524 (pt) cc_final: 0.8167 (mt) REVERT: A 71 TYR cc_start: 0.8448 (m-10) cc_final: 0.8014 (m-10) REVERT: A 114 MET cc_start: 0.8140 (mpp) cc_final: 0.7515 (mpp) REVERT: A 144 VAL cc_start: 0.8878 (t) cc_final: 0.8553 (m) REVERT: A 167 LYS cc_start: 0.8408 (mttt) cc_final: 0.8091 (mttp) REVERT: A 210 ARG cc_start: 0.7527 (mtp180) cc_final: 0.7043 (ttm-80) REVERT: A 266 ASP cc_start: 0.8053 (p0) cc_final: 0.7795 (p0) REVERT: A 322 TYR cc_start: 0.8449 (m-80) cc_final: 0.8197 (m-80) REVERT: A 335 LYS cc_start: 0.7497 (mttt) cc_final: 0.7273 (mttt) REVERT: A 338 ASP cc_start: 0.7544 (t0) cc_final: 0.7276 (t0) REVERT: B 40 GLU cc_start: 0.7092 (mp0) cc_final: 0.6600 (mp0) REVERT: B 54 GLU cc_start: 0.7012 (tp30) cc_final: 0.6002 (tp30) REVERT: B 90 GLU cc_start: 0.7898 (pt0) cc_final: 0.7606 (pt0) REVERT: B 92 LYS cc_start: 0.8496 (ttpp) cc_final: 0.8188 (ttmm) REVERT: B 109 GLN cc_start: 0.8141 (tt0) cc_final: 0.7892 (tt0) REVERT: B 127 GLU cc_start: 0.8290 (mp0) cc_final: 0.7950 (mp0) REVERT: B 204 LYS cc_start: 0.8863 (tttt) cc_final: 0.8611 (tttm) REVERT: B 277 GLU cc_start: 0.7949 (tt0) cc_final: 0.7139 (tp30) REVERT: B 291 MET cc_start: 0.7304 (mmm) cc_final: 0.7078 (mmm) REVERT: B 720 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8495 (p) REVERT: B 801 VAL cc_start: 0.9186 (t) cc_final: 0.8867 (m) REVERT: B 854 SER cc_start: 0.7706 (t) cc_final: 0.7407 (p) REVERT: B 857 LYS cc_start: 0.8328 (tppt) cc_final: 0.8094 (ttmm) REVERT: B 875 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7531 (tm-30) REVERT: B 947 ARG cc_start: 0.8159 (ptm160) cc_final: 0.7823 (ptm-80) REVERT: B 980 ASP cc_start: 0.6755 (t0) cc_final: 0.6083 (t0) REVERT: B 1014 MET cc_start: 0.6876 (mmm) cc_final: 0.6497 (mmm) REVERT: B 1100 ILE cc_start: 0.8583 (pt) cc_final: 0.8369 (pt) REVERT: B 1131 LYS cc_start: 0.8685 (tttp) cc_final: 0.8310 (tptp) REVERT: B 1134 GLU cc_start: 0.8669 (tp30) cc_final: 0.8101 (tp30) REVERT: B 1135 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8073 (tp30) REVERT: C 17 SER cc_start: 0.8546 (p) cc_final: 0.8313 (p) outliers start: 33 outliers final: 23 residues processed: 338 average time/residue: 0.7039 time to fit residues: 312.9853 Evaluate side-chains 349 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 325 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain B residue 1114 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 149 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 80 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 240 HIS ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.170820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122749 restraints weight = 48154.271| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.06 r_work: 0.3259 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13564 Z= 0.216 Angle : 0.508 5.665 18357 Z= 0.270 Chirality : 0.043 0.140 2082 Planarity : 0.003 0.062 2368 Dihedral : 4.229 15.607 1822 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.82 % Allowed : 16.69 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.84 (0.20), residues: 1669 helix: 2.50 (0.35), residues: 222 sheet: -0.86 (0.19), residues: 650 loop : -1.13 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1073 HIS 0.004 0.001 HIS B1070 PHE 0.014 0.001 PHE B 733 TYR 0.014 0.001 TYR B 935 ARG 0.009 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 528) hydrogen bonds : angle 5.02745 ( 1467) covalent geometry : bond 0.00458 (13564) covalent geometry : angle 0.50842 (18357) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 334 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.8273 (t0) cc_final: 0.7973 (t0) REVERT: A 39 GLU cc_start: 0.6803 (tm-30) cc_final: 0.5860 (tm-30) REVERT: A 46 ILE cc_start: 0.8724 (mm) cc_final: 0.8240 (mm) REVERT: A 47 ASN cc_start: 0.7825 (m110) cc_final: 0.7330 (m110) REVERT: A 50 ASP cc_start: 0.8175 (t0) cc_final: 0.7940 (t0) REVERT: A 55 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7761 (tt0) REVERT: A 71 TYR cc_start: 0.8443 (m-10) cc_final: 0.7962 (m-10) REVERT: A 114 MET cc_start: 0.8148 (mpp) cc_final: 0.7426 (mpp) REVERT: A 144 VAL cc_start: 0.8881 (t) cc_final: 0.8564 (m) REVERT: A 167 LYS cc_start: 0.8414 (mttt) cc_final: 0.8104 (mttp) REVERT: A 210 ARG cc_start: 0.7551 (mtp180) cc_final: 0.6982 (ttm-80) REVERT: A 266 ASP cc_start: 0.8083 (p0) cc_final: 0.7835 (p0) REVERT: A 281 LEU cc_start: 0.8851 (tp) cc_final: 0.8512 (tp) REVERT: A 322 TYR cc_start: 0.8509 (m-80) cc_final: 0.8264 (m-80) REVERT: A 335 LYS cc_start: 0.7519 (mttt) cc_final: 0.7290 (mttt) REVERT: A 338 ASP cc_start: 0.7564 (t0) cc_final: 0.7240 (t0) REVERT: B 40 GLU cc_start: 0.7143 (mp0) cc_final: 0.6624 (mp0) REVERT: B 54 GLU cc_start: 0.6933 (tp30) cc_final: 0.5900 (tp30) REVERT: B 90 GLU cc_start: 0.7913 (pt0) cc_final: 0.7593 (pt0) REVERT: B 92 LYS cc_start: 0.8537 (ttpp) cc_final: 0.8148 (ttmm) REVERT: B 109 GLN cc_start: 0.8219 (tt0) cc_final: 0.7965 (tt0) REVERT: B 127 GLU cc_start: 0.8313 (mp0) cc_final: 0.7965 (mp0) REVERT: B 204 LYS cc_start: 0.8867 (tttt) cc_final: 0.8626 (tttp) REVERT: B 277 GLU cc_start: 0.8010 (tt0) cc_final: 0.7132 (tp30) REVERT: B 291 MET cc_start: 0.7363 (mmm) cc_final: 0.7117 (mmm) REVERT: B 720 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8526 (p) REVERT: B 801 VAL cc_start: 0.9174 (t) cc_final: 0.8865 (m) REVERT: B 809 GLN cc_start: 0.8530 (mt0) cc_final: 0.8318 (mp10) REVERT: B 854 SER cc_start: 0.7744 (t) cc_final: 0.7467 (p) REVERT: B 857 LYS cc_start: 0.8317 (tppt) cc_final: 0.8074 (ttmm) REVERT: B 875 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7459 (tm-30) REVERT: B 898 GLU cc_start: 0.7596 (mp0) cc_final: 0.7016 (mm-30) REVERT: B 947 ARG cc_start: 0.8142 (ptm160) cc_final: 0.7846 (ptm-80) REVERT: B 989 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7632 (mtt90) REVERT: B 1100 ILE cc_start: 0.8581 (pt) cc_final: 0.8372 (pt) REVERT: B 1131 LYS cc_start: 0.8712 (tttp) cc_final: 0.8280 (tptp) REVERT: B 1134 GLU cc_start: 0.8628 (tp30) cc_final: 0.8223 (tp30) REVERT: B 1138 ARG cc_start: 0.8779 (ttm-80) cc_final: 0.8364 (ttm-80) REVERT: C 17 SER cc_start: 0.8535 (p) cc_final: 0.8297 (p) REVERT: C 18 ARG cc_start: 0.8555 (mtp85) cc_final: 0.8348 (mtp85) outliers start: 27 outliers final: 22 residues processed: 346 average time/residue: 0.6782 time to fit residues: 309.5575 Evaluate side-chains 354 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 331 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain B residue 1114 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 104 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 40.0000 chunk 11 optimal weight: 50.0000 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 153 optimal weight: 0.4980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 GLN ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.174021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126999 restraints weight = 48338.612| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.97 r_work: 0.3317 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 13564 Z= 0.341 Angle : 0.568 6.170 18357 Z= 0.304 Chirality : 0.044 0.144 2082 Planarity : 0.004 0.077 2368 Dihedral : 4.477 16.720 1822 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.02 % Allowed : 16.89 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.89 (0.20), residues: 1669 helix: 2.46 (0.36), residues: 222 sheet: -0.77 (0.19), residues: 636 loop : -1.28 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B1073 HIS 0.007 0.001 HIS B1070 PHE 0.021 0.002 PHE B 733 TYR 0.016 0.002 TYR B 171 ARG 0.009 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 528) hydrogen bonds : angle 5.18775 ( 1467) covalent geometry : bond 0.00718 (13564) covalent geometry : angle 0.56759 (18357) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 340 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.6870 (tm-30) cc_final: 0.5936 (tm-30) REVERT: A 46 ILE cc_start: 0.8774 (mm) cc_final: 0.8291 (mm) REVERT: A 50 ASP cc_start: 0.8139 (t0) cc_final: 0.7898 (t0) REVERT: A 55 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7781 (tt0) REVERT: A 71 TYR cc_start: 0.8438 (m-10) cc_final: 0.8012 (m-10) REVERT: A 114 MET cc_start: 0.8126 (mpp) cc_final: 0.7434 (mpp) REVERT: A 144 VAL cc_start: 0.8882 (t) cc_final: 0.8594 (m) REVERT: A 167 LYS cc_start: 0.8388 (mttt) cc_final: 0.8112 (mttp) REVERT: A 210 ARG cc_start: 0.7538 (mtp180) cc_final: 0.7115 (ttm-80) REVERT: A 212 LYS cc_start: 0.6956 (mttt) cc_final: 0.6744 (mttt) REVERT: A 266 ASP cc_start: 0.7940 (p0) cc_final: 0.7611 (p0) REVERT: A 281 LEU cc_start: 0.8822 (tp) cc_final: 0.8484 (tp) REVERT: A 322 TYR cc_start: 0.8514 (m-80) cc_final: 0.8266 (m-80) REVERT: A 335 LYS cc_start: 0.7577 (mttt) cc_final: 0.7360 (mttt) REVERT: A 338 ASP cc_start: 0.7595 (t0) cc_final: 0.7302 (t0) REVERT: B 40 GLU cc_start: 0.7084 (mp0) cc_final: 0.6606 (mp0) REVERT: B 54 GLU cc_start: 0.6962 (tp30) cc_final: 0.5891 (tp30) REVERT: B 90 GLU cc_start: 0.7801 (pt0) cc_final: 0.7555 (pt0) REVERT: B 92 LYS cc_start: 0.8510 (ttpp) cc_final: 0.8194 (ttmm) REVERT: B 109 GLN cc_start: 0.8218 (tt0) cc_final: 0.7955 (tt0) REVERT: B 127 GLU cc_start: 0.8323 (mp0) cc_final: 0.8032 (mp0) REVERT: B 204 LYS cc_start: 0.8815 (tttt) cc_final: 0.8587 (tttp) REVERT: B 277 GLU cc_start: 0.7995 (tt0) cc_final: 0.7140 (tp30) REVERT: B 291 MET cc_start: 0.7276 (mmm) cc_final: 0.7065 (mmm) REVERT: B 343 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8211 (mm-40) REVERT: B 720 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8665 (p) REVERT: B 728 GLU cc_start: 0.8444 (tp30) cc_final: 0.8192 (tp30) REVERT: B 801 VAL cc_start: 0.9194 (t) cc_final: 0.8909 (m) REVERT: B 854 SER cc_start: 0.7886 (t) cc_final: 0.7621 (p) REVERT: B 857 LYS cc_start: 0.8351 (tppt) cc_final: 0.8148 (ttmm) REVERT: B 898 GLU cc_start: 0.7608 (mp0) cc_final: 0.7040 (mm-30) REVERT: B 947 ARG cc_start: 0.8171 (ptm160) cc_final: 0.7897 (ptm-80) REVERT: B 980 ASP cc_start: 0.6679 (t0) cc_final: 0.6065 (t0) REVERT: B 1128 ASP cc_start: 0.8560 (m-30) cc_final: 0.8120 (t0) REVERT: B 1131 LYS cc_start: 0.8756 (tttp) cc_final: 0.8364 (tptm) REVERT: B 1134 GLU cc_start: 0.8659 (tp30) cc_final: 0.8162 (tp30) REVERT: C 17 SER cc_start: 0.8610 (p) cc_final: 0.8336 (p) outliers start: 30 outliers final: 27 residues processed: 352 average time/residue: 0.7124 time to fit residues: 330.9969 Evaluate side-chains 357 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 329 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain B residue 1114 TYR Chi-restraints excluded: chain C residue 43 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.170758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.124385 restraints weight = 47996.372| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.89 r_work: 0.3322 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13564 Z= 0.174 Angle : 0.520 6.881 18357 Z= 0.275 Chirality : 0.043 0.149 2082 Planarity : 0.003 0.067 2368 Dihedral : 4.282 15.541 1822 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.95 % Allowed : 17.83 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.73 (0.20), residues: 1669 helix: 2.67 (0.36), residues: 222 sheet: -0.65 (0.20), residues: 620 loop : -1.21 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 127 HIS 0.004 0.001 HIS C 20 PHE 0.013 0.001 PHE B 851 TYR 0.016 0.001 TYR A 350 ARG 0.007 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 528) hydrogen bonds : angle 5.02257 ( 1467) covalent geometry : bond 0.00374 (13564) covalent geometry : angle 0.52041 (18357) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 338 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.6848 (tm-30) cc_final: 0.5901 (tm-30) REVERT: A 46 ILE cc_start: 0.8756 (mm) cc_final: 0.8268 (mm) REVERT: A 47 ASN cc_start: 0.7789 (m110) cc_final: 0.7305 (m110) REVERT: A 50 ASP cc_start: 0.8173 (t0) cc_final: 0.7947 (t0) REVERT: A 55 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7740 (tt0) REVERT: A 71 TYR cc_start: 0.8375 (m-10) cc_final: 0.7933 (m-10) REVERT: A 114 MET cc_start: 0.8116 (mpp) cc_final: 0.7378 (mpp) REVERT: A 144 VAL cc_start: 0.8882 (t) cc_final: 0.8643 (m) REVERT: A 167 LYS cc_start: 0.8454 (mttt) cc_final: 0.8152 (mttp) REVERT: A 210 ARG cc_start: 0.7525 (mtp180) cc_final: 0.7022 (ttm-80) REVERT: A 266 ASP cc_start: 0.7922 (p0) cc_final: 0.7579 (p0) REVERT: A 276 ASN cc_start: 0.8219 (p0) cc_final: 0.7787 (p0) REVERT: A 281 LEU cc_start: 0.8794 (tp) cc_final: 0.8453 (tp) REVERT: A 338 ASP cc_start: 0.7574 (t0) cc_final: 0.7256 (t0) REVERT: B 40 GLU cc_start: 0.7092 (mp0) cc_final: 0.6585 (mp0) REVERT: B 54 GLU cc_start: 0.7003 (tp30) cc_final: 0.5901 (tp30) REVERT: B 90 GLU cc_start: 0.7869 (pt0) cc_final: 0.7536 (pt0) REVERT: B 92 LYS cc_start: 0.8458 (ttpp) cc_final: 0.8117 (ttmm) REVERT: B 109 GLN cc_start: 0.8080 (tt0) cc_final: 0.7870 (tt0) REVERT: B 116 SER cc_start: 0.8513 (m) cc_final: 0.8186 (t) REVERT: B 127 GLU cc_start: 0.8257 (mp0) cc_final: 0.7903 (mp0) REVERT: B 204 LYS cc_start: 0.8822 (tttt) cc_final: 0.8581 (tttp) REVERT: B 277 GLU cc_start: 0.7985 (tt0) cc_final: 0.7129 (tp30) REVERT: B 719 GLU cc_start: 0.8030 (pt0) cc_final: 0.7738 (pt0) REVERT: B 720 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8600 (p) REVERT: B 728 GLU cc_start: 0.8391 (tp30) cc_final: 0.8158 (tp30) REVERT: B 801 VAL cc_start: 0.9188 (t) cc_final: 0.8886 (m) REVERT: B 854 SER cc_start: 0.7893 (t) cc_final: 0.7650 (p) REVERT: B 875 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7424 (tm-30) REVERT: B 898 GLU cc_start: 0.7544 (mp0) cc_final: 0.6920 (mm-30) REVERT: B 947 ARG cc_start: 0.8109 (ptm160) cc_final: 0.7803 (ptm-80) REVERT: B 1122 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7716 (tmm-80) REVERT: B 1131 LYS cc_start: 0.8721 (tttp) cc_final: 0.8354 (tptm) REVERT: B 1134 GLU cc_start: 0.8594 (tp30) cc_final: 0.8053 (tp30) REVERT: B 1135 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7951 (tp30) REVERT: C 17 SER cc_start: 0.8569 (p) cc_final: 0.8319 (p) outliers start: 29 outliers final: 23 residues processed: 350 average time/residue: 0.7085 time to fit residues: 329.2185 Evaluate side-chains 360 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 336 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain B residue 1114 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 0.9980 chunk 135 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 HIS ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.171161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125016 restraints weight = 47666.499| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.86 r_work: 0.3253 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13564 Z= 0.158 Angle : 0.519 8.859 18357 Z= 0.273 Chirality : 0.043 0.149 2082 Planarity : 0.003 0.063 2368 Dihedral : 4.195 15.201 1822 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.75 % Allowed : 18.64 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.60 (0.20), residues: 1669 helix: 2.79 (0.36), residues: 222 sheet: -0.53 (0.20), residues: 617 loop : -1.15 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 127 HIS 0.004 0.001 HIS C 20 PHE 0.013 0.001 PHE B 851 TYR 0.014 0.001 TYR B 935 ARG 0.007 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 528) hydrogen bonds : angle 4.91313 ( 1467) covalent geometry : bond 0.00343 (13564) covalent geometry : angle 0.51915 (18357) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 334 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.6771 (tm-30) cc_final: 0.5819 (tm-30) REVERT: A 46 ILE cc_start: 0.8710 (mm) cc_final: 0.8190 (mm) REVERT: A 47 ASN cc_start: 0.7734 (m110) cc_final: 0.7209 (m110) REVERT: A 55 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7721 (tt0) REVERT: A 71 TYR cc_start: 0.8365 (m-10) cc_final: 0.7902 (m-10) REVERT: A 114 MET cc_start: 0.8122 (mpp) cc_final: 0.7325 (mpp) REVERT: A 144 VAL cc_start: 0.8871 (t) cc_final: 0.8640 (m) REVERT: A 167 LYS cc_start: 0.8468 (mttt) cc_final: 0.8170 (mttp) REVERT: A 210 ARG cc_start: 0.7501 (mtp180) cc_final: 0.6878 (ttm-80) REVERT: A 212 LYS cc_start: 0.6594 (mttt) cc_final: 0.6292 (mttt) REVERT: A 266 ASP cc_start: 0.7913 (p0) cc_final: 0.7592 (p0) REVERT: A 281 LEU cc_start: 0.8795 (tp) cc_final: 0.8443 (tp) REVERT: A 338 ASP cc_start: 0.7579 (t0) cc_final: 0.7228 (t0) REVERT: B 40 GLU cc_start: 0.7177 (mp0) cc_final: 0.6652 (mp0) REVERT: B 54 GLU cc_start: 0.6848 (tp30) cc_final: 0.5685 (tp30) REVERT: B 90 GLU cc_start: 0.7892 (pt0) cc_final: 0.7485 (pt0) REVERT: B 92 LYS cc_start: 0.8470 (ttpp) cc_final: 0.8178 (mtpp) REVERT: B 109 GLN cc_start: 0.8104 (tt0) cc_final: 0.7782 (tt0) REVERT: B 116 SER cc_start: 0.8505 (m) cc_final: 0.8141 (t) REVERT: B 127 GLU cc_start: 0.8288 (mp0) cc_final: 0.7891 (mp0) REVERT: B 166 ASP cc_start: 0.8062 (t0) cc_final: 0.7576 (p0) REVERT: B 204 LYS cc_start: 0.8840 (tttt) cc_final: 0.8545 (tttp) REVERT: B 277 GLU cc_start: 0.8037 (tt0) cc_final: 0.7139 (tp30) REVERT: B 343 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8162 (mm-40) REVERT: B 370 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6888 (pp30) REVERT: B 719 GLU cc_start: 0.8123 (pt0) cc_final: 0.7772 (pt0) REVERT: B 720 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8550 (p) REVERT: B 728 GLU cc_start: 0.8334 (tp30) cc_final: 0.8027 (tp30) REVERT: B 801 VAL cc_start: 0.9133 (t) cc_final: 0.8851 (m) REVERT: B 854 SER cc_start: 0.7863 (t) cc_final: 0.7620 (p) REVERT: B 898 GLU cc_start: 0.7494 (mp0) cc_final: 0.7089 (mp0) REVERT: B 947 ARG cc_start: 0.8164 (ptm160) cc_final: 0.7824 (ptm-80) REVERT: B 1122 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7663 (tmm-80) REVERT: B 1131 LYS cc_start: 0.8694 (tttp) cc_final: 0.8302 (tptm) REVERT: B 1134 GLU cc_start: 0.8619 (tp30) cc_final: 0.8105 (tp30) REVERT: B 1135 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7919 (tp30) REVERT: C 17 SER cc_start: 0.8533 (p) cc_final: 0.8251 (p) outliers start: 26 outliers final: 23 residues processed: 345 average time/residue: 0.7005 time to fit residues: 318.3459 Evaluate side-chains 358 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 333 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 991 HIS Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain B residue 1114 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 0 optimal weight: 50.0000 chunk 71 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 94 optimal weight: 50.0000 chunk 30 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.170983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124810 restraints weight = 47831.933| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.85 r_work: 0.3325 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13564 Z= 0.165 Angle : 0.525 9.930 18357 Z= 0.275 Chirality : 0.043 0.149 2082 Planarity : 0.004 0.068 2368 Dihedral : 4.163 15.122 1822 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.68 % Allowed : 18.91 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.56 (0.20), residues: 1669 helix: 2.78 (0.36), residues: 222 sheet: -0.48 (0.20), residues: 616 loop : -1.14 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1073 HIS 0.004 0.001 HIS C 20 PHE 0.015 0.001 PHE B 851 TYR 0.013 0.001 TYR B 935 ARG 0.007 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 528) hydrogen bonds : angle 4.87681 ( 1467) covalent geometry : bond 0.00358 (13564) covalent geometry : angle 0.52490 (18357) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 327 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8248 (mtm110) cc_final: 0.7981 (mtp-110) REVERT: A 39 GLU cc_start: 0.6840 (tm-30) cc_final: 0.5887 (tm-30) REVERT: A 46 ILE cc_start: 0.8759 (mm) cc_final: 0.8262 (mm) REVERT: A 55 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7721 (tt0) REVERT: A 71 TYR cc_start: 0.8339 (m-10) cc_final: 0.7926 (m-10) REVERT: A 114 MET cc_start: 0.8123 (mpp) cc_final: 0.7306 (mpp) REVERT: A 144 VAL cc_start: 0.8841 (t) cc_final: 0.8610 (m) REVERT: A 167 LYS cc_start: 0.8463 (mttt) cc_final: 0.8190 (mttp) REVERT: A 210 ARG cc_start: 0.7539 (mtp180) cc_final: 0.7018 (ttm-80) REVERT: A 212 LYS cc_start: 0.6843 (mttt) cc_final: 0.6563 (mttt) REVERT: A 266 ASP cc_start: 0.7830 (p0) cc_final: 0.7469 (p0) REVERT: A 281 LEU cc_start: 0.8748 (tp) cc_final: 0.8410 (tp) REVERT: A 338 ASP cc_start: 0.7563 (t0) cc_final: 0.7297 (t0) REVERT: A 340 CYS cc_start: 0.8292 (p) cc_final: 0.7973 (p) REVERT: B 40 GLU cc_start: 0.7074 (mp0) cc_final: 0.6627 (mp0) REVERT: B 54 GLU cc_start: 0.7026 (tp30) cc_final: 0.5892 (tp30) REVERT: B 92 LYS cc_start: 0.8519 (ttpp) cc_final: 0.8186 (ttmm) REVERT: B 109 GLN cc_start: 0.8001 (tt0) cc_final: 0.7725 (tt0) REVERT: B 116 SER cc_start: 0.8510 (m) cc_final: 0.8154 (t) REVERT: B 127 GLU cc_start: 0.8242 (mp0) cc_final: 0.7891 (mp0) REVERT: B 166 ASP cc_start: 0.7979 (t0) cc_final: 0.7635 (p0) REVERT: B 204 LYS cc_start: 0.8800 (tttt) cc_final: 0.8535 (tttp) REVERT: B 277 GLU cc_start: 0.7983 (tt0) cc_final: 0.7144 (tp30) REVERT: B 719 GLU cc_start: 0.7997 (pt0) cc_final: 0.7676 (pt0) REVERT: B 728 GLU cc_start: 0.8356 (tp30) cc_final: 0.8106 (tp30) REVERT: B 840 GLU cc_start: 0.7853 (mp0) cc_final: 0.7459 (mp0) REVERT: B 854 SER cc_start: 0.7928 (t) cc_final: 0.7683 (p) REVERT: B 898 GLU cc_start: 0.7507 (mp0) cc_final: 0.7124 (mp0) REVERT: B 947 ARG cc_start: 0.8147 (ptm160) cc_final: 0.7867 (ptm-80) REVERT: B 1131 LYS cc_start: 0.8698 (tttp) cc_final: 0.8300 (tptm) REVERT: B 1134 GLU cc_start: 0.8618 (tp30) cc_final: 0.8078 (tp30) REVERT: B 1135 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8102 (mm-30) REVERT: B 1138 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8521 (ttm-80) REVERT: C 17 SER cc_start: 0.8536 (p) cc_final: 0.8248 (p) outliers start: 25 outliers final: 23 residues processed: 337 average time/residue: 0.7049 time to fit residues: 311.7479 Evaluate side-chains 344 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 321 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 991 HIS Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain B residue 1114 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 113 optimal weight: 3.9990 chunk 135 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 59 optimal weight: 0.0020 chunk 145 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 81 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.180445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133265 restraints weight = 47525.520| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.04 r_work: 0.3304 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13564 Z= 0.127 Angle : 0.517 9.616 18357 Z= 0.269 Chirality : 0.043 0.146 2082 Planarity : 0.004 0.106 2368 Dihedral : 4.086 15.588 1822 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.48 % Allowed : 19.45 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.49 (0.20), residues: 1669 helix: 2.84 (0.36), residues: 222 sheet: -0.47 (0.20), residues: 621 loop : -1.07 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 127 HIS 0.004 0.001 HIS C 20 PHE 0.013 0.001 PHE B 851 TYR 0.011 0.001 TYR B 5 ARG 0.016 0.001 ARG B 989 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 528) hydrogen bonds : angle 4.78641 ( 1467) covalent geometry : bond 0.00282 (13564) covalent geometry : angle 0.51686 (18357) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14328.46 seconds wall clock time: 246 minutes 17.13 seconds (14777.13 seconds total)