Starting phenix.real_space_refine on Thu Jun 19 20:24:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qh5_18398/06_2025/8qh5_18398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qh5_18398/06_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_18398/06_2025/8qh5_18398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qh5_18398/06_2025/8qh5_18398.map" model { file = "/net/cci-nas-00/data/ceres_data/8qh5_18398/06_2025/8qh5_18398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qh5_18398/06_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-5710/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: 10.84, per 1000 atoms: 0.48 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: 5.45 Conformation dependent library (CDL) restraints added in 2.0 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: 2.43 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: 6.67 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.460 Extract box with map and model: 0.920 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 50.450 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.200 ------------------------------------------------------------------------------- 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 : 2.003 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: 0.6977 time to fit residues: 345.1025 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 : 1.740 ------------------------------------------------------------------------------- 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: 0.3405 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 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 : 2.064 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: 0.7963 (pp20) cc_final: 0.7707 (pp20) REVERT: A 32 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8143 (tt) REVERT: A 39 GLU cc_start: 0.6652 (tm-30) cc_final: 0.6137 (tm-30) REVERT: A 46 ILE cc_start: 0.8614 (mm) cc_final: 0.8037 (mm) REVERT: A 50 ASP cc_start: 0.8097 (t0) cc_final: 0.7740 (t0) REVERT: A 69 VAL cc_start: 0.8774 (t) cc_final: 0.8539 (m) REVERT: A 114 MET cc_start: 0.8008 (mpp) cc_final: 0.7518 (mpp) REVERT: A 122 LYS cc_start: 0.8665 (mmtp) cc_final: 0.8289 (mmtp) REVERT: A 136 ASP cc_start: 0.8152 (t0) cc_final: 0.7842 (t0) REVERT: A 138 PHE cc_start: 0.8581 (m-80) cc_final: 0.7979 (m-80) REVERT: A 210 ARG cc_start: 0.7529 (mtp180) cc_final: 0.7040 (ttm-80) REVERT: A 265 THR cc_start: 0.8328 (p) cc_final: 0.8118 (p) REVERT: A 266 ASP cc_start: 0.8131 (p0) cc_final: 0.7834 (p0) REVERT: A 281 LEU cc_start: 0.8896 (tp) cc_final: 0.8636 (tp) REVERT: A 306 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 338 ASP cc_start: 0.7571 (t0) cc_final: 0.7291 (t0) REVERT: B 28 ASP cc_start: 0.7508 (t0) cc_final: 0.7195 (t0) REVERT: B 30 ASN cc_start: 0.8319 (m-40) cc_final: 0.8084 (m-40) REVERT: B 40 GLU cc_start: 0.7104 (mp0) cc_final: 0.6700 (mp0) REVERT: B 54 GLU cc_start: 0.6989 (tp30) cc_final: 0.6033 (tp30) REVERT: B 92 LYS cc_start: 0.8488 (ttpp) cc_final: 0.8194 (ttmm) REVERT: B 117 GLU cc_start: 0.7462 (pm20) cc_final: 0.7176 (pm20) REVERT: B 127 GLU cc_start: 0.8332 (mp0) cc_final: 0.8037 (mp0) REVERT: B 151 GLU cc_start: 0.8181 (mp0) cc_final: 0.7948 (tp30) REVERT: B 196 SER cc_start: 0.8069 (t) cc_final: 0.7559 (p) REVERT: B 204 LYS cc_start: 0.8894 (tttt) cc_final: 0.8649 (tttp) REVERT: B 213 GLU cc_start: 0.7517 (tt0) cc_final: 0.6479 (tt0) REVERT: B 244 LYS cc_start: 0.8596 (tptm) cc_final: 0.8395 (tppp) REVERT: B 245 TYR cc_start: 0.8132 (t80) cc_final: 0.7911 (t80) REVERT: B 259 VAL cc_start: 0.8790 (m) cc_final: 0.8541 (p) REVERT: B 260 CYS cc_start: 0.7656 (p) cc_final: 0.7434 (p) REVERT: B 277 GLU cc_start: 0.8013 (tt0) cc_final: 0.7085 (tp30) REVERT: B 679 MET cc_start: 0.5732 (tmt) cc_final: 0.5364 (tmt) REVERT: B 730 SER cc_start: 0.8773 (m) cc_final: 0.7953 (p) REVERT: B 732 CYS cc_start: 0.8143 (p) cc_final: 0.7834 (p) REVERT: B 857 LYS cc_start: 0.8372 (tppt) cc_final: 0.8062 (ttmm) REVERT: B 889 ARG cc_start: 0.8126 (mtp85) cc_final: 0.7913 (mtp85) REVERT: B 898 GLU cc_start: 0.7670 (mp0) cc_final: 0.7318 (mp0) REVERT: B 927 MET cc_start: 0.8300 (ptp) cc_final: 0.8058 (ptm) REVERT: B 1014 MET cc_start: 0.6868 (mmm) cc_final: 0.6623 (mmm) REVERT: B 1036 MET cc_start: 0.8738 (tmt) cc_final: 0.8308 (tmt) REVERT: B 1083 GLU cc_start: 0.7982 (mp0) cc_final: 0.7711 (mp0) REVERT: B 1131 LYS cc_start: 0.8658 (tttp) cc_final: 0.8367 (tptt) REVERT: B 1135 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7853 (tp30) REVERT: C 14 SER cc_start: 0.8479 (t) cc_final: 0.8165 (p) outliers start: 20 outliers final: 9 residues processed: 343 average time/residue: 0.7398 time to fit residues: 338.1928 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 : 2.947 ------------------------------------------------------------------------------- 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: 0.9980 chunk 113 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 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: 0.6738 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.173285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.126481 restraints weight = 48032.445| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.93 r_work: 0.3292 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13564 Z= 0.159 Angle : 0.514 6.197 18357 Z= 0.273 Chirality : 0.043 0.161 2082 Planarity : 0.004 0.102 2368 Dihedral : 4.256 14.769 1822 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.48 % Allowed : 16.02 % 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: -0.79 (0.20), residues: 634 loop : -1.18 (0.20), residues: 819 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 0.019 0.001 TYR A 71 ARG 0.005 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 528) hydrogen bonds : angle 5.22290 ( 1467) covalent geometry : bond 0.00344 (13564) covalent geometry : angle 0.51438 (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 345 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 323 time to evaluate : 1.949 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: A 31 GLU cc_start: 0.7853 (pp20) cc_final: 0.7604 (pp20) REVERT: A 39 GLU cc_start: 0.6565 (tm-30) cc_final: 0.5960 (tm-30) REVERT: A 46 ILE cc_start: 0.8611 (mm) cc_final: 0.8220 (mm) REVERT: A 50 ASP cc_start: 0.8161 (t0) cc_final: 0.7684 (t0) REVERT: A 51 ILE cc_start: 0.8595 (pt) cc_final: 0.8131 (mt) REVERT: A 114 MET cc_start: 0.8040 (mpp) cc_final: 0.7481 (mpp) REVERT: A 122 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8264 (mmtp) REVERT: A 210 ARG cc_start: 0.7620 (mtp180) cc_final: 0.7069 (ttm-80) REVERT: A 266 ASP cc_start: 0.8225 (p0) cc_final: 0.7956 (p0) REVERT: A 281 LEU cc_start: 0.8887 (tp) cc_final: 0.8629 (tp) REVERT: A 322 TYR cc_start: 0.8296 (m-80) cc_final: 0.7964 (m-80) REVERT: A 325 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 338 ASP cc_start: 0.7515 (t0) cc_final: 0.7256 (t0) REVERT: B 28 ASP cc_start: 0.7451 (t0) cc_final: 0.7216 (t70) REVERT: B 40 GLU cc_start: 0.7160 (mp0) cc_final: 0.6750 (mp0) REVERT: B 54 GLU cc_start: 0.6916 (tp30) cc_final: 0.5963 (tp30) REVERT: B 92 LYS cc_start: 0.8442 (ttpp) cc_final: 0.8129 (ttmm) REVERT: B 117 GLU cc_start: 0.7493 (pm20) cc_final: 0.7219 (pm20) REVERT: B 127 GLU cc_start: 0.8315 (mp0) cc_final: 0.8030 (mp0) REVERT: B 191 LYS cc_start: 0.8680 (tttt) cc_final: 0.8319 (ttmt) REVERT: B 196 SER cc_start: 0.8025 (t) cc_final: 0.7451 (p) REVERT: B 204 LYS cc_start: 0.8915 (tttt) cc_final: 0.8596 (tttp) REVERT: B 213 GLU cc_start: 0.7336 (tt0) cc_final: 0.6986 (tm-30) REVERT: B 215 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7863 (mm-30) REVERT: B 277 GLU cc_start: 0.7990 (tt0) cc_final: 0.7056 (tp30) REVERT: B 679 MET cc_start: 0.5913 (tmt) cc_final: 0.5684 (tmt) REVERT: B 719 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: B 801 VAL cc_start: 0.9073 (t) cc_final: 0.8770 (m) REVERT: B 857 LYS cc_start: 0.8309 (tppt) cc_final: 0.7991 (ttmm) REVERT: B 898 GLU cc_start: 0.7724 (mp0) cc_final: 0.7490 (mp0) REVERT: B 927 MET cc_start: 0.8269 (ptp) cc_final: 0.8054 (ptm) REVERT: B 980 ASP cc_start: 0.6804 (t0) cc_final: 0.6275 (t0) REVERT: B 989 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7439 (mtt90) REVERT: B 1014 MET cc_start: 0.6899 (mmm) cc_final: 0.6524 (mmm) REVERT: B 1083 GLU cc_start: 0.8051 (mp0) cc_final: 0.7783 (mp0) REVERT: B 1131 LYS cc_start: 0.8642 (tttp) cc_final: 0.8185 (tptp) REVERT: C 14 SER cc_start: 0.8526 (t) cc_final: 0.8176 (p) REVERT: C 18 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7733 (ttp-110) outliers start: 22 outliers final: 16 residues processed: 333 average time/residue: 0.6848 time to fit residues: 303.0371 Evaluate side-chains 333 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 316 time to evaluate : 2.127 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 88 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 11 optimal weight: 50.0000 chunk 42 optimal weight: 0.0070 chunk 153 optimal weight: 0.9980 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.172017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.125289 restraints weight = 48249.168| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.92 r_work: 0.3354 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3138 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= 0.165 Angle : 0.496 5.615 18357 Z= 0.263 Chirality : 0.043 0.145 2082 Planarity : 0.003 0.063 2368 Dihedral : 4.179 14.931 1822 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.28 % Allowed : 16.62 % Favored : 82.10 % 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: -0.88 (0.20), residues: 1669 helix: 2.32 (0.36), residues: 216 sheet: -0.77 (0.20), residues: 637 loop : -1.18 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 561 HIS 0.007 0.001 HIS A 333 PHE 0.016 0.001 PHE B 829 TYR 0.015 0.001 TYR C 35 ARG 0.006 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 528) hydrogen bonds : angle 5.01160 ( 1467) covalent geometry : bond 0.00353 (13564) covalent geometry : angle 0.49566 (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 338 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 319 time to evaluate : 2.020 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: A 31 GLU cc_start: 0.7844 (pp20) cc_final: 0.7634 (pp20) REVERT: A 39 GLU cc_start: 0.6653 (tm-30) cc_final: 0.5975 (tm-30) REVERT: A 46 ILE cc_start: 0.8666 (mm) cc_final: 0.8231 (mm) REVERT: A 50 ASP cc_start: 0.8123 (t0) cc_final: 0.7665 (t0) REVERT: A 51 ILE cc_start: 0.8566 (pt) cc_final: 0.8154 (mt) REVERT: A 114 MET cc_start: 0.8053 (mpp) cc_final: 0.7517 (mpp) REVERT: A 136 ASP cc_start: 0.8140 (t0) cc_final: 0.7799 (t0) REVERT: A 210 ARG cc_start: 0.7615 (mtp180) cc_final: 0.7039 (ttm-80) REVERT: A 266 ASP cc_start: 0.8234 (p0) cc_final: 0.7992 (p0) REVERT: A 281 LEU cc_start: 0.8845 (tp) cc_final: 0.8588 (tp) REVERT: A 322 TYR cc_start: 0.8355 (m-80) cc_final: 0.8022 (m-80) REVERT: A 325 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 338 ASP cc_start: 0.7513 (t0) cc_final: 0.7224 (t0) REVERT: B 40 GLU cc_start: 0.7188 (mp0) cc_final: 0.6595 (mp0) REVERT: B 54 GLU cc_start: 0.6983 (tp30) cc_final: 0.5812 (tp30) REVERT: B 90 GLU cc_start: 0.7984 (pt0) cc_final: 0.7773 (pt0) REVERT: B 92 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8136 (ttmm) REVERT: B 127 GLU cc_start: 0.8260 (mp0) cc_final: 0.7938 (mp0) REVERT: B 191 LYS cc_start: 0.8680 (tttt) cc_final: 0.8337 (ttmt) REVERT: B 204 LYS cc_start: 0.8893 (tttt) cc_final: 0.8615 (tttm) REVERT: B 213 GLU cc_start: 0.7170 (tt0) cc_final: 0.6839 (tt0) REVERT: B 215 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8021 (mm-30) REVERT: B 277 GLU cc_start: 0.7949 (tt0) cc_final: 0.7106 (tp30) REVERT: B 291 MET cc_start: 0.7406 (mmm) cc_final: 0.7166 (mmm) REVERT: B 739 ARG cc_start: 0.7739 (ptt-90) cc_final: 0.7471 (ptt90) REVERT: B 801 VAL cc_start: 0.9147 (t) cc_final: 0.8840 (m) REVERT: B 857 LYS cc_start: 0.8346 (tppt) cc_final: 0.8069 (ttmm) REVERT: B 875 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7390 (tm-30) REVERT: B 898 GLU cc_start: 0.7716 (mp0) cc_final: 0.7083 (mm-30) REVERT: B 927 MET cc_start: 0.8253 (ptp) cc_final: 0.8045 (ptm) REVERT: B 980 ASP cc_start: 0.6753 (t0) cc_final: 0.6159 (t0) REVERT: B 989 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7584 (mtt90) REVERT: B 1083 GLU cc_start: 0.8125 (mp0) cc_final: 0.7715 (mp0) REVERT: B 1131 LYS cc_start: 0.8700 (tttp) cc_final: 0.8251 (tptp) REVERT: C 14 SER cc_start: 0.8419 (t) cc_final: 0.8189 (p) outliers start: 19 outliers final: 16 residues processed: 327 average time/residue: 0.6896 time to fit residues: 298.8052 Evaluate side-chains 332 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 316 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 225 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain B residue 70 LYS 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 576 LEU Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 991 HIS 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: 1.9990 chunk 145 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 8 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.175020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127458 restraints weight = 48317.401| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.04 r_work: 0.3349 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 13564 Z= 0.254 Angle : 0.523 5.726 18357 Z= 0.279 Chirality : 0.043 0.141 2082 Planarity : 0.003 0.066 2368 Dihedral : 4.272 15.922 1822 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.29 % Allowed : 16.08 % Favored : 81.63 % 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: -0.94 (0.20), residues: 1669 helix: 2.32 (0.35), residues: 222 sheet: -0.90 (0.19), residues: 651 loop : -1.17 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1073 HIS 0.006 0.001 HIS B1070 PHE 0.017 0.002 PHE B 733 TYR 0.014 0.001 TYR B 171 ARG 0.007 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 528) hydrogen bonds : angle 5.09114 ( 1467) covalent geometry : bond 0.00538 (13564) covalent geometry : angle 0.52336 (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 367 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 333 time to evaluate : 1.985 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 39 GLU cc_start: 0.6812 (tm-30) cc_final: 0.5884 (tm-30) REVERT: A 46 ILE cc_start: 0.8759 (mm) cc_final: 0.8306 (mm) REVERT: A 50 ASP cc_start: 0.8111 (t0) cc_final: 0.7688 (t0) REVERT: A 51 ILE cc_start: 0.8554 (pt) cc_final: 0.8200 (mt) REVERT: A 71 TYR cc_start: 0.8465 (m-10) cc_final: 0.7933 (m-10) REVERT: A 114 MET cc_start: 0.8115 (mpp) cc_final: 0.7451 (mpp) REVERT: A 136 ASP cc_start: 0.8168 (t0) cc_final: 0.7958 (t0) REVERT: A 167 LYS cc_start: 0.8397 (mttt) cc_final: 0.8091 (mttp) REVERT: A 210 ARG cc_start: 0.7518 (mtp180) cc_final: 0.6993 (ttm-80) REVERT: A 265 THR cc_start: 0.8506 (p) cc_final: 0.8305 (p) REVERT: A 266 ASP cc_start: 0.8165 (p0) cc_final: 0.7862 (p0) REVERT: A 281 LEU cc_start: 0.8811 (tp) cc_final: 0.8550 (tp) REVERT: A 322 TYR cc_start: 0.8444 (m-80) cc_final: 0.8144 (m-80) REVERT: A 325 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7502 (tm-30) REVERT: A 335 LYS cc_start: 0.7523 (mttt) cc_final: 0.7321 (mttt) REVERT: A 338 ASP cc_start: 0.7547 (t0) cc_final: 0.7259 (t0) REVERT: B 40 GLU cc_start: 0.7129 (mp0) cc_final: 0.6767 (mp0) REVERT: B 54 GLU cc_start: 0.7103 (tp30) cc_final: 0.6016 (tp30) REVERT: B 90 GLU cc_start: 0.7935 (pt0) cc_final: 0.7715 (pt0) REVERT: B 92 LYS cc_start: 0.8445 (ttpp) cc_final: 0.8154 (ttmm) REVERT: B 109 GLN cc_start: 0.8199 (tt0) cc_final: 0.7945 (tt0) REVERT: B 127 GLU cc_start: 0.8285 (mp0) cc_final: 0.7945 (mp0) REVERT: B 204 LYS cc_start: 0.8848 (tttt) cc_final: 0.8619 (tttp) REVERT: B 209 GLN cc_start: 0.7904 (tm130) cc_final: 0.7704 (tm-30) REVERT: B 213 GLU cc_start: 0.7250 (tt0) cc_final: 0.6962 (tt0) REVERT: B 277 GLU cc_start: 0.7981 (tt0) cc_final: 0.7096 (tp30) REVERT: B 291 MET cc_start: 0.7334 (mmm) cc_final: 0.7106 (mmm) REVERT: B 720 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8506 (p) REVERT: B 739 ARG cc_start: 0.7989 (ptt-90) cc_final: 0.7779 (ptt90) REVERT: B 801 VAL cc_start: 0.9194 (t) cc_final: 0.8894 (m) REVERT: B 854 SER cc_start: 0.7710 (t) cc_final: 0.7392 (p) REVERT: B 857 LYS cc_start: 0.8342 (tppt) cc_final: 0.8111 (ttmm) REVERT: B 875 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7461 (tm-30) REVERT: B 898 GLU cc_start: 0.7730 (mp0) cc_final: 0.7146 (mm-30) REVERT: B 927 MET cc_start: 0.8275 (ptp) cc_final: 0.8030 (ptm) REVERT: B 935 TYR cc_start: 0.8108 (t80) cc_final: 0.7865 (t80) REVERT: B 947 ARG cc_start: 0.8119 (ptm160) cc_final: 0.7794 (ptm-80) REVERT: B 980 ASP cc_start: 0.6742 (t0) cc_final: 0.6069 (t0) REVERT: B 1014 MET cc_start: 0.6814 (mmm) cc_final: 0.6465 (mmm) REVERT: B 1131 LYS cc_start: 0.8695 (tttp) cc_final: 0.8290 (tptp) REVERT: B 1134 GLU cc_start: 0.8615 (tp30) cc_final: 0.8059 (tp30) REVERT: C 14 SER cc_start: 0.8469 (t) cc_final: 0.8038 (p) REVERT: C 17 SER cc_start: 0.8485 (p) cc_final: 0.8265 (p) outliers start: 34 outliers final: 25 residues processed: 349 average time/residue: 0.7117 time to fit residues: 332.7787 Evaluate side-chains 344 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 318 time to evaluate : 2.035 ------------------------------------------------------------------------------- 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 A residue 315 THR Chi-restraints excluded: chain B residue 28 ASP 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 260 CYS 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 805 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 80 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN A 47 ASN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.171367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124336 restraints weight = 48210.545| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.90 r_work: 0.3317 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3712 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= 0.166 Angle : 0.500 5.631 18357 Z= 0.264 Chirality : 0.043 0.143 2082 Planarity : 0.003 0.065 2368 Dihedral : 4.157 15.346 1822 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.82 % Allowed : 16.22 % 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: -0.80 (0.20), residues: 1669 helix: 2.58 (0.35), residues: 222 sheet: -0.82 (0.19), residues: 646 loop : -1.12 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1073 HIS 0.004 0.001 HIS C 20 PHE 0.013 0.001 PHE B 851 TYR 0.011 0.001 TYR B 171 ARG 0.007 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 528) hydrogen bonds : angle 4.95536 ( 1467) covalent geometry : bond 0.00358 (13564) covalent geometry : angle 0.50041 (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 : 1.807 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 33 ASN cc_start: 0.8264 (t0) cc_final: 0.8003 (t0) REVERT: A 39 GLU cc_start: 0.6804 (tm-30) cc_final: 0.5849 (tm-30) REVERT: A 46 ILE cc_start: 0.8707 (mm) cc_final: 0.8223 (mm) REVERT: A 50 ASP cc_start: 0.8129 (t0) cc_final: 0.7889 (t0) REVERT: A 55 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7742 (tt0) REVERT: A 71 TYR cc_start: 0.8385 (m-10) cc_final: 0.7886 (m-10) REVERT: A 114 MET cc_start: 0.8105 (mpp) cc_final: 0.7407 (mpp) REVERT: A 136 ASP cc_start: 0.8171 (t0) cc_final: 0.7967 (t0) REVERT: A 167 LYS cc_start: 0.8378 (mttt) cc_final: 0.8071 (mttp) REVERT: A 210 ARG cc_start: 0.7511 (mtp180) cc_final: 0.6976 (ttm-80) REVERT: A 266 ASP cc_start: 0.8116 (p0) cc_final: 0.7833 (p0) REVERT: A 276 ASN cc_start: 0.8318 (p0) cc_final: 0.7851 (p0) REVERT: A 322 TYR cc_start: 0.8442 (m-80) cc_final: 0.8215 (m-80) REVERT: A 325 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7461 (tm-30) REVERT: A 335 LYS cc_start: 0.7525 (mttt) cc_final: 0.7314 (mttt) REVERT: A 338 ASP cc_start: 0.7557 (t0) cc_final: 0.7258 (t0) REVERT: B 40 GLU cc_start: 0.7082 (mp0) cc_final: 0.6729 (mp0) REVERT: B 54 GLU cc_start: 0.7089 (tp30) cc_final: 0.5989 (tp30) REVERT: B 90 GLU cc_start: 0.7898 (pt0) cc_final: 0.7683 (pt0) REVERT: B 92 LYS cc_start: 0.8446 (ttpp) cc_final: 0.8119 (ttmm) REVERT: B 109 GLN cc_start: 0.8134 (tt0) cc_final: 0.7930 (tt0) REVERT: B 127 GLU cc_start: 0.8265 (mp0) cc_final: 0.7931 (mp0) REVERT: B 158 ARG cc_start: 0.8621 (mmm-85) cc_final: 0.8387 (mmm-85) REVERT: B 204 LYS cc_start: 0.8845 (tttt) cc_final: 0.8619 (tttp) REVERT: B 209 GLN cc_start: 0.7888 (tm130) cc_final: 0.7661 (tm-30) REVERT: B 277 GLU cc_start: 0.7960 (tt0) cc_final: 0.7086 (tp30) REVERT: B 319 ASN cc_start: 0.8354 (t0) cc_final: 0.7786 (m-40) REVERT: B 720 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8521 (p) REVERT: B 801 VAL cc_start: 0.9196 (t) cc_final: 0.8881 (m) REVERT: B 854 SER cc_start: 0.7738 (t) cc_final: 0.7456 (p) REVERT: B 857 LYS cc_start: 0.8326 (tppt) cc_final: 0.8106 (ttmm) REVERT: B 875 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7446 (tm-30) REVERT: B 898 GLU cc_start: 0.7628 (mp0) cc_final: 0.7062 (mm-30) REVERT: B 927 MET cc_start: 0.8222 (ptp) cc_final: 0.7965 (ptm) REVERT: B 947 ARG cc_start: 0.8109 (ptm160) cc_final: 0.7859 (ptm-80) REVERT: B 989 ARG cc_start: 0.7965 (mtt90) cc_final: 0.7724 (mtt90) REVERT: B 1014 MET cc_start: 0.6857 (mmm) cc_final: 0.6492 (mmm) REVERT: B 1100 ILE cc_start: 0.8645 (pt) cc_final: 0.8444 (pt) REVERT: B 1131 LYS cc_start: 0.8674 (tttp) cc_final: 0.8296 (tptp) REVERT: B 1134 GLU cc_start: 0.8601 (tp30) cc_final: 0.8048 (tp30) REVERT: B 1135 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8073 (tp30) REVERT: B 1138 ARG cc_start: 0.8778 (ttm-80) cc_final: 0.8345 (ttm-80) REVERT: C 14 SER cc_start: 0.8367 (t) cc_final: 0.8005 (p) outliers start: 27 outliers final: 22 residues processed: 344 average time/residue: 0.6925 time to fit residues: 315.0689 Evaluate side-chains 351 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 328 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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 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 593 MET Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 750 THR 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=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: 1.9990 chunk 108 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 40.0000 chunk 11 optimal weight: 50.0000 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 163 HIS ** 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 = 0.4114 r_free = 0.4114 target = 0.168069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.121711 restraints weight = 48956.291| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.86 r_work: 0.3321 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.130 13564 Z= 0.413 Angle : 0.603 6.092 18357 Z= 0.323 Chirality : 0.045 0.145 2082 Planarity : 0.004 0.073 2368 Dihedral : 4.618 17.848 1822 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.09 % Allowed : 16.69 % Favored : 81.22 % 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: -0.99 (0.20), residues: 1669 helix: 2.46 (0.36), residues: 222 sheet: -0.83 (0.19), residues: 639 loop : -1.37 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 214 HIS 0.009 0.001 HIS B1070 PHE 0.025 0.002 PHE B 733 TYR 0.018 0.002 TYR B 171 ARG 0.008 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 528) hydrogen bonds : angle 5.25600 ( 1467) covalent geometry : bond 0.00870 (13564) covalent geometry : angle 0.60258 (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 365 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 334 time to evaluate : 1.929 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: 0.6906 (tm-30) cc_final: 0.5970 (tm-30) REVERT: A 46 ILE cc_start: 0.8817 (mm) cc_final: 0.8369 (mm) REVERT: A 50 ASP cc_start: 0.8162 (t0) cc_final: 0.7927 (t0) REVERT: A 55 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7757 (tt0) REVERT: A 71 TYR cc_start: 0.8417 (m-10) cc_final: 0.7980 (m-10) REVERT: A 114 MET cc_start: 0.8109 (mpp) cc_final: 0.7433 (mpp) REVERT: A 167 LYS cc_start: 0.8394 (mttt) cc_final: 0.8121 (mttp) REVERT: A 210 ARG cc_start: 0.7499 (mtp180) cc_final: 0.7059 (ttm-80) REVERT: A 266 ASP cc_start: 0.8001 (p0) cc_final: 0.7642 (p0) REVERT: A 281 LEU cc_start: 0.8818 (tp) cc_final: 0.8492 (tp) REVERT: A 322 TYR cc_start: 0.8523 (m-80) cc_final: 0.8312 (m-80) REVERT: A 325 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 335 LYS cc_start: 0.7584 (mttt) cc_final: 0.7382 (mttt) REVERT: A 338 ASP cc_start: 0.7634 (t0) cc_final: 0.7360 (t0) REVERT: B 40 GLU cc_start: 0.7100 (mp0) cc_final: 0.6804 (mp0) REVERT: B 54 GLU cc_start: 0.7088 (tp30) cc_final: 0.5974 (tp30) REVERT: B 92 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8187 (ttmm) REVERT: B 109 GLN cc_start: 0.8179 (tt0) cc_final: 0.7924 (tt0) REVERT: B 127 GLU cc_start: 0.8285 (mp0) cc_final: 0.7994 (mp0) REVERT: B 158 ARG cc_start: 0.8572 (mmm-85) cc_final: 0.8323 (mmm-85) REVERT: B 204 LYS cc_start: 0.8824 (tttt) cc_final: 0.8604 (tttp) REVERT: B 277 GLU cc_start: 0.7987 (tt0) cc_final: 0.7139 (tp30) REVERT: B 319 ASN cc_start: 0.8476 (t0) cc_final: 0.8270 (t0) REVERT: B 679 MET cc_start: 0.6638 (tmt) cc_final: 0.6425 (tmt) REVERT: B 801 VAL cc_start: 0.9167 (t) cc_final: 0.8896 (m) REVERT: B 854 SER cc_start: 0.7904 (t) cc_final: 0.7644 (p) REVERT: B 857 LYS cc_start: 0.8350 (tppt) cc_final: 0.8147 (ttmm) REVERT: B 898 GLU cc_start: 0.7559 (mp0) cc_final: 0.7043 (mm-30) REVERT: B 927 MET cc_start: 0.8282 (ptp) cc_final: 0.8024 (ptm) REVERT: B 935 TYR cc_start: 0.8104 (t80) cc_final: 0.7802 (t80) REVERT: B 947 ARG cc_start: 0.8144 (ptm160) cc_final: 0.7828 (ptm-80) REVERT: B 980 ASP cc_start: 0.6673 (t0) cc_final: 0.6058 (t0) REVERT: B 989 ARG cc_start: 0.7974 (mtt90) cc_final: 0.7767 (mtt90) REVERT: B 1128 ASP cc_start: 0.8554 (m-30) cc_final: 0.8111 (t0) REVERT: B 1131 LYS cc_start: 0.8761 (tttp) cc_final: 0.8375 (tptm) REVERT: B 1134 GLU cc_start: 0.8663 (tp30) cc_final: 0.8183 (tp30) REVERT: C 14 SER cc_start: 0.8443 (t) cc_final: 0.8199 (p) REVERT: C 19 PHE cc_start: 0.8738 (t80) cc_final: 0.8351 (t80) outliers start: 31 outliers final: 28 residues processed: 345 average time/residue: 0.7917 time to fit residues: 360.7725 Evaluate side-chains 351 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 323 time to evaluate : 1.949 ------------------------------------------------------------------------------- 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 132 LEU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 230 ASN 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 235 GLU 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 593 MET Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 931 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 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: 0.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 121 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 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 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 = 0.4142 r_free = 0.4142 target = 0.170319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.122895 restraints weight = 48150.551| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.92 r_work: 0.3313 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13564 Z= 0.166 Angle : 0.526 8.123 18357 Z= 0.277 Chirality : 0.043 0.152 2082 Planarity : 0.003 0.066 2368 Dihedral : 4.337 18.171 1822 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.02 % Allowed : 17.90 % Favored : 80.08 % 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: -0.79 (0.20), residues: 1669 helix: 2.70 (0.36), residues: 222 sheet: -0.75 (0.20), residues: 626 loop : -1.22 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 207 HIS 0.004 0.001 HIS C 20 PHE 0.015 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 0.03509 ( 528) hydrogen bonds : angle 5.03312 ( 1467) covalent geometry : bond 0.00361 (13564) covalent geometry : angle 0.52648 (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 365 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 335 time to evaluate : 2.070 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: 0.6872 (tm-30) cc_final: 0.5902 (tm-30) REVERT: A 46 ILE cc_start: 0.8784 (mm) cc_final: 0.8329 (mm) REVERT: A 50 ASP cc_start: 0.8165 (t0) cc_final: 0.7920 (t0) REVERT: A 55 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7739 (tt0) REVERT: A 71 TYR cc_start: 0.8385 (m-10) cc_final: 0.7900 (m-10) REVERT: A 114 MET cc_start: 0.8131 (mpp) cc_final: 0.7400 (mpp) REVERT: A 144 VAL cc_start: 0.8892 (t) cc_final: 0.8639 (m) REVERT: A 167 LYS cc_start: 0.8468 (mttt) cc_final: 0.8173 (mttp) REVERT: A 210 ARG cc_start: 0.7489 (mtp180) cc_final: 0.6964 (ttm-80) REVERT: A 212 LYS cc_start: 0.6861 (mttt) cc_final: 0.6554 (mttt) REVERT: A 276 ASN cc_start: 0.8216 (p0) cc_final: 0.7771 (p0) REVERT: A 281 LEU cc_start: 0.8798 (tp) cc_final: 0.8467 (tp) REVERT: A 325 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7421 (tm-30) REVERT: A 338 ASP cc_start: 0.7617 (t0) cc_final: 0.7354 (t0) REVERT: A 355 ASP cc_start: 0.8278 (p0) cc_final: 0.7980 (p0) REVERT: B 40 GLU cc_start: 0.7075 (mp0) cc_final: 0.6732 (mp0) REVERT: B 54 GLU cc_start: 0.7129 (tp30) cc_final: 0.5952 (tp30) REVERT: B 92 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8182 (mtpp) REVERT: B 116 SER cc_start: 0.8416 (m) cc_final: 0.8166 (t) REVERT: B 127 GLU cc_start: 0.8254 (mp0) cc_final: 0.7900 (mp0) REVERT: B 204 LYS cc_start: 0.8817 (tttt) cc_final: 0.8580 (tttp) REVERT: B 277 GLU cc_start: 0.8014 (tt0) cc_final: 0.7132 (tp30) REVERT: B 801 VAL cc_start: 0.9188 (t) cc_final: 0.8887 (m) REVERT: B 854 SER cc_start: 0.7902 (t) cc_final: 0.7655 (p) REVERT: B 875 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7418 (tm-30) REVERT: B 898 GLU cc_start: 0.7517 (mp0) cc_final: 0.7010 (mm-30) REVERT: B 910 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7109 (mtp) REVERT: B 927 MET cc_start: 0.8216 (ptp) cc_final: 0.7939 (ptm) REVERT: B 935 TYR cc_start: 0.8181 (t80) cc_final: 0.7885 (t80) REVERT: B 947 ARG cc_start: 0.8193 (ptm160) cc_final: 0.7894 (ptm-80) REVERT: B 980 ASP cc_start: 0.6674 (t0) cc_final: 0.6064 (t0) REVERT: B 1122 ARG cc_start: 0.7974 (ttp80) cc_final: 0.7706 (tmm-80) REVERT: B 1131 LYS cc_start: 0.8721 (tttp) cc_final: 0.8323 (tptm) REVERT: B 1134 GLU cc_start: 0.8642 (tp30) cc_final: 0.8124 (tp30) REVERT: B 1138 ARG cc_start: 0.8773 (ttm-80) cc_final: 0.8508 (ttm-80) outliers start: 30 outliers final: 23 residues processed: 344 average time/residue: 0.6927 time to fit residues: 313.1910 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 : 1.892 ------------------------------------------------------------------------------- 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 254 LYS Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 910 MET 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: 0.9990 chunk 135 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 123 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 145 optimal weight: 0.4980 chunk 130 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.171299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.123595 restraints weight = 47942.446| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.00 r_work: 0.3351 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13564 Z= 0.146 Angle : 0.519 8.713 18357 Z= 0.271 Chirality : 0.043 0.150 2082 Planarity : 0.003 0.063 2368 Dihedral : 4.188 16.621 1822 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.55 % Allowed : 18.51 % Favored : 79.95 % 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: -0.65 (0.20), residues: 1669 helix: 2.85 (0.36), residues: 222 sheet: -0.64 (0.20), residues: 624 loop : -1.16 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 127 HIS 0.005 0.001 HIS D 140 PHE 0.014 0.001 PHE B 851 TYR 0.013 0.001 TYR A 319 ARG 0.006 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 528) hydrogen bonds : angle 4.90155 ( 1467) covalent geometry : bond 0.00318 (13564) covalent geometry : angle 0.51900 (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 348 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 325 time to evaluate : 1.863 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: 0.6871 (tm-30) cc_final: 0.5907 (tm-30) REVERT: A 46 ILE cc_start: 0.8748 (mm) cc_final: 0.8299 (mm) REVERT: A 50 ASP cc_start: 0.8174 (t0) cc_final: 0.7932 (t0) REVERT: A 55 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7738 (tt0) REVERT: A 71 TYR cc_start: 0.8366 (m-10) cc_final: 0.7899 (m-10) REVERT: A 114 MET cc_start: 0.8137 (mpp) cc_final: 0.7418 (mpp) REVERT: A 167 LYS cc_start: 0.8483 (mttt) cc_final: 0.8199 (mttp) REVERT: A 210 ARG cc_start: 0.7499 (mtp180) cc_final: 0.7009 (ttm-80) REVERT: A 276 ASN cc_start: 0.8251 (p0) cc_final: 0.7807 (p0) REVERT: A 281 LEU cc_start: 0.8783 (tp) cc_final: 0.8450 (tp) REVERT: A 325 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7442 (tm-30) REVERT: A 338 ASP cc_start: 0.7616 (t0) cc_final: 0.7353 (t0) REVERT: B 40 GLU cc_start: 0.7129 (mp0) cc_final: 0.6767 (mp0) REVERT: B 54 GLU cc_start: 0.7095 (tp30) cc_final: 0.5914 (tp30) REVERT: B 92 LYS cc_start: 0.8433 (ttpp) cc_final: 0.8116 (ttmm) REVERT: B 116 SER cc_start: 0.8416 (m) cc_final: 0.8160 (t) REVERT: B 127 GLU cc_start: 0.8259 (mp0) cc_final: 0.7914 (mp0) REVERT: B 166 ASP cc_start: 0.8010 (t0) cc_final: 0.7549 (p0) REVERT: B 204 LYS cc_start: 0.8825 (tttt) cc_final: 0.8571 (tttp) REVERT: B 277 GLU cc_start: 0.8003 (tt0) cc_final: 0.7178 (tp30) REVERT: B 343 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8166 (mm-40) REVERT: B 801 VAL cc_start: 0.9175 (t) cc_final: 0.8870 (m) REVERT: B 854 SER cc_start: 0.7913 (t) cc_final: 0.7675 (p) REVERT: B 875 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7366 (tm-30) REVERT: B 898 GLU cc_start: 0.7509 (mp0) cc_final: 0.6890 (mm-30) REVERT: B 910 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.7105 (mtp) REVERT: B 927 MET cc_start: 0.8210 (ptp) cc_final: 0.7947 (ptm) REVERT: B 935 TYR cc_start: 0.8194 (t80) cc_final: 0.7912 (t80) REVERT: B 947 ARG cc_start: 0.8173 (ptm160) cc_final: 0.7885 (ptm-80) REVERT: B 980 ASP cc_start: 0.6702 (t0) cc_final: 0.6092 (t0) REVERT: B 1122 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7695 (tmm-80) REVERT: B 1131 LYS cc_start: 0.8714 (tttp) cc_final: 0.8344 (tptm) REVERT: B 1134 GLU cc_start: 0.8628 (tp30) cc_final: 0.8126 (tp30) outliers start: 23 outliers final: 21 residues processed: 333 average time/residue: 0.7263 time to fit residues: 316.9803 Evaluate side-chains 343 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 321 time to evaluate : 1.968 ------------------------------------------------------------------------------- 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 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 719 GLU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 910 MET Chi-restraints excluded: chain B residue 991 HIS Chi-restraints excluded: chain B residue 1025 GLN 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: 1.9990 chunk 72 optimal weight: 0.0980 chunk 94 optimal weight: 40.0000 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 46 optimal weight: 0.3980 chunk 51 optimal weight: 0.0270 chunk 93 optimal weight: 10.0000 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.172158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125109 restraints weight = 47936.796| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.91 r_work: 0.3362 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13564 Z= 0.116 Angle : 0.514 10.005 18357 Z= 0.266 Chirality : 0.043 0.149 2082 Planarity : 0.003 0.069 2368 Dihedral : 4.064 15.783 1822 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.48 % Allowed : 18.84 % Favored : 79.68 % 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: 2.96 (0.36), residues: 222 sheet: -0.50 (0.20), residues: 619 loop : -1.08 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.004 0.000 HIS C 20 PHE 0.013 0.001 PHE B 851 TYR 0.011 0.001 TYR A 319 ARG 0.007 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 528) hydrogen bonds : angle 4.77376 ( 1467) covalent geometry : bond 0.00263 (13564) covalent geometry : angle 0.51350 (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 349 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 327 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8243 (mtm110) cc_final: 0.7996 (mtp-110) REVERT: A 39 GLU cc_start: 0.6853 (tm-30) cc_final: 0.5889 (tm-30) REVERT: A 46 ILE cc_start: 0.8733 (mm) cc_final: 0.8431 (mm) REVERT: A 50 ASP cc_start: 0.8146 (t0) cc_final: 0.7912 (t0) REVERT: A 55 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7696 (tt0) REVERT: A 71 TYR cc_start: 0.8323 (m-10) cc_final: 0.7873 (m-10) REVERT: A 114 MET cc_start: 0.8118 (mpp) cc_final: 0.7409 (mpp) REVERT: A 144 VAL cc_start: 0.8855 (t) cc_final: 0.8619 (m) REVERT: A 167 LYS cc_start: 0.8468 (mttt) cc_final: 0.8184 (mttp) REVERT: A 210 ARG cc_start: 0.7453 (mtp180) cc_final: 0.6910 (ttm-80) REVERT: A 212 LYS cc_start: 0.6772 (mttt) cc_final: 0.6536 (mttt) REVERT: A 276 ASN cc_start: 0.8224 (p0) cc_final: 0.7776 (p0) REVERT: A 281 LEU cc_start: 0.8757 (tp) cc_final: 0.8410 (tp) REVERT: A 325 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 338 ASP cc_start: 0.7605 (t0) cc_final: 0.7275 (t0) REVERT: B 40 GLU cc_start: 0.7104 (mp0) cc_final: 0.6732 (mp0) REVERT: B 54 GLU cc_start: 0.7060 (tp30) cc_final: 0.5874 (tp30) REVERT: B 92 LYS cc_start: 0.8412 (ttpp) cc_final: 0.8096 (ttmm) REVERT: B 127 GLU cc_start: 0.8251 (mp0) cc_final: 0.7905 (mp0) REVERT: B 166 ASP cc_start: 0.7854 (t0) cc_final: 0.7588 (p0) REVERT: B 204 LYS cc_start: 0.8848 (tttt) cc_final: 0.8565 (tttp) REVERT: B 277 GLU cc_start: 0.7993 (tt0) cc_final: 0.7204 (tp30) REVERT: B 319 ASN cc_start: 0.8291 (t0) cc_final: 0.7980 (m-40) REVERT: B 327 ARG cc_start: 0.8341 (ttp80) cc_final: 0.8104 (ttp80) REVERT: B 801 VAL cc_start: 0.9179 (t) cc_final: 0.8870 (m) REVERT: B 854 SER cc_start: 0.7914 (t) cc_final: 0.7687 (p) REVERT: B 875 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7330 (tm-30) REVERT: B 898 GLU cc_start: 0.7482 (mp0) cc_final: 0.6869 (mm-30) REVERT: B 927 MET cc_start: 0.8164 (ptp) cc_final: 0.7924 (ptm) REVERT: B 935 TYR cc_start: 0.8130 (t80) cc_final: 0.7890 (t80) REVERT: B 989 ARG cc_start: 0.7791 (mtt90) cc_final: 0.7566 (mtm-85) REVERT: B 1131 LYS cc_start: 0.8683 (tttp) cc_final: 0.8260 (tptm) REVERT: B 1134 GLU cc_start: 0.8618 (tp30) cc_final: 0.8372 (tp30) REVERT: B 1138 ARG cc_start: 0.8792 (tpp80) cc_final: 0.8564 (ttm-80) outliers start: 22 outliers final: 19 residues processed: 335 average time/residue: 0.7162 time to fit residues: 316.7296 Evaluate side-chains 339 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 320 time to evaluate : 1.807 ------------------------------------------------------------------------------- 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 B residue 70 LYS 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 800 GLU Chi-restraints excluded: chain B residue 991 HIS Chi-restraints excluded: chain B residue 1105 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 113 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 67 optimal weight: 0.0970 chunk 81 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 805 HIS 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 = 0.171148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124768 restraints weight = 48053.618| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.86 r_work: 0.3354 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13564 Z= 0.175 Angle : 0.527 9.720 18357 Z= 0.273 Chirality : 0.042 0.144 2082 Planarity : 0.003 0.068 2368 Dihedral : 4.086 17.421 1822 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.41 % Allowed : 19.18 % 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: -0.49 (0.20), residues: 1669 helix: 2.93 (0.36), residues: 222 sheet: -0.45 (0.20), residues: 615 loop : -1.11 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1073 HIS 0.004 0.001 HIS C 20 PHE 0.013 0.001 PHE B 851 TYR 0.012 0.001 TYR A 319 ARG 0.007 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 528) hydrogen bonds : angle 4.78460 ( 1467) covalent geometry : bond 0.00378 (13564) covalent geometry : angle 0.52652 (18357) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15101.73 seconds wall clock time: 259 minutes 52.27 seconds (15592.27 seconds total)