Starting phenix.real_space_refine on Sun Oct 12 08:48:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qh5_18398/10_2025/8qh5_18398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qh5_18398/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8qh5_18398/10_2025/8qh5_18398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qh5_18398/10_2025/8qh5_18398.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qh5_18398/10_2025/8qh5_18398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qh5_18398/10_2025/8qh5_18398.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.61, per 1000 atoms: 0.16 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: 1.93 Conformation dependent library (CDL) restraints added in 597.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.80 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: 5.98 Time building geometry restraints manager: 2.64 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.140 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.880 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.070 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG D 115 TYR 0.019 0.002 TYR B 613 PHE 0.018 0.002 PHE C 19 TRP 0.020 0.002 TRP A 272 HIS 0.008 0.001 HIS B1070 Details of bonding type rmsd covalent geometry : bond 0.00536 (13564) covalent geometry : angle 0.82975 (18357) hydrogen bonds : bond 0.16307 ( 528) hydrogen bonds : angle 7.36287 ( 1467) *********************** 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 : 0.602 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: 0.7893 (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: 0.7291 (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: 0.6714 (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: 0.6614 (t70) REVERT: B 30 ASN cc_start: 0.7398 (m110) cc_final: 0.7026 (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: 0.5307 (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: 0.7509 (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: 0.7429 (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: 0.2861 time to fit residues: 139.0479 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 : 0.664 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.7980 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.175658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.129171 restraints weight = 48370.962| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.93 r_work: 0.3339 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13564 Z= 0.156 Angle : 0.539 5.619 18357 Z= 0.291 Chirality : 0.044 0.162 2082 Planarity : 0.008 0.266 2368 Dihedral : 4.924 67.323 1830 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.14 % Allowed : 15.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.20), residues: 1669 helix: 1.78 (0.36), residues: 215 sheet: -0.83 (0.20), residues: 625 loop : -1.26 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 369 TYR 0.020 0.001 TYR A 71 PHE 0.012 0.001 PHE B 614 TRP 0.018 0.001 TRP B 561 HIS 0.007 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00334 (13564) covalent geometry : angle 0.53917 (18357) hydrogen bonds : bond 0.04468 ( 528) hydrogen bonds : angle 5.61186 ( 1467) *********************** 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 344 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 327 time to evaluate : 0.551 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 31 GLU cc_start: 0.7956 (pp20) cc_final: 0.7695 (pp20) REVERT: A 39 GLU cc_start: 0.6580 (tm-30) cc_final: 0.6092 (tm-30) REVERT: A 46 ILE cc_start: 0.8558 (mm) cc_final: 0.7933 (mm) REVERT: A 50 ASP cc_start: 0.8089 (t0) cc_final: 0.7643 (t0) REVERT: A 69 VAL cc_start: 0.8725 (t) cc_final: 0.8413 (m) REVERT: A 122 LYS cc_start: 0.8644 (mmtp) cc_final: 0.8222 (mmtm) REVERT: A 136 ASP cc_start: 0.8114 (t0) cc_final: 0.7669 (t0) REVERT: A 138 PHE cc_start: 0.8559 (m-80) cc_final: 0.7929 (m-80) REVERT: A 195 SER cc_start: 0.8946 (t) cc_final: 0.8722 (t) REVERT: A 210 ARG cc_start: 0.7476 (mtp180) cc_final: 0.6937 (ttm-80) REVERT: A 256 ASP cc_start: 0.8485 (p0) cc_final: 0.8281 (p0) REVERT: A 265 THR cc_start: 0.8257 (p) cc_final: 0.8057 (p) REVERT: A 266 ASP cc_start: 0.8184 (p0) cc_final: 0.7898 (p0) REVERT: A 281 LEU cc_start: 0.8889 (tp) cc_final: 0.8615 (tp) REVERT: A 338 ASP cc_start: 0.7584 (t0) cc_final: 0.7257 (t0) REVERT: B 28 ASP cc_start: 0.7512 (t0) cc_final: 0.7299 (t0) REVERT: B 40 GLU cc_start: 0.7102 (mp0) cc_final: 0.6678 (mp0) REVERT: B 47 GLU cc_start: 0.8270 (mp0) cc_final: 0.7924 (mm-30) REVERT: B 54 GLU cc_start: 0.6907 (tp30) cc_final: 0.5896 (tp30) REVERT: B 64 MET cc_start: 0.8369 (ttp) cc_final: 0.8168 (ttp) REVERT: B 90 GLU cc_start: 0.8060 (pt0) cc_final: 0.7608 (pt0) REVERT: B 92 LYS cc_start: 0.8427 (ttpp) cc_final: 0.8108 (ttmm) REVERT: B 127 GLU cc_start: 0.8291 (mp0) cc_final: 0.7967 (mp0) REVERT: B 191 LYS cc_start: 0.8668 (tttt) cc_final: 0.8374 (ttmt) REVERT: B 196 SER cc_start: 0.7947 (t) cc_final: 0.7401 (p) REVERT: B 204 LYS cc_start: 0.8929 (tttt) cc_final: 0.8664 (tttp) REVERT: B 213 GLU cc_start: 0.7563 (tt0) cc_final: 0.6505 (tt0) REVERT: B 244 LYS cc_start: 0.8562 (tptm) cc_final: 0.8344 (tppp) REVERT: B 245 TYR cc_start: 0.8135 (t80) cc_final: 0.7856 (t80) REVERT: B 259 VAL cc_start: 0.8673 (m) cc_final: 0.8427 (p) REVERT: B 260 CYS cc_start: 0.7633 (p) cc_final: 0.7424 (p) REVERT: B 277 GLU cc_start: 0.8081 (tt0) cc_final: 0.7234 (tp30) REVERT: B 679 MET cc_start: 0.5756 (tmt) cc_final: 0.5409 (tmt) REVERT: B 730 SER cc_start: 0.8754 (m) cc_final: 0.7922 (p) REVERT: B 732 CYS cc_start: 0.8042 (p) cc_final: 0.7715 (p) REVERT: B 801 VAL cc_start: 0.8990 (t) cc_final: 0.8751 (m) REVERT: B 857 LYS cc_start: 0.8321 (tppt) cc_final: 0.7990 (ttmm) REVERT: B 864 LYS cc_start: 0.8535 (tptt) cc_final: 0.8321 (tptm) REVERT: B 879 LYS cc_start: 0.8542 (mttt) cc_final: 0.8308 (mttp) REVERT: B 898 GLU cc_start: 0.7596 (mp0) cc_final: 0.7173 (mp0) REVERT: B 927 MET cc_start: 0.8215 (ptp) cc_final: 0.7985 (ptm) REVERT: B 944 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7258 (tm-30) REVERT: B 947 ARG cc_start: 0.8123 (ptm160) cc_final: 0.7721 (ttp-110) REVERT: B 989 ARG cc_start: 0.7820 (mtm-85) cc_final: 0.7579 (mtt180) REVERT: B 1014 MET cc_start: 0.6800 (mmm) cc_final: 0.6468 (mmm) REVERT: B 1036 MET cc_start: 0.8700 (tmt) cc_final: 0.8269 (tmt) REVERT: B 1083 GLU cc_start: 0.8023 (mp0) cc_final: 0.7724 (mp0) REVERT: B 1131 LYS cc_start: 0.8632 (tttp) cc_final: 0.8226 (tptm) REVERT: B 1135 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7782 (tp30) REVERT: C 14 SER cc_start: 0.8429 (t) cc_final: 0.7924 (p) REVERT: C 15 ASN cc_start: 0.8479 (m-40) cc_final: 0.8190 (m110) REVERT: C 18 ARG cc_start: 0.8005 (mtp85) cc_final: 0.7709 (mtp85) outliers start: 17 outliers final: 6 residues processed: 336 average time/residue: 0.3066 time to fit residues: 135.1240 Evaluate side-chains 322 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 315 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 225 THR 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 1135 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 57 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 160 optimal weight: 0.0770 chunk 2 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 7 optimal weight: 30.0000 chunk 148 optimal weight: 2.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.173348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125278 restraints weight = 48357.577| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.05 r_work: 0.3351 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13564 Z= 0.174 Angle : 0.521 6.254 18357 Z= 0.277 Chirality : 0.043 0.176 2082 Planarity : 0.004 0.096 2368 Dihedral : 4.248 14.580 1822 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.28 % Allowed : 16.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.20), residues: 1669 helix: 2.11 (0.36), residues: 216 sheet: -0.81 (0.20), residues: 636 loop : -1.15 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 38 TYR 0.017 0.001 TYR A 71 PHE 0.012 0.001 PHE B 829 TRP 0.010 0.001 TRP A 127 HIS 0.011 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00377 (13564) covalent geometry : angle 0.52083 (18357) hydrogen bonds : bond 0.03786 ( 528) hydrogen bonds : angle 5.21635 ( 1467) *********************** 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 357 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 338 time to evaluate : 0.577 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: 0.7877 (pp20) cc_final: 0.7623 (pp20) REVERT: A 32 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8000 (tt) REVERT: A 39 GLU cc_start: 0.6495 (tm-30) cc_final: 0.5881 (tm-30) REVERT: A 46 ILE cc_start: 0.8613 (mm) cc_final: 0.8037 (mm) REVERT: A 50 ASP cc_start: 0.8171 (t0) cc_final: 0.7753 (t0) REVERT: A 114 MET cc_start: 0.8035 (mpp) cc_final: 0.7510 (mpp) REVERT: A 195 SER cc_start: 0.8949 (t) cc_final: 0.8742 (t) REVERT: A 210 ARG cc_start: 0.7735 (mtp180) cc_final: 0.7226 (ttm-80) REVERT: A 266 ASP cc_start: 0.8246 (p0) cc_final: 0.7975 (p0) REVERT: A 281 LEU cc_start: 0.8882 (tp) cc_final: 0.8626 (tp) REVERT: A 338 ASP cc_start: 0.7573 (t0) cc_final: 0.7271 (t0) REVERT: B 28 ASP cc_start: 0.7443 (t0) cc_final: 0.7230 (t70) REVERT: B 40 GLU cc_start: 0.7163 (mp0) cc_final: 0.6745 (mp0) REVERT: B 54 GLU cc_start: 0.6971 (tp30) cc_final: 0.6045 (tp30) REVERT: B 92 LYS cc_start: 0.8452 (ttpp) cc_final: 0.8162 (ttmm) REVERT: B 117 GLU cc_start: 0.7502 (pm20) cc_final: 0.7220 (pm20) REVERT: B 127 GLU cc_start: 0.8330 (mp0) cc_final: 0.8080 (mp0) REVERT: B 191 LYS cc_start: 0.8698 (tttt) cc_final: 0.8360 (ttmt) REVERT: B 196 SER cc_start: 0.8045 (t) cc_final: 0.7505 (p) REVERT: B 204 LYS cc_start: 0.8920 (tttt) cc_final: 0.8612 (tttp) REVERT: B 213 GLU cc_start: 0.7304 (tt0) cc_final: 0.6985 (tm-30) REVERT: B 215 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7878 (mm-30) REVERT: B 245 TYR cc_start: 0.8210 (t80) cc_final: 0.8004 (t80) REVERT: B 259 VAL cc_start: 0.8806 (m) cc_final: 0.8579 (p) REVERT: B 277 GLU cc_start: 0.8074 (tt0) cc_final: 0.7084 (tp30) REVERT: B 291 MET cc_start: 0.7385 (mmm) cc_final: 0.7142 (mmm) REVERT: B 679 MET cc_start: 0.5910 (tmt) cc_final: 0.5674 (tmt) REVERT: B 801 VAL cc_start: 0.9047 (t) cc_final: 0.8754 (m) REVERT: B 857 LYS cc_start: 0.8317 (tppt) cc_final: 0.8028 (ttmm) REVERT: B 864 LYS cc_start: 0.8639 (tptt) cc_final: 0.8426 (tptm) REVERT: B 898 GLU cc_start: 0.7750 (mp0) cc_final: 0.7532 (mp0) REVERT: B 980 ASP cc_start: 0.6886 (t0) cc_final: 0.6420 (t0) REVERT: B 989 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7453 (mtt90) REVERT: B 1014 MET cc_start: 0.6902 (mmm) cc_final: 0.6635 (mmm) REVERT: B 1036 MET cc_start: 0.8727 (tmt) cc_final: 0.8301 (tmt) REVERT: B 1083 GLU cc_start: 0.8076 (mp0) cc_final: 0.7828 (mp0) REVERT: B 1131 LYS cc_start: 0.8655 (tttp) cc_final: 0.8231 (tptp) REVERT: B 1135 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: C 14 SER cc_start: 0.8470 (t) cc_final: 0.8154 (p) outliers start: 19 outliers final: 14 residues processed: 346 average time/residue: 0.3058 time to fit residues: 139.5381 Evaluate side-chains 334 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 318 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 88 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 339 CYS 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 480 SER Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 805 HIS Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 926 LEU 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 119 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 ASN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 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 = 0.4147 r_free = 0.4147 target = 0.173681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126069 restraints weight = 48646.266| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.05 r_work: 0.3337 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 13564 Z= 0.339 Angle : 0.579 5.590 18357 Z= 0.312 Chirality : 0.045 0.141 2082 Planarity : 0.004 0.047 2368 Dihedral : 4.559 16.967 1822 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.09 % Allowed : 16.02 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.20), residues: 1669 helix: 2.13 (0.35), residues: 216 sheet: -0.85 (0.19), residues: 644 loop : -1.33 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 38 TYR 0.017 0.002 TYR B 171 PHE 0.022 0.002 PHE B 733 TRP 0.011 0.002 TRP B1073 HIS 0.010 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00715 (13564) covalent geometry : angle 0.57850 (18357) hydrogen bonds : bond 0.04196 ( 528) hydrogen bonds : angle 5.29242 ( 1467) *********************** 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 355 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 324 time to evaluate : 0.446 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: 0.6736 (tm-30) cc_final: 0.6051 (tm-30) REVERT: A 46 ILE cc_start: 0.8699 (mm) cc_final: 0.8321 (mm) REVERT: A 47 ASN cc_start: 0.7846 (m110) cc_final: 0.7335 (m110) REVERT: A 50 ASP cc_start: 0.8128 (t0) cc_final: 0.7738 (t0) REVERT: A 51 ILE cc_start: 0.8562 (pt) cc_final: 0.8222 (mt) REVERT: A 114 MET cc_start: 0.8092 (mpp) cc_final: 0.7447 (mpp) REVERT: A 167 LYS cc_start: 0.8469 (mttt) cc_final: 0.8169 (mttp) REVERT: A 210 ARG cc_start: 0.7657 (mtp180) cc_final: 0.7183 (ttm-80) REVERT: A 266 ASP cc_start: 0.8199 (p0) cc_final: 0.7930 (p0) REVERT: A 281 LEU cc_start: 0.8824 (tp) cc_final: 0.8556 (tp) REVERT: A 322 TYR cc_start: 0.8421 (m-80) cc_final: 0.8189 (m-80) REVERT: A 338 ASP cc_start: 0.7582 (t0) cc_final: 0.7270 (t0) REVERT: B 40 GLU cc_start: 0.7124 (mp0) cc_final: 0.6588 (mp0) REVERT: B 54 GLU cc_start: 0.7011 (tp30) cc_final: 0.5927 (tp30) REVERT: B 90 GLU cc_start: 0.7917 (pt0) cc_final: 0.7563 (pt0) REVERT: B 92 LYS cc_start: 0.8521 (ttpp) cc_final: 0.8220 (ttmm) REVERT: B 127 GLU cc_start: 0.8289 (mp0) cc_final: 0.7957 (mp0) REVERT: B 204 LYS cc_start: 0.8839 (tttt) cc_final: 0.8574 (tttm) REVERT: B 213 GLU cc_start: 0.7190 (tt0) cc_final: 0.6832 (tm-30) REVERT: B 215 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7898 (mm-30) REVERT: B 259 VAL cc_start: 0.8877 (m) cc_final: 0.8666 (p) REVERT: B 277 GLU cc_start: 0.8024 (tt0) cc_final: 0.7159 (tp30) REVERT: B 288 GLU cc_start: 0.6568 (pm20) cc_final: 0.6291 (pm20) REVERT: B 291 MET cc_start: 0.7323 (mmm) cc_final: 0.7105 (mmm) REVERT: B 801 VAL cc_start: 0.9136 (t) cc_final: 0.8847 (m) REVERT: B 854 SER cc_start: 0.7696 (t) cc_final: 0.7404 (p) REVERT: B 857 LYS cc_start: 0.8346 (tppt) cc_final: 0.8120 (ttmm) REVERT: B 864 LYS cc_start: 0.8677 (tptt) cc_final: 0.8463 (tptm) REVERT: B 875 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7449 (tm-30) REVERT: B 898 GLU cc_start: 0.7757 (mp0) cc_final: 0.7155 (mm-30) REVERT: B 944 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7710 (tm-30) REVERT: B 980 ASP cc_start: 0.6784 (t0) cc_final: 0.6189 (t0) REVERT: B 989 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7683 (mtt90) REVERT: B 1014 MET cc_start: 0.6786 (mmm) cc_final: 0.6392 (mmm) REVERT: B 1069 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8222 (mm-30) REVERT: B 1131 LYS cc_start: 0.8745 (tttp) cc_final: 0.8313 (tptp) REVERT: B 1134 GLU cc_start: 0.8641 (tp30) cc_final: 0.8096 (tp30) REVERT: C 14 SER cc_start: 0.8533 (t) cc_final: 0.8331 (p) outliers start: 31 outliers final: 21 residues processed: 338 average time/residue: 0.2995 time to fit residues: 133.8193 Evaluate side-chains 346 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 325 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 74 GLU Chi-restraints excluded: chain A residue 88 CYS 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 125 ASP Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 805 HIS Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1105 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 2 optimal weight: 30.0000 chunk 72 optimal weight: 0.2980 chunk 149 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 4 optimal weight: 50.0000 chunk 136 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 600 HIS ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.170796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122788 restraints weight = 47905.275| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.02 r_work: 0.3347 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13564 Z= 0.198 Angle : 0.517 5.695 18357 Z= 0.274 Chirality : 0.043 0.150 2082 Planarity : 0.003 0.057 2368 Dihedral : 4.344 16.070 1822 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.29 % Allowed : 16.76 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.20), residues: 1669 helix: 2.28 (0.35), residues: 222 sheet: -0.91 (0.19), residues: 646 loop : -1.22 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.012 0.001 TYR A 71 PHE 0.013 0.001 PHE B 733 TRP 0.008 0.001 TRP B1073 HIS 0.006 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00421 (13564) covalent geometry : angle 0.51673 (18357) hydrogen bonds : bond 0.03601 ( 528) hydrogen bonds : angle 5.13698 ( 1467) *********************** 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 : 0.644 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: 0.6733 (tm-30) cc_final: 0.5978 (tm-30) REVERT: A 46 ILE cc_start: 0.8751 (mm) cc_final: 0.8314 (mm) REVERT: A 50 ASP cc_start: 0.8172 (t0) cc_final: 0.7725 (t0) REVERT: A 51 ILE cc_start: 0.8481 (pt) cc_final: 0.8167 (mt) REVERT: A 55 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7826 (tt0) REVERT: A 114 MET cc_start: 0.8067 (mpp) cc_final: 0.7379 (mpp) REVERT: A 167 LYS cc_start: 0.8403 (mttt) cc_final: 0.8084 (mttp) REVERT: A 210 ARG cc_start: 0.7555 (mtp180) cc_final: 0.7019 (ttm-80) REVERT: A 266 ASP cc_start: 0.8063 (p0) cc_final: 0.7801 (p0) REVERT: A 276 ASN cc_start: 0.8423 (p0) cc_final: 0.8050 (p0) REVERT: A 338 ASP cc_start: 0.7589 (t0) cc_final: 0.7279 (t0) REVERT: B 40 GLU cc_start: 0.7143 (mp0) cc_final: 0.6605 (mp0) REVERT: B 54 GLU cc_start: 0.7023 (tp30) cc_final: 0.5943 (tp30) REVERT: B 90 GLU cc_start: 0.7932 (pt0) cc_final: 0.7624 (pt0) REVERT: B 92 LYS cc_start: 0.8524 (ttpp) cc_final: 0.8194 (ttmm) REVERT: B 109 GLN cc_start: 0.8186 (tt0) cc_final: 0.7923 (tt0) REVERT: B 127 GLU cc_start: 0.8280 (mp0) cc_final: 0.7920 (mp0) REVERT: B 158 ARG cc_start: 0.8630 (mmm-85) cc_final: 0.8415 (mmm-85) REVERT: B 204 LYS cc_start: 0.8853 (tttt) cc_final: 0.8588 (tttm) REVERT: B 213 GLU cc_start: 0.7253 (tt0) cc_final: 0.6970 (tt0) REVERT: B 259 VAL cc_start: 0.8835 (m) cc_final: 0.8601 (p) REVERT: B 277 GLU cc_start: 0.7968 (tt0) cc_final: 0.7116 (tp30) REVERT: B 288 GLU cc_start: 0.6632 (pm20) cc_final: 0.6338 (pm20) REVERT: B 291 MET cc_start: 0.7371 (mmm) cc_final: 0.7134 (mmm) REVERT: B 720 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8572 (p) REVERT: B 801 VAL cc_start: 0.9128 (t) cc_final: 0.8840 (m) REVERT: B 854 SER cc_start: 0.7691 (t) cc_final: 0.7404 (p) REVERT: B 857 LYS cc_start: 0.8328 (tppt) cc_final: 0.8096 (ttmm) REVERT: B 864 LYS cc_start: 0.8689 (tptt) cc_final: 0.8471 (tptm) REVERT: B 875 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7551 (tm-30) REVERT: B 980 ASP cc_start: 0.6752 (t0) cc_final: 0.6087 (t0) REVERT: B 989 ARG cc_start: 0.7962 (mtm-85) cc_final: 0.7708 (mtt90) REVERT: B 1014 MET cc_start: 0.6818 (mmm) cc_final: 0.6429 (mmm) REVERT: B 1128 ASP cc_start: 0.8469 (m-30) cc_final: 0.8056 (t0) REVERT: B 1131 LYS cc_start: 0.8668 (tttp) cc_final: 0.8265 (tptp) REVERT: B 1134 GLU cc_start: 0.8634 (tp30) cc_final: 0.8142 (tp30) REVERT: C 14 SER cc_start: 0.8525 (t) cc_final: 0.8004 (p) REVERT: C 17 SER cc_start: 0.8553 (p) cc_final: 0.8312 (p) outliers start: 34 outliers final: 25 residues processed: 347 average time/residue: 0.3146 time to fit residues: 144.0859 Evaluate side-chains 353 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 327 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 61 SER Chi-restraints excluded: chain A residue 68 ILE 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 B residue 87 CYS Chi-restraints excluded: chain B residue 114 ARG 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 480 SER Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain B residue 1114 TYR Chi-restraints excluded: chain C residue 43 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 117 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 84 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 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 = 0.4141 r_free = 0.4141 target = 0.169889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122739 restraints weight = 48372.283| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.95 r_work: 0.3230 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 13564 Z= 0.252 Angle : 0.530 5.605 18357 Z= 0.283 Chirality : 0.043 0.142 2082 Planarity : 0.003 0.061 2368 Dihedral : 4.359 16.448 1822 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.22 % Allowed : 16.69 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.20), residues: 1669 helix: 2.43 (0.35), residues: 222 sheet: -0.82 (0.19), residues: 637 loop : -1.29 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 20 TYR 0.014 0.001 TYR B 171 PHE 0.016 0.002 PHE B 733 TRP 0.010 0.001 TRP B1073 HIS 0.004 0.001 HIS B1070 Details of bonding type rmsd covalent geometry : bond 0.00534 (13564) covalent geometry : angle 0.53007 (18357) hydrogen bonds : bond 0.03732 ( 528) hydrogen bonds : angle 5.13727 ( 1467) *********************** 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 369 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 336 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.8350 (t0) cc_final: 0.8045 (t0) REVERT: A 39 GLU cc_start: 0.6712 (tm-30) cc_final: 0.5946 (tm-30) REVERT: A 46 ILE cc_start: 0.8697 (mm) cc_final: 0.8205 (mm) REVERT: A 55 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7758 (tt0) REVERT: A 114 MET cc_start: 0.8113 (mpp) cc_final: 0.7346 (mpp) REVERT: A 167 LYS cc_start: 0.8411 (mttt) cc_final: 0.8107 (mttp) REVERT: A 210 ARG cc_start: 0.7546 (mtp180) cc_final: 0.6990 (ttm-80) REVERT: A 266 ASP cc_start: 0.8056 (p0) cc_final: 0.7842 (p0) REVERT: A 281 LEU cc_start: 0.8782 (tp) cc_final: 0.8460 (tp) REVERT: A 338 ASP cc_start: 0.7614 (t0) cc_final: 0.7254 (t0) REVERT: B 40 GLU cc_start: 0.7247 (mp0) cc_final: 0.6659 (mp0) REVERT: B 54 GLU cc_start: 0.6933 (tp30) cc_final: 0.5763 (tp30) REVERT: B 92 LYS cc_start: 0.8488 (ttpp) cc_final: 0.8066 (ttmm) REVERT: B 109 GLN cc_start: 0.8278 (tt0) cc_final: 0.8023 (tt0) REVERT: B 127 GLU cc_start: 0.8351 (mp0) cc_final: 0.8032 (mp0) REVERT: B 204 LYS cc_start: 0.8865 (tttt) cc_final: 0.8604 (tttp) REVERT: B 259 VAL cc_start: 0.8840 (m) cc_final: 0.8606 (p) REVERT: B 277 GLU cc_start: 0.8052 (tt0) cc_final: 0.7138 (tp30) REVERT: B 288 GLU cc_start: 0.6427 (pm20) cc_final: 0.6213 (pm20) REVERT: B 291 MET cc_start: 0.7412 (mmm) cc_final: 0.7155 (mmm) REVERT: B 720 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8519 (p) REVERT: B 728 GLU cc_start: 0.8376 (tp30) cc_final: 0.8094 (tp30) REVERT: B 801 VAL cc_start: 0.9094 (t) cc_final: 0.8825 (m) REVERT: B 809 GLN cc_start: 0.8581 (mt0) cc_final: 0.8312 (mp10) REVERT: B 840 GLU cc_start: 0.7847 (mp0) cc_final: 0.7644 (mp0) REVERT: B 854 SER cc_start: 0.7774 (t) cc_final: 0.7490 (p) REVERT: B 857 LYS cc_start: 0.8278 (tppt) cc_final: 0.8037 (ttmm) REVERT: B 864 LYS cc_start: 0.8692 (tptt) cc_final: 0.8416 (tptm) REVERT: B 875 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7473 (tm-30) REVERT: B 898 GLU cc_start: 0.7569 (mp0) cc_final: 0.6981 (mm-30) REVERT: B 980 ASP cc_start: 0.6679 (t0) cc_final: 0.6005 (t0) REVERT: B 989 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7702 (mtt90) REVERT: B 1014 MET cc_start: 0.6706 (mmm) cc_final: 0.6328 (mmm) REVERT: B 1128 ASP cc_start: 0.8567 (m-30) cc_final: 0.8060 (t0) REVERT: B 1131 LYS cc_start: 0.8687 (tttp) cc_final: 0.8249 (tptp) REVERT: B 1134 GLU cc_start: 0.8636 (tp30) cc_final: 0.8241 (tp30) REVERT: B 1138 ARG cc_start: 0.8790 (ttm-80) cc_final: 0.8364 (ttm-80) REVERT: C 14 SER cc_start: 0.8352 (t) cc_final: 0.7861 (p) REVERT: C 17 SER cc_start: 0.8503 (p) cc_final: 0.8267 (p) outliers start: 33 outliers final: 26 residues processed: 350 average time/residue: 0.3207 time to fit residues: 147.6195 Evaluate side-chains 349 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 322 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 61 SER 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 260 CYS Chi-restraints excluded: chain B residue 363 CYS 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 800 GLU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain B residue 1114 TYR Chi-restraints excluded: chain C residue 43 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 123 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 14 optimal weight: 20.0000 chunk 87 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 796 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.170677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.123243 restraints weight = 48414.925| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.98 r_work: 0.3312 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13564 Z= 0.183 Angle : 0.518 6.071 18357 Z= 0.274 Chirality : 0.043 0.149 2082 Planarity : 0.003 0.062 2368 Dihedral : 4.279 15.825 1822 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.95 % Allowed : 18.17 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.20), residues: 1669 helix: 2.62 (0.36), residues: 222 sheet: -0.81 (0.19), residues: 635 loop : -1.22 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 20 TYR 0.016 0.001 TYR A 350 PHE 0.013 0.001 PHE B 851 TRP 0.007 0.001 TRP A 127 HIS 0.004 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00393 (13564) covalent geometry : angle 0.51801 (18357) hydrogen bonds : bond 0.03495 ( 528) hydrogen bonds : angle 5.02559 ( 1467) *********************** 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 363 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 334 time to evaluate : 0.576 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: A 39 GLU cc_start: 0.6790 (tm-30) cc_final: 0.5868 (tm-30) REVERT: A 46 ILE cc_start: 0.8769 (mm) cc_final: 0.8327 (mm) REVERT: A 55 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7765 (tt0) REVERT: A 71 TYR cc_start: 0.8501 (m-10) cc_final: 0.8160 (m-10) REVERT: A 114 MET cc_start: 0.8106 (mpp) cc_final: 0.7389 (mpp) REVERT: A 144 VAL cc_start: 0.8872 (t) cc_final: 0.8616 (m) REVERT: A 167 LYS cc_start: 0.8386 (mttt) cc_final: 0.8094 (mttp) REVERT: A 210 ARG cc_start: 0.7533 (mtp180) cc_final: 0.6957 (ttm-80) REVERT: A 266 ASP cc_start: 0.7984 (p0) cc_final: 0.7735 (p0) REVERT: A 276 ASN cc_start: 0.8262 (p0) cc_final: 0.7849 (p0) REVERT: A 281 LEU cc_start: 0.8812 (tp) cc_final: 0.8473 (tp) REVERT: A 338 ASP cc_start: 0.7632 (t0) cc_final: 0.7351 (t0) REVERT: B 40 GLU cc_start: 0.7154 (mp0) cc_final: 0.6606 (mp0) REVERT: B 54 GLU cc_start: 0.7019 (tp30) cc_final: 0.5903 (tp30) REVERT: B 92 LYS cc_start: 0.8491 (ttpp) cc_final: 0.8127 (ttmm) REVERT: B 114 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7582 (mtm-85) REVERT: B 127 GLU cc_start: 0.8306 (mp0) cc_final: 0.7999 (mp0) REVERT: B 204 LYS cc_start: 0.8836 (tttt) cc_final: 0.8595 (tttp) REVERT: B 259 VAL cc_start: 0.8804 (m) cc_final: 0.8582 (p) REVERT: B 277 GLU cc_start: 0.8000 (tt0) cc_final: 0.7119 (tp30) REVERT: B 288 GLU cc_start: 0.6642 (pm20) cc_final: 0.6440 (pm20) REVERT: B 720 SER cc_start: 0.8825 (OUTLIER) cc_final: 0.8581 (p) REVERT: B 728 GLU cc_start: 0.8389 (tp30) cc_final: 0.8123 (tp30) REVERT: B 801 VAL cc_start: 0.9152 (t) cc_final: 0.8846 (m) REVERT: B 809 GLN cc_start: 0.8563 (mt0) cc_final: 0.8271 (mp10) REVERT: B 854 SER cc_start: 0.7851 (t) cc_final: 0.7582 (p) REVERT: B 864 LYS cc_start: 0.8690 (tptt) cc_final: 0.8444 (tptm) REVERT: B 875 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7440 (tm-30) REVERT: B 898 GLU cc_start: 0.7571 (mp0) cc_final: 0.7239 (mp0) REVERT: B 980 ASP cc_start: 0.6737 (t0) cc_final: 0.6056 (t0) REVERT: B 989 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7760 (mtt90) REVERT: B 1128 ASP cc_start: 0.8522 (m-30) cc_final: 0.8072 (t0) REVERT: B 1131 LYS cc_start: 0.8704 (tttp) cc_final: 0.8330 (tptm) REVERT: B 1134 GLU cc_start: 0.8631 (tp30) cc_final: 0.8080 (tp30) REVERT: B 1135 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8052 (tp30) REVERT: B 1138 ARG cc_start: 0.8803 (ttm-80) cc_final: 0.8358 (ttm-80) REVERT: C 14 SER cc_start: 0.8362 (t) cc_final: 0.7881 (p) REVERT: C 17 SER cc_start: 0.8521 (p) cc_final: 0.8288 (p) REVERT: C 19 PHE cc_start: 0.8743 (t80) cc_final: 0.8392 (t80) outliers start: 29 outliers final: 24 residues processed: 344 average time/residue: 0.3082 time to fit residues: 139.6009 Evaluate side-chains 356 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 330 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 61 SER 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 B residue 87 CYS Chi-restraints excluded: chain B residue 114 ARG 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 720 SER Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain B residue 1114 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 105 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 240 HIS ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.170158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123745 restraints weight = 47764.002| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.85 r_work: 0.3250 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13564 Z= 0.223 Angle : 0.532 6.672 18357 Z= 0.281 Chirality : 0.043 0.147 2082 Planarity : 0.003 0.064 2368 Dihedral : 4.294 16.442 1822 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.36 % Allowed : 18.37 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.20), residues: 1669 helix: 2.67 (0.36), residues: 222 sheet: -0.73 (0.20), residues: 627 loop : -1.25 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 20 TYR 0.014 0.001 TYR B 171 PHE 0.015 0.001 PHE B 733 TRP 0.009 0.001 TRP B1073 HIS 0.004 0.001 HIS B1070 Details of bonding type rmsd covalent geometry : bond 0.00475 (13564) covalent geometry : angle 0.53161 (18357) hydrogen bonds : bond 0.03610 ( 528) hydrogen bonds : angle 5.04617 ( 1467) *********************** 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 366 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 331 time to evaluate : 0.680 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: A 39 GLU cc_start: 0.6786 (tm-30) cc_final: 0.5874 (tm-30) REVERT: A 46 ILE cc_start: 0.8747 (mm) cc_final: 0.8290 (mm) REVERT: A 55 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7730 (tt0) REVERT: A 71 TYR cc_start: 0.8494 (m-10) cc_final: 0.8152 (m-10) REVERT: A 114 MET cc_start: 0.8172 (mpp) cc_final: 0.7410 (mpp) REVERT: A 144 VAL cc_start: 0.8875 (t) cc_final: 0.8604 (m) REVERT: A 167 LYS cc_start: 0.8381 (mttt) cc_final: 0.8076 (mttp) REVERT: A 210 ARG cc_start: 0.7519 (mtp180) cc_final: 0.6978 (ttm-80) REVERT: A 266 ASP cc_start: 0.7936 (p0) cc_final: 0.7616 (p0) REVERT: A 281 LEU cc_start: 0.8795 (tp) cc_final: 0.8454 (tp) REVERT: A 338 ASP cc_start: 0.7624 (t0) cc_final: 0.7321 (t0) REVERT: B 40 GLU cc_start: 0.7175 (mp0) cc_final: 0.6632 (mp0) REVERT: B 54 GLU cc_start: 0.6963 (tp30) cc_final: 0.5701 (tp30) REVERT: B 92 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8215 (mtpp) REVERT: B 114 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7557 (mtm-85) REVERT: B 166 ASP cc_start: 0.8033 (t0) cc_final: 0.7616 (p0) REVERT: B 204 LYS cc_start: 0.8822 (tttt) cc_final: 0.8563 (tttp) REVERT: B 259 VAL cc_start: 0.8836 (m) cc_final: 0.8603 (p) REVERT: B 277 GLU cc_start: 0.8012 (tt0) cc_final: 0.7190 (tp30) REVERT: B 288 GLU cc_start: 0.6732 (pm20) cc_final: 0.6508 (pm20) REVERT: B 343 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8159 (mm-40) REVERT: B 728 GLU cc_start: 0.8364 (tp30) cc_final: 0.8105 (tp30) REVERT: B 801 VAL cc_start: 0.9132 (t) cc_final: 0.8845 (m) REVERT: B 854 SER cc_start: 0.7883 (t) cc_final: 0.7633 (p) REVERT: B 864 LYS cc_start: 0.8706 (tptt) cc_final: 0.8494 (tptm) REVERT: B 875 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7405 (tm-30) REVERT: B 898 GLU cc_start: 0.7555 (mp0) cc_final: 0.7195 (mp0) REVERT: B 928 ARG cc_start: 0.7978 (mmm-85) cc_final: 0.7703 (mmt180) REVERT: B 980 ASP cc_start: 0.6682 (t0) cc_final: 0.5984 (t0) REVERT: B 989 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7724 (mtt90) REVERT: B 1128 ASP cc_start: 0.8533 (m-30) cc_final: 0.8050 (t0) REVERT: B 1131 LYS cc_start: 0.8714 (tttp) cc_final: 0.8322 (tptm) REVERT: B 1134 GLU cc_start: 0.8631 (tp30) cc_final: 0.8098 (tp30) REVERT: B 1135 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8159 (mm-30) REVERT: C 17 SER cc_start: 0.8545 (p) cc_final: 0.8290 (p) REVERT: C 19 PHE cc_start: 0.8709 (t80) cc_final: 0.8345 (t80) outliers start: 35 outliers final: 30 residues processed: 345 average time/residue: 0.3251 time to fit residues: 147.4028 Evaluate side-chains 358 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 327 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 61 SER 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 114 ARG 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 370 GLN Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain B residue 1114 TYR Chi-restraints excluded: chain C residue 43 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 135 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** B 36 ASN ** 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 = 0.4151 r_free = 0.4151 target = 0.170890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124592 restraints weight = 47831.805| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.86 r_work: 0.3329 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13564 Z= 0.176 Angle : 0.528 8.990 18357 Z= 0.278 Chirality : 0.043 0.153 2082 Planarity : 0.003 0.062 2368 Dihedral : 4.225 16.137 1822 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.09 % Allowed : 18.78 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.20), residues: 1669 helix: 2.81 (0.36), residues: 222 sheet: -0.61 (0.20), residues: 625 loop : -1.20 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 20 TYR 0.013 0.001 TYR B 171 PHE 0.013 0.001 PHE B 851 TRP 0.007 0.001 TRP B1073 HIS 0.004 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00379 (13564) covalent geometry : angle 0.52770 (18357) hydrogen bonds : bond 0.03425 ( 528) hydrogen bonds : angle 4.94509 ( 1467) *********************** 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 362 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 331 time to evaluate : 0.633 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: A 39 GLU cc_start: 0.6808 (tm-30) cc_final: 0.5902 (tm-30) REVERT: A 46 ILE cc_start: 0.8770 (mm) cc_final: 0.8366 (mm) REVERT: A 55 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7699 (tt0) REVERT: A 71 TYR cc_start: 0.8447 (m-10) cc_final: 0.8148 (m-10) REVERT: A 114 MET cc_start: 0.8111 (mpp) cc_final: 0.7300 (mpp) REVERT: A 167 LYS cc_start: 0.8450 (mttt) cc_final: 0.8162 (mttp) REVERT: A 210 ARG cc_start: 0.7465 (mtp180) cc_final: 0.6944 (ttm-80) REVERT: A 266 ASP cc_start: 0.7872 (p0) cc_final: 0.7531 (p0) REVERT: A 276 ASN cc_start: 0.8302 (p0) cc_final: 0.7876 (p0) REVERT: A 281 LEU cc_start: 0.8746 (tp) cc_final: 0.8403 (tp) REVERT: A 307 PHE cc_start: 0.8630 (m-80) cc_final: 0.8386 (m-80) REVERT: A 338 ASP cc_start: 0.7616 (t0) cc_final: 0.7334 (t0) REVERT: B 40 GLU cc_start: 0.7090 (mp0) cc_final: 0.6637 (mp0) REVERT: B 54 GLU cc_start: 0.6996 (tp30) cc_final: 0.5831 (tp30) REVERT: B 92 LYS cc_start: 0.8477 (ttpp) cc_final: 0.8141 (ttmm) REVERT: B 114 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7512 (mtm-85) REVERT: B 166 ASP cc_start: 0.7886 (t0) cc_final: 0.7622 (p0) REVERT: B 204 LYS cc_start: 0.8795 (tttt) cc_final: 0.8560 (tttp) REVERT: B 259 VAL cc_start: 0.8800 (m) cc_final: 0.8566 (p) REVERT: B 277 GLU cc_start: 0.7982 (tt0) cc_final: 0.7186 (tp30) REVERT: B 288 GLU cc_start: 0.6932 (pm20) cc_final: 0.6697 (pm20) REVERT: B 343 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8145 (mm-40) REVERT: B 728 GLU cc_start: 0.8405 (tp30) cc_final: 0.8142 (tp30) REVERT: B 801 VAL cc_start: 0.9162 (t) cc_final: 0.8866 (m) REVERT: B 809 GLN cc_start: 0.8485 (mt0) cc_final: 0.8229 (mp10) REVERT: B 854 SER cc_start: 0.7912 (t) cc_final: 0.7690 (p) REVERT: B 864 LYS cc_start: 0.8700 (tptt) cc_final: 0.8434 (tptm) REVERT: B 875 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7349 (tm-30) REVERT: B 898 GLU cc_start: 0.7556 (mp0) cc_final: 0.7192 (mp0) REVERT: B 980 ASP cc_start: 0.6754 (t0) cc_final: 0.6081 (t0) REVERT: B 989 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7449 (mtt90) REVERT: B 1128 ASP cc_start: 0.8468 (m-30) cc_final: 0.8047 (t0) REVERT: B 1131 LYS cc_start: 0.8716 (tttp) cc_final: 0.8336 (tptm) REVERT: B 1134 GLU cc_start: 0.8620 (tp30) cc_final: 0.8133 (tp30) REVERT: C 17 SER cc_start: 0.8556 (p) cc_final: 0.8315 (p) REVERT: C 19 PHE cc_start: 0.8695 (t80) cc_final: 0.8320 (t80) outliers start: 31 outliers final: 29 residues processed: 340 average time/residue: 0.3198 time to fit residues: 141.6144 Evaluate side-chains 358 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 328 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 61 SER 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 B residue 87 CYS Chi-restraints excluded: chain B residue 114 ARG 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 719 GLU Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 991 HIS Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain B residue 1114 TYR Chi-restraints excluded: chain C residue 43 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 165 optimal weight: 0.0670 chunk 113 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.179832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132546 restraints weight = 47580.136| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.02 r_work: 0.3318 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13564 Z= 0.144 Angle : 0.521 9.095 18357 Z= 0.273 Chirality : 0.043 0.152 2082 Planarity : 0.003 0.065 2368 Dihedral : 4.154 15.657 1822 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.02 % Allowed : 19.11 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.20), residues: 1669 helix: 2.88 (0.36), residues: 222 sheet: -0.55 (0.20), residues: 626 loop : -1.16 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 20 TYR 0.012 0.001 TYR B 935 PHE 0.014 0.001 PHE B 851 TRP 0.008 0.001 TRP A 127 HIS 0.004 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00316 (13564) covalent geometry : angle 0.52133 (18357) hydrogen bonds : bond 0.03291 ( 528) hydrogen bonds : angle 4.86438 ( 1467) ********************** 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 360 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 330 time to evaluate : 0.628 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: A 39 GLU cc_start: 0.6800 (tm-30) cc_final: 0.5885 (tm-30) REVERT: A 46 ILE cc_start: 0.8760 (mm) cc_final: 0.8336 (mm) REVERT: A 47 ASN cc_start: 0.8071 (m110) cc_final: 0.7857 (m-40) REVERT: A 55 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7727 (tt0) REVERT: A 71 TYR cc_start: 0.8422 (m-10) cc_final: 0.8112 (m-10) REVERT: A 114 MET cc_start: 0.8111 (mpp) cc_final: 0.7286 (mpp) REVERT: A 167 LYS cc_start: 0.8467 (mttt) cc_final: 0.8194 (mttp) REVERT: A 210 ARG cc_start: 0.7488 (mtp180) cc_final: 0.6978 (ttm-80) REVERT: A 266 ASP cc_start: 0.7860 (p0) cc_final: 0.7515 (p0) REVERT: A 276 ASN cc_start: 0.8218 (p0) cc_final: 0.7769 (p0) REVERT: A 281 LEU cc_start: 0.8752 (tp) cc_final: 0.8411 (tp) REVERT: A 297 PHE cc_start: 0.8927 (p90) cc_final: 0.8095 (p90) REVERT: A 307 PHE cc_start: 0.8616 (m-80) cc_final: 0.8381 (m-80) REVERT: A 338 ASP cc_start: 0.7575 (t0) cc_final: 0.7268 (t0) REVERT: B 40 GLU cc_start: 0.7136 (mp0) cc_final: 0.6660 (mp0) REVERT: B 54 GLU cc_start: 0.6999 (tp30) cc_final: 0.5723 (tp30) REVERT: B 92 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8134 (ttmm) REVERT: B 114 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7539 (mtm-85) REVERT: B 166 ASP cc_start: 0.7892 (t0) cc_final: 0.7636 (p0) REVERT: B 204 LYS cc_start: 0.8834 (tttt) cc_final: 0.8549 (tttp) REVERT: B 259 VAL cc_start: 0.8798 (m) cc_final: 0.8561 (p) REVERT: B 277 GLU cc_start: 0.7994 (tt0) cc_final: 0.7180 (tp30) REVERT: B 288 GLU cc_start: 0.6962 (pm20) cc_final: 0.6733 (pm20) REVERT: B 728 GLU cc_start: 0.8383 (tp30) cc_final: 0.8127 (tp30) REVERT: B 801 VAL cc_start: 0.9160 (t) cc_final: 0.8859 (m) REVERT: B 809 GLN cc_start: 0.8512 (mt0) cc_final: 0.8243 (mp10) REVERT: B 840 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7580 (mp0) REVERT: B 854 SER cc_start: 0.7917 (t) cc_final: 0.7688 (p) REVERT: B 864 LYS cc_start: 0.8669 (tptt) cc_final: 0.8429 (tptm) REVERT: B 875 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7351 (tm-30) REVERT: B 898 GLU cc_start: 0.7538 (mp0) cc_final: 0.7168 (mp0) REVERT: B 980 ASP cc_start: 0.6721 (t0) cc_final: 0.6035 (t0) REVERT: B 989 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7463 (mtt90) REVERT: B 1128 ASP cc_start: 0.8480 (m-30) cc_final: 0.8048 (t0) REVERT: B 1131 LYS cc_start: 0.8723 (tttp) cc_final: 0.8323 (tptm) REVERT: B 1134 GLU cc_start: 0.8663 (tp30) cc_final: 0.8131 (tp30) REVERT: B 1138 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8517 (ttm-80) REVERT: C 17 SER cc_start: 0.8521 (p) cc_final: 0.8275 (p) outliers start: 30 outliers final: 27 residues processed: 339 average time/residue: 0.3225 time to fit residues: 142.4380 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 : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 61 SER 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 225 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 209 GLN 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 719 GLU Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain B residue 1114 TYR Chi-restraints excluded: chain C residue 43 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 87 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 156 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 8 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 B 261 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.180473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133157 restraints weight = 47581.423| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.07 r_work: 0.3352 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 13564 Z= 0.188 Angle : 0.779 59.185 18357 Z= 0.445 Chirality : 0.043 0.338 2082 Planarity : 0.003 0.062 2368 Dihedral : 4.148 15.651 1822 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.95 % Allowed : 18.98 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.20), residues: 1669 helix: 2.90 (0.36), residues: 222 sheet: -0.55 (0.20), residues: 626 loop : -1.16 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 20 TYR 0.012 0.001 TYR B 171 PHE 0.015 0.001 PHE B 851 TRP 0.038 0.002 TRP A 214 HIS 0.004 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00403 (13564) covalent geometry : angle 0.77941 (18357) hydrogen bonds : bond 0.03321 ( 528) hydrogen bonds : angle 4.86170 ( 1467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6657.79 seconds wall clock time: 113 minutes 44.44 seconds (6824.44 seconds total)