Starting phenix.real_space_refine on Tue Sep 15 22:18:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5anc_3147/09_2026/5anc_3147.cif Found real_map, /net/cci-nas-00/data/ceres_data/5anc_3147/09_2026/5anc_3147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5anc_3147/09_2026/5anc_3147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5anc_3147/09_2026/5anc_3147.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5anc_3147/09_2026/5anc_3147.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5anc_3147/09_2026/5anc_3147.cif" model { file = "/net/cci-nas-00/data/ceres_data/5anc_3147/09_2026/5anc_3147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5anc_3147/09_2026/5anc_3147.cif" } resolution = 4.2 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= 0.003 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1158 5.49 5 S 128 5.16 5 C 25017 2.51 5 N 8368 2.21 5 O 12136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 46807 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3176 Classifications: {'peptide': 398} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 12, 'TRANS': 382} Chain: "B" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1491 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 184} Chain: "C" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1571 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain: "D" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1245 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 150} Chain: "E" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1017 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 6, 'TRANS': 125} Chain: "F" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "G" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 586 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "H" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 427 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "J" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2015 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 241} Chain: "K" Number of atoms: 8800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8800 Classifications: {'peptide': 1120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 62, 'TRANS': 1057} Chain: "N" Number of atoms: 24758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1162, 24758 Classifications: {'RNAv2': 1162} Modifications used: {'rna2p_pur': 109, 'rna2p_pyr': 57, 'rna3p_pur': 515, 'rna3p_pyr': 481} Link IDs: {'rna2p': 166, 'rna3p': 995} Unresolved chain links: 3 Unresolved chain link angles: 12 Unresolved chain link dihedrals: 9 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 10.80, per 1000 atoms: 0.23 Number of scatterers: 46807 At special positions: 0 Unit cell: (206.15, 194.18, 214.13, 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 128 16.00 P 1158 15.00 O 12136 8.00 N 8368 7.00 C 25017 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 33 " distance=2.94 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: 4.13 Conformation dependent library (CDL) restraints added in 1.6 seconds 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5216 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 31 sheets defined 26.1% alpha, 12.9% beta 321 base pairs and 519 stacking pairs defined. Time for finding SS restraints: 6.68 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.990A pdb=" N PHE A 16 " --> pdb=" O ASN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 140 through 157 removed outlier: 4.571A pdb=" N LYS A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 203 removed outlier: 3.958A pdb=" N GLU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 377 through 389 Processing helix chain 'B' and resid 61 through 84 Processing helix chain 'B' and resid 148 through 163 removed outlier: 3.764A pdb=" N GLN B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 12 removed outlier: 3.774A pdb=" N VAL C 11 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 42 removed outlier: 3.549A pdb=" N LEU C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 50 removed outlier: 3.926A pdb=" N ILE C 46 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY C 48 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 95 through 100 removed outlier: 3.611A pdb=" N VAL C 100 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 137 Processing helix chain 'D' and resid 41 through 43 No H-bonds generated for 'chain 'D' and resid 41 through 43' Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 77 through 86 removed outlier: 4.032A pdb=" N ILE D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.813A pdb=" N ASP D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 118 removed outlier: 4.335A pdb=" N MET D 116 " --> pdb=" O ILE D 112 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 134 removed outlier: 3.718A pdb=" N ILE D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 125 Processing helix chain 'E' and resid 125 through 131 Processing helix chain 'F' and resid 62 through 73 removed outlier: 3.514A pdb=" N CYS F 72 " --> pdb=" O GLY F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 85 Processing helix chain 'F' and resid 145 through 158 removed outlier: 3.647A pdb=" N GLU F 150 " --> pdb=" O ALA F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 188 removed outlier: 3.956A pdb=" N LYS F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LYS F 185 " --> pdb=" O TYR F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 217 removed outlier: 3.943A pdb=" N ASN F 217 " --> pdb=" O ALA F 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 43 Processing helix chain 'G' and resid 53 through 60 removed outlier: 3.619A pdb=" N ILE G 58 " --> pdb=" O VAL G 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 13 removed outlier: 4.032A pdb=" N LEU H 8 " --> pdb=" O SER H 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 41 removed outlier: 4.073A pdb=" N VAL J 37 " --> pdb=" O LYS J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 76 Processing helix chain 'J' and resid 79 through 91 removed outlier: 3.553A pdb=" N ILE J 83 " --> pdb=" O ASP J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 Processing helix chain 'J' and resid 129 through 140 removed outlier: 4.102A pdb=" N LYS J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP J 139 " --> pdb=" O ARG J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 163 removed outlier: 3.647A pdb=" N LYS J 159 " --> pdb=" O LEU J 155 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU J 163 " --> pdb=" O LYS J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.935A pdb=" N LYS J 185 " --> pdb=" O ASN J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 removed outlier: 3.566A pdb=" N ASP J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS J 226 " --> pdb=" O GLU J 222 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU J 227 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR J 228 " --> pdb=" O ILE J 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 13 removed outlier: 3.784A pdb=" N MET K 9 " --> pdb=" O SER K 5 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN K 11 " --> pdb=" O ASP K 7 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU K 12 " --> pdb=" O LYS K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 43 removed outlier: 3.810A pdb=" N LEU K 35 " --> pdb=" O GLY K 31 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER K 42 " --> pdb=" O CYS K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 67 removed outlier: 3.965A pdb=" N GLN K 64 " --> pdb=" O ARG K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 108 removed outlier: 4.005A pdb=" N SER K 104 " --> pdb=" O SER K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 135 removed outlier: 4.109A pdb=" N ALA K 134 " --> pdb=" O VAL K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 155 removed outlier: 5.236A pdb=" N LEU K 155 " --> pdb=" O LEU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 178 removed outlier: 4.302A pdb=" N TYR K 163 " --> pdb=" O PRO K 159 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER K 164 " --> pdb=" O GLN K 160 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA K 175 " --> pdb=" O GLU K 171 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU K 176 " --> pdb=" O GLN K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 204 removed outlier: 3.519A pdb=" N GLN K 204 " --> pdb=" O PRO K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 256 removed outlier: 3.506A pdb=" N LYS K 255 " --> pdb=" O ILE K 251 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE K 256 " --> pdb=" O TYR K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 269 removed outlier: 3.912A pdb=" N GLY K 269 " --> pdb=" O LYS K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 296 Processing helix chain 'K' and resid 297 through 311 removed outlier: 3.624A pdb=" N ILE K 301 " --> pdb=" O ILE K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 323 removed outlier: 4.167A pdb=" N ASP K 317 " --> pdb=" O LYS K 313 " (cutoff:3.500A) Processing helix chain 'K' and resid 337 through 348 removed outlier: 3.972A pdb=" N ILE K 341 " --> pdb=" O PRO K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 363 removed outlier: 3.785A pdb=" N LEU K 356 " --> pdb=" O SER K 352 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ALA K 357 " --> pdb=" O HIS K 353 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET K 358 " --> pdb=" O ALA K 354 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 371 removed outlier: 4.170A pdb=" N ILE K 369 " --> pdb=" O SER K 365 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR K 370 " --> pdb=" O PRO K 366 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA K 371 " --> pdb=" O LEU K 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 365 through 371' Processing helix chain 'K' and resid 397 through 402 removed outlier: 3.842A pdb=" N LYS K 401 " --> pdb=" O ALA K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 429 through 434 Processing helix chain 'K' and resid 434 through 445 removed outlier: 3.709A pdb=" N ILE K 438 " --> pdb=" O THR K 434 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA K 439 " --> pdb=" O GLN K 435 " (cutoff:3.500A) Processing helix chain 'K' and resid 448 through 459 removed outlier: 4.428A pdb=" N LYS K 452 " --> pdb=" O ARG K 448 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 483 removed outlier: 3.574A pdb=" N GLY K 482 " --> pdb=" O GLU K 478 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP K 483 " --> pdb=" O GLU K 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 478 through 483' Processing helix chain 'K' and resid 529 through 536 Processing helix chain 'K' and resid 626 through 628 No H-bonds generated for 'chain 'K' and resid 626 through 628' Processing helix chain 'K' and resid 629 through 644 removed outlier: 3.909A pdb=" N LEU K 633 " --> pdb=" O GLU K 629 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL K 634 " --> pdb=" O MET K 630 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU K 639 " --> pdb=" O LYS K 635 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN K 642 " --> pdb=" O LYS K 638 " (cutoff:3.500A) Processing helix chain 'K' and resid 665 through 674 removed outlier: 3.605A pdb=" N LEU K 674 " --> pdb=" O CYS K 670 " (cutoff:3.500A) Processing helix chain 'K' and resid 759 through 769 Processing helix chain 'K' and resid 786 through 796 removed outlier: 4.186A pdb=" N HIS K 790 " --> pdb=" O GLY K 786 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET K 791 " --> pdb=" O GLU K 787 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS K 793 " --> pdb=" O THR K 789 " (cutoff:3.500A) Processing helix chain 'K' and resid 806 through 812 Processing helix chain 'K' and resid 865 through 877 removed outlier: 3.685A pdb=" N ILE K 869 " --> pdb=" O LEU K 865 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER K 871 " --> pdb=" O ASN K 867 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY K 872 " --> pdb=" O SER K 868 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU K 875 " --> pdb=" O SER K 871 " (cutoff:3.500A) Processing helix chain 'K' and resid 907 through 918 Processing helix chain 'K' and resid 936 through 942 removed outlier: 3.595A pdb=" N THR K 942 " --> pdb=" O PHE K 938 " (cutoff:3.500A) Processing helix chain 'K' and resid 957 through 976 removed outlier: 3.670A pdb=" N LYS K 966 " --> pdb=" O ILE K 962 " (cutoff:3.500A) Processing helix chain 'K' and resid 992 through 994 No H-bonds generated for 'chain 'K' and resid 992 through 994' Processing helix chain 'K' and resid 995 through 1006 removed outlier: 3.828A pdb=" N VAL K 999 " --> pdb=" O VAL K 995 " (cutoff:3.500A) Processing helix chain 'K' and resid 1035 through 1044 Processing sheet with id=AA, first strand: chain 'A' and resid 329 through 333 removed outlier: 6.533A pdb=" N ILE A 72 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A 57 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU A 74 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N HIS A 55 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 76 " --> pdb=" O MET A 53 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N MET A 53 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE A 78 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 51 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 344 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 105 through 106 Processing sheet with id=AC, first strand: chain 'A' and resid 181 through 185 removed outlier: 7.209A pdb=" N ARG A 162 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU A 89 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 164 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 181 through 185 removed outlier: 7.209A pdb=" N ARG A 162 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU A 89 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 164 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'A' and resid 218 through 223 removed outlier: 5.427A pdb=" N ILE A 218 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A 222 " --> pdb=" O ARG A 278 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 278 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=BA, first strand: chain 'B' and resid 8 through 11 removed outlier: 4.080A pdb=" N ARG B 8 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing sheet with id=BB, first strand: chain 'B' and resid 17 through 20 removed outlier: 3.591A pdb=" N ASP B 19 " --> pdb=" O LYS B 26 " (cutoff:3.500A) Processing sheet with id=BC, first strand: chain 'B' and resid 130 through 131 removed outlier: 7.360A pdb=" N GLU B 87 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG B 182 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYS B 89 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 176 " --> pdb=" O VAL B 93 " (cutoff:3.500A) Processing sheet with id=BD, first strand: chain 'B' and resid 101 through 104 Processing sheet with id=CA, first strand: chain 'C' and resid 86 through 90 removed outlier: 7.872A pdb=" N MET C 26 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE C 191 " --> pdb=" O MET C 26 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL C 28 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 13 through 16 removed outlier: 4.032A pdb=" N PHE D 14 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR D 63 " --> pdb=" O PHE D 14 " (cutoff:3.500A) Processing sheet with id=EA, first strand: chain 'E' and resid 22 through 24 removed outlier: 6.908A pdb=" N MET E 59 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL E 39 " --> pdb=" O MET E 57 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N MET E 57 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 58 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA E 99 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 85 through 86 Processing sheet with id=FA, first strand: chain 'F' and resid 134 through 139 removed outlier: 6.606A pdb=" N ILE F 134 " --> pdb=" O SER F 54 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER F 54 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE F 136 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N CYS F 49 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing sheet with id=FB, first strand: chain 'F' and resid 59 through 61 removed outlier: 6.184A pdb=" N ILE F 99 " --> pdb=" O PRO F 122 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY F 124 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing sheet with id=FC, first strand: chain 'F' and resid 192 through 193 removed outlier: 3.642A pdb=" N ASN F 196 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing sheet with id=GA, first strand: chain 'G' and resid 19 through 21 Processing sheet with id=JA, first strand: chain 'J' and resid 20 through 22 Processing sheet with id=JB, first strand: chain 'J' and resid 57 through 59 removed outlier: 7.158A pdb=" N GLN J 64 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id=JC, first strand: chain 'J' and resid 195 through 197 removed outlier: 4.276A pdb=" N LYS J 195 " --> pdb=" O ILE J 212 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS J 210 " --> pdb=" O ILE J 197 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG J 175 " --> pdb=" O VAL J 236 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU J 234 " --> pdb=" O ILE J 177 " (cutoff:3.500A) Processing sheet with id=KA, first strand: chain 'K' and resid 23 through 26 removed outlier: 3.879A pdb=" N VAL K 142 " --> pdb=" O CYS K 113 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE K 115 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL K 144 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL K 233 " --> pdb=" O LEU K 143 " (cutoff:3.500A) Processing sheet with id=KB, first strand: chain 'K' and resid 73 through 75 removed outlier: 3.667A pdb=" N SER K 73 " --> pdb=" O ASP K 92 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP K 92 " --> pdb=" O SER K 73 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE K 75 " --> pdb=" O LEU K 90 " (cutoff:3.500A) Processing sheet with id=KC, first strand: chain 'K' and resid 520 through 522 removed outlier: 3.529A pdb=" N LYS K 520 " --> pdb=" O LEU K 560 " (cutoff:3.500A) Processing sheet with id=KD, first strand: chain 'K' and resid 618 through 620 removed outlier: 4.000A pdb=" N VAL K 620 " --> pdb=" O LEU K 659 " (cutoff:3.500A) Processing sheet with id=KE, first strand: chain 'K' and resid 623 through 624 removed outlier: 3.659A pdb=" N GLU K 623 " --> pdb=" O SER K 684 " (cutoff:3.500A) Processing sheet with id=KF, first strand: chain 'K' and resid 693 through 696 removed outlier: 7.296A pdb=" N ARG K 979 " --> pdb=" O ARG K 693 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR K 695 " --> pdb=" O ARG K 979 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N MET K 981 " --> pdb=" O THR K 695 " (cutoff:3.500A) No H-bonds generated for sheet with id=KF Processing sheet with id=KG, first strand: chain 'K' and resid 1009 through 1015 removed outlier: 5.630A pdb=" N VAL K1010 " --> pdb=" O VAL K1027 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL K1027 " --> pdb=" O VAL K1010 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN K1012 " --> pdb=" O LYS K1025 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU K 980 " --> pdb=" O ILE K1059 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE K1059 " --> pdb=" O LEU K 980 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA K 982 " --> pdb=" O TRP K1057 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TRP K1057 " --> pdb=" O ALA K 982 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N MET K 984 " --> pdb=" O SER K1055 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER K1055 " --> pdb=" O MET K 984 " (cutoff:3.500A) Processing sheet with id=KH, first strand: chain 'K' and resid 1009 through 1015 removed outlier: 5.630A pdb=" N VAL K1010 " --> pdb=" O VAL K1027 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL K1027 " --> pdb=" O VAL K1010 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN K1012 " --> pdb=" O LYS K1025 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ARG K 693 " --> pdb=" O ARG K 979 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR K 695 " --> pdb=" O MET K 981 " (cutoff:3.500A) removed outlier: 11.869A pdb=" N ALA K 983 " --> pdb=" O THR K 695 " (cutoff:3.500A) Processing sheet with id=KI, first strand: chain 'K' and resid 1052 through 1059 removed outlier: 6.569A pdb=" N LEU K1052 " --> pdb=" O ASP K 988 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP K 988 " --> pdb=" O LEU K1052 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N PHE K1054 " --> pdb=" O THR K 986 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N THR K 986 " --> pdb=" O PHE K1054 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N HIS K1056 " --> pdb=" O MET K 984 " (cutoff:3.500A) Processing sheet with id=KJ, first strand: chain 'K' and resid 750 through 757 removed outlier: 7.462A pdb=" N THR K 750 " --> pdb=" O TRP K 897 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TRP K 897 " --> pdb=" O THR K 750 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER K 752 " --> pdb=" O GLU K 895 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET K 756 " --> pdb=" O CYS K 891 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS K 891 " --> pdb=" O MET K 756 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 787 hydrogen bonds 1360 hydrogen bond angles 0 basepair planarities 321 basepair parallelities 519 stacking parallelities Total time for adding SS restraints: 26.38 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5625 1.32 - 1.45: 19879 1.45 - 1.58: 22157 1.58 - 1.70: 2273 1.70 - 1.83: 200 Bond restraints: 50134 Sorted by residual: bond pdb=" O3' A N2405 " pdb=" P A N2406 " ideal model delta sigma weight residual 1.607 1.668 -0.061 1.20e-02 6.94e+03 2.57e+01 bond pdb=" O3' U N1550 " pdb=" P A N1551 " ideal model delta sigma weight residual 1.607 1.668 -0.061 1.20e-02 6.94e+03 2.57e+01 bond pdb=" O3' G N1384 " pdb=" P G N1385 " ideal model delta sigma weight residual 1.607 1.551 0.056 1.20e-02 6.94e+03 2.21e+01 bond pdb=" CG ASP A 295 " pdb=" OD1 ASP A 295 " ideal model delta sigma weight residual 1.249 1.337 -0.088 1.90e-02 2.77e+03 2.14e+01 bond pdb=" O3' A N2611 " pdb=" P C N2612 " ideal model delta sigma weight residual 1.607 1.659 -0.052 1.20e-02 6.94e+03 1.88e+01 ... (remaining 50129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 70015 3.38 - 6.76: 3140 6.76 - 10.14: 174 10.14 - 13.52: 15 13.52 - 16.90: 3 Bond angle restraints: 73347 Sorted by residual: angle pdb=" O3' A N3477 " pdb=" C3' A N3477 " pdb=" C2' A N3477 " ideal model delta sigma weight residual 113.80 96.90 16.90 2.00e+00 2.50e-01 7.14e+01 angle pdb=" C HIS A 259 " pdb=" N PRO A 260 " pdb=" CA PRO A 260 " ideal model delta sigma weight residual 121.00 111.79 9.21 1.16e+00 7.43e-01 6.31e+01 angle pdb=" C4' G N3231 " pdb=" C3' G N3231 " pdb=" O3' G N3231 " ideal model delta sigma weight residual 112.50 98.82 13.68 2.00e+00 2.50e-01 4.68e+01 angle pdb=" N PRO D 88 " pdb=" CA PRO D 88 " pdb=" C PRO D 88 " ideal model delta sigma weight residual 110.70 118.69 -7.99 1.22e+00 6.72e-01 4.29e+01 angle pdb=" N ILE A 362 " pdb=" CA ILE A 362 " pdb=" C ILE A 362 " ideal model delta sigma weight residual 108.35 116.53 -8.18 1.32e+00 5.74e-01 3.84e+01 ... (remaining 73342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 25014 35.37 - 70.74: 2645 70.74 - 106.11: 161 106.11 - 141.48: 5 141.48 - 176.84: 4 Dihedral angle restraints: 27829 sinusoidal: 19754 harmonic: 8075 Sorted by residual: dihedral pdb=" C4' G N1368 " pdb=" C3' G N1368 " pdb=" C2' G N1368 " pdb=" C1' G N1368 " ideal model delta sinusoidal sigma weight residual 36.35 -41.13 77.47 1 3.10e+00 1.04e-01 7.82e+02 dihedral pdb=" C4' G N1542 " pdb=" C3' G N1542 " pdb=" C2' G N1542 " pdb=" C1' G N1542 " ideal model delta sinusoidal sigma weight residual 36.34 -40.48 76.82 1 3.10e+00 1.04e-01 7.71e+02 dihedral pdb=" C4' A N2989 " pdb=" C3' A N2989 " pdb=" C2' A N2989 " pdb=" C1' A N2989 " ideal model delta sinusoidal sigma weight residual 36.35 -40.38 76.73 1 3.10e+00 1.04e-01 7.70e+02 ... (remaining 27826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 8187 0.225 - 0.451: 995 0.451 - 0.676: 3 0.676 - 0.902: 0 0.902 - 1.127: 1 Chirality restraints: 9186 Sorted by residual: chirality pdb=" C4' A N1221 " pdb=" C5' A N1221 " pdb=" O4' A N1221 " pdb=" C3' A N1221 " both_signs ideal model delta sigma weight residual False -2.49 -1.36 -1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" C2' U N1550 " pdb=" C3' U N1550 " pdb=" O2' U N1550 " pdb=" C1' U N1550 " both_signs ideal model delta sigma weight residual False -2.79 -2.31 -0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C3' G N1565 " pdb=" C4' G N1565 " pdb=" O3' G N1565 " pdb=" C2' G N1565 " both_signs ideal model delta sigma weight residual False -2.50 -2.04 -0.46 2.00e-01 2.50e+01 5.29e+00 ... (remaining 9183 not shown) Planarity restraints: 5036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C N3379 " 0.003 2.00e-02 2.50e+03 5.85e-02 7.70e+01 pdb=" N1 C N3379 " -0.007 2.00e-02 2.50e+03 pdb=" C2 C N3379 " 0.003 2.00e-02 2.50e+03 pdb=" O2 C N3379 " -0.071 2.00e-02 2.50e+03 pdb=" N3 C N3379 " 0.144 2.00e-02 2.50e+03 pdb=" C4 C N3379 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C N3379 " -0.070 2.00e-02 2.50e+03 pdb=" C5 C N3379 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C N3379 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C N3349 " -0.018 2.00e-02 2.50e+03 4.24e-02 4.05e+01 pdb=" N1 C N3349 " 0.013 2.00e-02 2.50e+03 pdb=" C2 C N3349 " -0.008 2.00e-02 2.50e+03 pdb=" O2 C N3349 " 0.062 2.00e-02 2.50e+03 pdb=" N3 C N3349 " -0.101 2.00e-02 2.50e+03 pdb=" C4 C N3349 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C N3349 " 0.038 2.00e-02 2.50e+03 pdb=" C5 C N3349 " 0.010 2.00e-02 2.50e+03 pdb=" C6 C N3349 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U N1598 " -0.060 2.00e-02 2.50e+03 4.08e-02 3.74e+01 pdb=" N1 U N1598 " 0.038 2.00e-02 2.50e+03 pdb=" C2 U N1598 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U N1598 " -0.009 2.00e-02 2.50e+03 pdb=" N3 U N1598 " 0.060 2.00e-02 2.50e+03 pdb=" C4 U N1598 " 0.012 2.00e-02 2.50e+03 pdb=" O4 U N1598 " -0.074 2.00e-02 2.50e+03 pdb=" C5 U N1598 " 0.023 2.00e-02 2.50e+03 pdb=" C6 U N1598 " 0.014 2.00e-02 2.50e+03 ... (remaining 5033 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 2 1.97 - 2.70: 2790 2.70 - 3.43: 63348 3.43 - 4.17: 140159 4.17 - 4.90: 201938 Nonbonded interactions: 408237 Sorted by model distance: nonbonded pdb=" N1 A N2425 " pdb=" O4 U N2442 " model vdw 1.236 2.496 nonbonded pdb=" C2 A N2425 " pdb=" O4 U N2442 " model vdw 1.928 3.340 nonbonded pdb=" OH TYR E 92 " pdb=" O2 C N3386 " model vdw 2.014 3.040 nonbonded pdb=" O2' U N3287 " pdb=" OP2 U N3288 " model vdw 2.116 3.040 nonbonded pdb=" O ALA B 66 " pdb=" O2' A N3449 " model vdw 2.164 3.040 ... (remaining 408232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 64.870 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 : 0.009 0.911 50135 Z= 0.564 Angle : 1.464 16.897 73349 Z= 0.770 Chirality : 0.134 1.127 9186 Planarity : 0.007 0.075 5036 Dihedral : 21.930 176.844 22610 Min Nonbonded Distance : 1.236 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 3.63 % Allowed : 13.63 % Favored : 82.74 % Rotamer: Outliers : 4.21 % Allowed : 9.42 % Favored : 86.36 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.33 (0.12), residues: 2781 helix: -0.87 (0.17), residues: 618 sheet: -3.37 (0.26), residues: 237 loop : -3.81 (0.11), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 21 TYR 0.040 0.003 TYR A 275 PHE 0.043 0.003 PHE A 229 TRP 0.017 0.003 TRP K 824 HIS 0.012 0.003 HIS E 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00806 / 0.53 (50134) covalent geometry : angle 1.46447 / 0.77 (73347) SS BOND : bond 0.91078 / 47.94 ( 1) SS BOND : angle 0.98689 / 0.57 ( 2) hydrogen bonds : bond 0.16873 / 11.52 ( 1289) hydrogen bonds : angle 9.56154 / 6.79 ( 2809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 590 time to evaluate : 1.135 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: A 9 PRO cc_start: 0.6565 (Cg_endo) cc_final: 0.5867 (Cg_exo) REVERT: A 35 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.5762 (m-30) REVERT: A 62 LYS cc_start: 0.7857 (tttt) cc_final: 0.7290 (ttpt) REVERT: A 97 GLN cc_start: 0.5759 (OUTLIER) cc_final: 0.4958 (mp10) REVERT: A 100 LYS cc_start: 0.5195 (OUTLIER) cc_final: 0.4763 (tptp) REVERT: A 113 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.7971 (p0) REVERT: A 121 ASN cc_start: 0.5098 (OUTLIER) cc_final: 0.4725 (m-40) REVERT: A 135 VAL cc_start: 0.5432 (OUTLIER) cc_final: 0.5121 (m) REVERT: A 154 ILE cc_start: 0.8736 (pt) cc_final: 0.8433 (mt) REVERT: A 155 LYS cc_start: 0.6911 (tttt) cc_final: 0.6634 (ttpt) REVERT: A 170 HIS cc_start: 0.6371 (m90) cc_final: 0.6091 (m-70) REVERT: A 180 HIS cc_start: 0.7169 (OUTLIER) cc_final: 0.6833 (m170) REVERT: A 201 ASN cc_start: 0.8195 (m-40) cc_final: 0.7886 (m-40) REVERT: A 230 ASN cc_start: 0.9132 (p0) cc_final: 0.8858 (p0) REVERT: A 235 ARG cc_start: 0.9002 (ttt180) cc_final: 0.8249 (ttt180) REVERT: A 269 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8635 (tpt-90) REVERT: A 319 PHE cc_start: 0.7401 (m-80) cc_final: 0.6656 (m-10) REVERT: A 332 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7604 (mp) REVERT: A 335 CYS cc_start: 0.8214 (m) cc_final: 0.8010 (p) REVERT: A 347 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.5777 (mtm110) REVERT: A 348 LYS cc_start: 0.8753 (mttm) cc_final: 0.8327 (tttt) REVERT: A 349 SER cc_start: 0.8883 (m) cc_final: 0.8653 (m) REVERT: A 366 PHE cc_start: 0.5858 (m-80) cc_final: 0.5224 (m-80) REVERT: B 51 LYS cc_start: 0.8014 (pttm) cc_final: 0.7606 (mmmm) REVERT: B 67 CYS cc_start: 0.8516 (m) cc_final: 0.7766 (t) REVERT: B 69 LYS cc_start: 0.8042 (tttt) cc_final: 0.7655 (tptm) REVERT: B 71 ILE cc_start: 0.8384 (mt) cc_final: 0.8005 (mt) REVERT: B 90 MET cc_start: 0.6814 (mtp) cc_final: 0.5934 (mtm) REVERT: B 97 PHE cc_start: 0.6662 (m-80) cc_final: 0.6417 (m-80) REVERT: B 99 ILE cc_start: 0.8951 (tt) cc_final: 0.8705 (mt) REVERT: B 105 ASP cc_start: 0.7181 (m-30) cc_final: 0.6938 (p0) REVERT: B 126 LEU cc_start: 0.9393 (mt) cc_final: 0.9102 (mp) REVERT: B 155 SER cc_start: 0.9018 (m) cc_final: 0.8557 (p) REVERT: B 179 VAL cc_start: 0.9091 (t) cc_final: 0.8738 (t) REVERT: C 15 LYS cc_start: 0.4562 (tttm) cc_final: 0.3542 (mttt) REVERT: C 32 ASP cc_start: 0.3037 (OUTLIER) cc_final: 0.2101 (t0) REVERT: C 159 ILE cc_start: 0.5472 (pt) cc_final: 0.5212 (tt) REVERT: D 21 GLU cc_start: 0.3698 (pt0) cc_final: 0.3390 (pm20) REVERT: E 48 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6679 (ttt90) REVERT: E 81 GLN cc_start: 0.8622 (mp10) cc_final: 0.7909 (mp10) REVERT: E 94 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.5231 (t80) REVERT: F 9 TYR cc_start: 0.8561 (m-80) cc_final: 0.8186 (m-10) REVERT: F 10 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.5105 (tmt90) REVERT: F 18 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8232 (pt) REVERT: F 39 LYS cc_start: 0.8860 (mtmt) cc_final: 0.8502 (mtmm) REVERT: F 99 ILE cc_start: 0.7615 (mt) cc_final: 0.7355 (mt) REVERT: F 115 MET cc_start: 0.8169 (ttt) cc_final: 0.7687 (ttt) REVERT: F 125 THR cc_start: 0.8540 (m) cc_final: 0.8171 (p) REVERT: F 126 VAL cc_start: 0.9083 (p) cc_final: 0.8698 (m) REVERT: F 154 ARG cc_start: 0.8086 (mtp180) cc_final: 0.7575 (mpt180) REVERT: F 179 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.4044 (pp20) REVERT: F 181 TYR cc_start: 0.7645 (t80) cc_final: 0.7385 (t80) REVERT: F 197 VAL cc_start: 0.8466 (m) cc_final: 0.8042 (t) REVERT: G 1 MET cc_start: 0.5604 (mmm) cc_final: 0.4736 (tpp) REVERT: G 25 ASP cc_start: 0.7696 (p0) cc_final: 0.7114 (p0) REVERT: H 26 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8484 (mp) REVERT: H 42 ASN cc_start: 0.6853 (m110) cc_final: 0.6459 (m-40) REVERT: J 45 LYS cc_start: 0.6299 (mtpt) cc_final: 0.5592 (mptt) REVERT: J 58 VAL cc_start: 0.8841 (m) cc_final: 0.8485 (t) REVERT: J 67 LYS cc_start: 0.8273 (mttt) cc_final: 0.7826 (mttm) REVERT: K 9 MET cc_start: -0.0526 (mtt) cc_final: -0.0808 (mtt) REVERT: K 252 TYR cc_start: 0.4229 (OUTLIER) cc_final: 0.3703 (m-80) REVERT: K 264 MET cc_start: 0.6041 (mtm) cc_final: 0.5616 (ttp) REVERT: K 337 PRO cc_start: 0.7094 (Cg_endo) cc_final: 0.6869 (Cg_exo) REVERT: K 349 LEU cc_start: 0.4854 (OUTLIER) cc_final: 0.4376 (mt) REVERT: K 358 MET cc_start: 0.0574 (mmt) cc_final: 0.0182 (mmt) REVERT: K 373 ARG cc_start: 0.2411 (ptt180) cc_final: 0.1878 (ptt180) REVERT: K 378 MET cc_start: 0.1297 (mtp) cc_final: 0.0917 (mmm) REVERT: K 431 ARG cc_start: 0.2960 (OUTLIER) cc_final: 0.1529 (ptp-110) REVERT: K 530 SER cc_start: 0.4402 (m) cc_final: 0.4074 (p) REVERT: K 536 ARG cc_start: 0.1028 (ptp-170) cc_final: 0.0662 (ptp90) REVERT: K 555 MET cc_start: 0.1843 (mmt) cc_final: 0.1522 (mmt) REVERT: K 630 MET cc_start: 0.4727 (mtt) cc_final: 0.4110 (mtp) REVERT: K 721 MET cc_start: -0.0765 (OUTLIER) cc_final: -0.1787 (pmm) REVERT: K 838 ASN cc_start: 0.5757 (m110) cc_final: 0.5556 (p0) REVERT: K 849 THR cc_start: 0.3838 (m) cc_final: 0.3468 (m) REVERT: K 862 TYR cc_start: 0.0359 (m-80) cc_final: 0.0018 (m-80) REVERT: K 965 MET cc_start: 0.5330 (mtt) cc_final: 0.5100 (mmt) REVERT: K 1015 MET cc_start: 0.1984 (mtt) cc_final: -0.0900 (tpt) REVERT: K 1021 MET cc_start: 0.2775 (mmt) cc_final: 0.2216 (ptm) REVERT: K 1039 GLU cc_start: 0.2450 (tp30) cc_final: 0.2122 (tm-30) REVERT: K 1091 MET cc_start: 0.3203 (ptp) cc_final: 0.2332 (ptp) outliers start: 102 outliers final: 33 residues processed: 667 average time/residue: 0.3172 time to fit residues: 338.8856 Evaluate side-chains 440 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 387 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 HIS A 68 HIS A 108 GLN A 166 HIS A 170 HIS A 180 HIS ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN A 215 ASN A 277 HIS ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS C 93 ASN ** E 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN E 98 ASN F 59 GLN F 73 ASN F 143 ASN J 34 ASN J 52 GLN J 54 HIS J 147 ASN ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN K 138 ASN K 172 GLN K 247 HIS K 459 GLN K 632 GLN K 641 ASN K 793 HIS K 809 GLN K 844 GLN K 925 ASN ** K1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1076 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.186924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.170451 restraints weight = 111099.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.170717 restraints weight = 110787.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.170260 restraints weight = 59213.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.169937 restraints weight = 52881.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.170250 restraints weight = 39939.837| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 50135 Z= 0.263 Angle : 1.508 24.422 73349 Z= 0.612 Chirality : 0.122 1.232 9186 Planarity : 0.006 0.074 5036 Dihedral : 19.220 167.593 16959 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 1.19 % Allowed : 10.82 % Favored : 87.99 % Rotamer: Outliers : 0.04 % Allowed : 4.92 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.14), residues: 2781 helix: 0.17 (0.22), residues: 636 sheet: -3.20 (0.24), residues: 296 loop : -3.47 (0.12), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 278 TYR 0.025 0.002 TYR F 17 PHE 0.027 0.002 PHE C 33 TRP 0.040 0.003 TRP K 135 HIS 0.010 0.002 HIS F 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.26 (50134) covalent geometry : angle 1.50846 / 0.61 (73347) SS BOND : bond 0.01319 / 0.69 ( 1) SS BOND : angle 1.32320 / 0.75 ( 2) hydrogen bonds : bond 0.07801 / 5.42 ( 1289) hydrogen bonds : angle 4.83779 / 3.43 ( 2809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 479 time to evaluate : 1.138 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 9 PRO cc_start: 0.6488 (Cg_endo) cc_final: 0.6159 (Cg_exo) REVERT: A 62 LYS cc_start: 0.7530 (tttt) cc_final: 0.7303 (ttpt) REVERT: A 154 ILE cc_start: 0.8586 (pt) cc_final: 0.8128 (mt) REVERT: A 183 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 348 LYS cc_start: 0.8564 (mttm) cc_final: 0.7917 (mtpt) REVERT: B 55 VAL cc_start: 0.9305 (t) cc_final: 0.9094 (t) REVERT: B 69 LYS cc_start: 0.7809 (tttt) cc_final: 0.7588 (tppp) REVERT: B 155 SER cc_start: 0.9078 (m) cc_final: 0.8726 (p) REVERT: C 159 ILE cc_start: 0.6974 (pt) cc_final: 0.6611 (mt) REVERT: D 82 ILE cc_start: 0.2915 (tp) cc_final: 0.2649 (mt) REVERT: E 59 MET cc_start: 0.7824 (mmm) cc_final: 0.7368 (mmm) REVERT: E 120 GLU cc_start: 0.6246 (mp0) cc_final: 0.5921 (mp0) REVERT: F 19 LYS cc_start: 0.6478 (mttm) cc_final: 0.5527 (mttm) REVERT: F 39 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8414 (mtmm) REVERT: F 125 THR cc_start: 0.8592 (m) cc_final: 0.8280 (p) REVERT: F 154 ARG cc_start: 0.8108 (mtp180) cc_final: 0.7833 (mtp180) REVERT: F 157 TYR cc_start: 0.8282 (m-80) cc_final: 0.7866 (m-10) REVERT: F 174 THR cc_start: 0.7310 (t) cc_final: 0.7088 (m) REVERT: G 1 MET cc_start: 0.3875 (mmm) cc_final: 0.3510 (mtp) REVERT: H 14 CYS cc_start: 0.6977 (m) cc_final: 0.6671 (m) REVERT: J 1 MET cc_start: 0.4018 (mmp) cc_final: 0.3713 (mmt) REVERT: J 21 LYS cc_start: 0.6521 (mtmt) cc_final: 0.5795 (ptpp) REVERT: J 67 LYS cc_start: 0.7625 (mttt) cc_final: 0.7297 (mttm) REVERT: J 164 LYS cc_start: 0.8365 (ttmm) cc_final: 0.8147 (ttpp) REVERT: K 139 ILE cc_start: 0.4975 (pt) cc_final: 0.4774 (mt) REVERT: K 221 SER cc_start: 0.6164 (m) cc_final: 0.5581 (p) REVERT: K 378 MET cc_start: 0.2176 (mtp) cc_final: 0.1547 (mmm) REVERT: K 536 ARG cc_start: 0.0980 (ptp-170) cc_final: 0.0611 (ptp90) REVERT: K 555 MET cc_start: 0.1884 (mmt) cc_final: 0.1189 (mmt) REVERT: K 564 TYR cc_start: 0.1959 (p90) cc_final: 0.1034 (p90) REVERT: K 705 VAL cc_start: 0.5124 (m) cc_final: 0.4842 (p) REVERT: K 791 MET cc_start: 0.0963 (mmp) cc_final: -0.1341 (ttt) REVERT: K 849 THR cc_start: 0.5166 (m) cc_final: 0.4824 (p) REVERT: K 1015 MET cc_start: 0.1593 (mtt) cc_final: -0.1072 (tpt) REVERT: K 1021 MET cc_start: 0.3129 (mmt) cc_final: 0.2753 (ptm) outliers start: 1 outliers final: 0 residues processed: 480 average time/residue: 0.2980 time to fit residues: 233.4501 Evaluate side-chains 353 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 120 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 363 optimal weight: 7.9990 chunk 380 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 177 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 206 optimal weight: 4.9990 chunk 171 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN A 215 ASN A 246 HIS ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS E 10 ASN F 51 HIS F 177 ASN G 33 ASN G 61 ASN J 171 HIS ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 818 ASN K 844 GLN K 915 GLN K1109 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.184680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.168675 restraints weight = 110443.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.167718 restraints weight = 102510.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.162995 restraints weight = 65710.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.164021 restraints weight = 69579.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.164016 restraints weight = 49107.207| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 50135 Z= 0.259 Angle : 1.272 15.011 73349 Z= 0.525 Chirality : 0.100 1.124 9186 Planarity : 0.006 0.071 5036 Dihedral : 19.131 177.305 16959 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 1.11 % Allowed : 12.51 % Favored : 86.37 % Rotamer: Outliers : 0.12 % Allowed : 4.38 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.14), residues: 2781 helix: -0.19 (0.21), residues: 650 sheet: -2.85 (0.26), residues: 283 loop : -3.33 (0.12), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 66 TYR 0.027 0.002 TYR F 17 PHE 0.020 0.002 PHE K 512 TRP 0.046 0.003 TRP F 171 HIS 0.010 0.002 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.26 (50134) covalent geometry : angle 1.27167 / 0.52 (73347) SS BOND : bond 0.00016 / 0.01 ( 1) SS BOND : angle 1.65003 / 0.88 ( 2) hydrogen bonds : bond 0.07530 / 5.29 ( 1289) hydrogen bonds : angle 4.56544 / 3.26 ( 2809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 432 time to evaluate : 1.063 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: A 9 PRO cc_start: 0.5299 (Cg_endo) cc_final: 0.4990 (Cg_exo) REVERT: A 49 TYR cc_start: 0.8091 (m-80) cc_final: 0.7753 (m-80) REVERT: A 59 ASP cc_start: 0.7734 (m-30) cc_final: 0.7351 (m-30) REVERT: A 62 LYS cc_start: 0.7618 (tttt) cc_final: 0.7313 (ttpt) REVERT: A 80 GLU cc_start: 0.6533 (tm-30) cc_final: 0.6055 (tm-30) REVERT: A 183 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7879 (mm-30) REVERT: A 235 ARG cc_start: 0.9070 (ttt180) cc_final: 0.8396 (ttt180) REVERT: A 340 ARG cc_start: 0.7523 (mpp80) cc_final: 0.7103 (mpt180) REVERT: A 348 LYS cc_start: 0.8548 (mttm) cc_final: 0.7986 (mtpt) REVERT: B 1 MET cc_start: 0.2874 (mmt) cc_final: 0.2617 (mmt) REVERT: B 15 ASN cc_start: 0.7849 (p0) cc_final: 0.7384 (p0) REVERT: B 69 LYS cc_start: 0.7963 (tttt) cc_final: 0.7667 (tptm) REVERT: B 155 SER cc_start: 0.9111 (m) cc_final: 0.8755 (p) REVERT: C 159 ILE cc_start: 0.6997 (pt) cc_final: 0.6609 (mt) REVERT: D 82 ILE cc_start: 0.2783 (tp) cc_final: 0.2428 (mt) REVERT: D 97 ASN cc_start: 0.6629 (m-40) cc_final: 0.6385 (m-40) REVERT: E 35 TYR cc_start: 0.8283 (t80) cc_final: 0.8063 (t80) REVERT: E 135 ILE cc_start: 0.7215 (mm) cc_final: 0.6996 (mp) REVERT: F 19 LYS cc_start: 0.5593 (mttm) cc_final: 0.5045 (mttm) REVERT: F 154 ARG cc_start: 0.8115 (mtp180) cc_final: 0.7481 (mtm110) REVERT: H 20 ARG cc_start: 0.8510 (mtt-85) cc_final: 0.8123 (mtt-85) REVERT: J 1 MET cc_start: 0.4421 (mmp) cc_final: 0.4102 (mmt) REVERT: J 21 LYS cc_start: 0.6437 (mtmt) cc_final: 0.5786 (ptpp) REVERT: J 44 GLU cc_start: 0.5255 (mm-30) cc_final: 0.4847 (tm-30) REVERT: J 51 LEU cc_start: 0.8015 (mp) cc_final: 0.7685 (pp) REVERT: J 67 LYS cc_start: 0.7762 (mttt) cc_final: 0.7288 (mttm) REVERT: J 164 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8135 (ttpp) REVERT: K 189 ARG cc_start: 0.5873 (tpm170) cc_final: 0.4992 (ptm160) REVERT: K 349 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.5885 (mt) REVERT: K 378 MET cc_start: 0.1438 (mtp) cc_final: 0.0877 (mmm) REVERT: K 447 GLN cc_start: 0.3900 (pt0) cc_final: 0.3259 (tp40) REVERT: K 536 ARG cc_start: 0.1450 (ptp-170) cc_final: 0.1058 (ttm170) REVERT: K 555 MET cc_start: 0.2431 (mmt) cc_final: 0.1794 (mmt) REVERT: K 564 TYR cc_start: 0.2110 (p90) cc_final: 0.1100 (p90) REVERT: K 630 MET cc_start: 0.4272 (mmm) cc_final: 0.3757 (mmm) REVERT: K 776 MET cc_start: 0.3989 (tpp) cc_final: 0.3520 (tpp) REVERT: K 791 MET cc_start: 0.0893 (mmp) cc_final: -0.0471 (mpp) REVERT: K 1015 MET cc_start: 0.1403 (mtt) cc_final: -0.1154 (tpt) REVERT: K 1021 MET cc_start: 0.3182 (mmt) cc_final: 0.2542 (ptm) REVERT: K 1091 MET cc_start: 0.5664 (mpp) cc_final: 0.5066 (mpp) outliers start: 3 outliers final: 0 residues processed: 435 average time/residue: 0.2931 time to fit residues: 209.0154 Evaluate side-chains 354 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 210 optimal weight: 5.9990 chunk 296 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 93 optimal weight: 0.1980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS E 10 ASN F 51 HIS F 177 ASN ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 466 GLN K 844 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.187745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.173055 restraints weight = 111585.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.173108 restraints weight = 105404.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.172925 restraints weight = 68144.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.172987 restraints weight = 56731.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.173017 restraints weight = 42595.876| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 50135 Z= 0.197 Angle : 1.154 14.970 73349 Z= 0.476 Chirality : 0.091 1.029 9186 Planarity : 0.005 0.089 5036 Dihedral : 18.864 178.157 16959 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.93 % Allowed : 10.93 % Favored : 88.13 % Rotamer: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.14), residues: 2781 helix: -0.12 (0.21), residues: 637 sheet: -2.57 (0.26), residues: 302 loop : -3.21 (0.12), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 278 TYR 0.031 0.002 TYR F 17 PHE 0.019 0.002 PHE K 225 TRP 0.044 0.003 TRP K 135 HIS 0.011 0.001 HIS K1056 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 (50134) covalent geometry : angle 1.15377 / 0.48 (73347) SS BOND : bond 0.04543 / 2.39 ( 1) SS BOND : angle 1.64822 / 0.89 ( 2) hydrogen bonds : bond 0.06743 / 4.79 ( 1289) hydrogen bonds : angle 4.33929 / 3.09 ( 2809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 427 time to evaluate : 1.187 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: A 59 ASP cc_start: 0.7641 (m-30) cc_final: 0.7354 (m-30) REVERT: A 183 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7919 (mm-30) REVERT: A 192 VAL cc_start: 0.8492 (t) cc_final: 0.8231 (t) REVERT: A 348 LYS cc_start: 0.8589 (mttm) cc_final: 0.7943 (mtpt) REVERT: A 349 SER cc_start: 0.9126 (m) cc_final: 0.8903 (m) REVERT: B 15 ASN cc_start: 0.7673 (p0) cc_final: 0.7315 (p0) REVERT: B 55 VAL cc_start: 0.9315 (t) cc_final: 0.9092 (t) REVERT: B 155 SER cc_start: 0.9061 (m) cc_final: 0.8755 (p) REVERT: C 159 ILE cc_start: 0.6896 (pt) cc_final: 0.6643 (mt) REVERT: D 82 ILE cc_start: 0.2610 (tp) cc_final: 0.2209 (mt) REVERT: F 156 SER cc_start: 0.8168 (m) cc_final: 0.7547 (t) REVERT: F 157 TYR cc_start: 0.7826 (m-80) cc_final: 0.7599 (m-10) REVERT: F 191 MET cc_start: 0.5062 (mpp) cc_final: 0.4597 (mtm) REVERT: F 200 ILE cc_start: 0.7792 (mt) cc_final: 0.7480 (mt) REVERT: H 14 CYS cc_start: 0.6661 (m) cc_final: 0.6361 (m) REVERT: J 21 LYS cc_start: 0.6584 (mtmt) cc_final: 0.5864 (ptpp) REVERT: J 44 GLU cc_start: 0.5370 (mm-30) cc_final: 0.4963 (tm-30) REVERT: J 67 LYS cc_start: 0.7732 (mttt) cc_final: 0.7288 (mttm) REVERT: K 1 MET cc_start: 0.2901 (ptt) cc_final: 0.2341 (mmp) REVERT: K 189 ARG cc_start: 0.4970 (tpm170) cc_final: 0.4306 (ptm160) REVERT: K 378 MET cc_start: 0.1577 (mtp) cc_final: 0.0979 (mmm) REVERT: K 447 GLN cc_start: 0.4335 (pt0) cc_final: 0.3822 (tp40) REVERT: K 536 ARG cc_start: 0.1387 (ptp-170) cc_final: 0.1052 (ttm170) REVERT: K 555 MET cc_start: 0.2399 (mmt) cc_final: 0.1740 (mmt) REVERT: K 564 TYR cc_start: 0.1608 (p90) cc_final: 0.0772 (p90) REVERT: K 630 MET cc_start: 0.4009 (mmm) cc_final: 0.3660 (mmm) REVERT: K 776 MET cc_start: 0.3939 (tpp) cc_final: 0.3391 (tpp) REVERT: K 791 MET cc_start: 0.1313 (mmp) cc_final: 0.0237 (mpp) REVERT: K 1015 MET cc_start: 0.1072 (mtt) cc_final: -0.1061 (tpt) REVERT: K 1021 MET cc_start: 0.3521 (mmt) cc_final: 0.3202 (ptm) REVERT: K 1091 MET cc_start: 0.6045 (mpp) cc_final: 0.5459 (mpp) outliers start: 1 outliers final: 0 residues processed: 428 average time/residue: 0.3013 time to fit residues: 211.9369 Evaluate side-chains 346 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 123 optimal weight: 0.9990 chunk 335 optimal weight: 10.0000 chunk 301 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 377 optimal weight: 8.9990 chunk 329 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 201 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN C 138 GLN C 155 ASN E 10 ASN E 33 ASN E 104 ASN J 153 GLN J 171 HIS ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 GLN ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN K 435 GLN K 554 HIS ** K 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.180917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.165524 restraints weight = 112547.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.165967 restraints weight = 104444.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161919 restraints weight = 56650.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.162407 restraints weight = 61099.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.162379 restraints weight = 47183.872| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 50135 Z= 0.328 Angle : 1.365 15.875 73349 Z= 0.557 Chirality : 0.100 1.303 9186 Planarity : 0.006 0.081 5036 Dihedral : 19.208 177.383 16959 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.93 % Allowed : 13.77 % Favored : 85.29 % Rotamer: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.14), residues: 2781 helix: -0.64 (0.20), residues: 646 sheet: -2.71 (0.26), residues: 301 loop : -3.30 (0.12), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 278 TYR 0.038 0.003 TYR F 181 PHE 0.061 0.003 PHE B 116 TRP 0.067 0.004 TRP F 171 HIS 0.009 0.002 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.33 (50134) covalent geometry : angle 1.36465 / 0.56 (73347) SS BOND : bond 0.00312 / 0.16 ( 1) SS BOND : angle 2.21238 / 1.17 ( 2) hydrogen bonds : bond 0.08529 / 5.96 ( 1289) hydrogen bonds : angle 4.62707 / 3.30 ( 2809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 384 time to evaluate : 1.047 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: A 59 ASP cc_start: 0.7597 (m-30) cc_final: 0.7305 (m-30) REVERT: A 60 LEU cc_start: 0.7607 (tp) cc_final: 0.7343 (tp) REVERT: A 348 LYS cc_start: 0.8556 (mttm) cc_final: 0.8009 (mtpt) REVERT: B 19 ASP cc_start: 0.7413 (t0) cc_final: 0.7075 (t0) REVERT: B 69 LYS cc_start: 0.7783 (tptm) cc_final: 0.7470 (tptp) REVERT: C 159 ILE cc_start: 0.6972 (pt) cc_final: 0.6676 (mt) REVERT: D 82 ILE cc_start: 0.2554 (tp) cc_final: 0.2197 (mt) REVERT: E 59 MET cc_start: 0.6743 (mmm) cc_final: 0.6451 (mmm) REVERT: E 70 ARG cc_start: 0.8606 (mtt180) cc_final: 0.7993 (ttm-80) REVERT: F 43 THR cc_start: 0.7107 (t) cc_final: 0.6738 (m) REVERT: F 157 TYR cc_start: 0.7933 (m-80) cc_final: 0.7695 (m-10) REVERT: F 191 MET cc_start: 0.4608 (mpp) cc_final: 0.4373 (mtm) REVERT: G 1 MET cc_start: 0.5610 (ttt) cc_final: 0.4262 (ttm) REVERT: H 14 CYS cc_start: 0.6961 (m) cc_final: 0.6757 (m) REVERT: H 29 ARG cc_start: 0.7159 (ttp-110) cc_final: 0.6938 (mtm110) REVERT: J 21 LYS cc_start: 0.6530 (mtmt) cc_final: 0.5852 (ptpp) REVERT: J 67 LYS cc_start: 0.8022 (mttt) cc_final: 0.7497 (mttm) REVERT: K 1 MET cc_start: 0.3288 (ptt) cc_final: 0.1942 (mmp) REVERT: K 447 GLN cc_start: 0.4488 (pt0) cc_final: 0.3765 (tp40) REVERT: K 555 MET cc_start: 0.2742 (mmt) cc_final: 0.2110 (mmt) REVERT: K 564 TYR cc_start: 0.2180 (p90) cc_final: 0.1091 (p90) REVERT: K 776 MET cc_start: 0.3954 (tpp) cc_final: 0.3050 (tpp) REVERT: K 791 MET cc_start: 0.1739 (mmp) cc_final: 0.0664 (mpp) REVERT: K 1015 MET cc_start: 0.0817 (mtt) cc_final: -0.1315 (tpt) REVERT: K 1021 MET cc_start: 0.3660 (mmt) cc_final: 0.2953 (ptt) REVERT: K 1091 MET cc_start: 0.5887 (mpp) cc_final: 0.5421 (mpp) outliers start: 2 outliers final: 0 residues processed: 386 average time/residue: 0.2932 time to fit residues: 186.9060 Evaluate side-chains 317 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 111 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 282 optimal weight: 7.9990 chunk 332 optimal weight: 7.9990 chunk 255 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 256 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 343 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS D 97 ASN E 10 ASN E 98 ASN J 121 ASN ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN K 247 HIS K 334 HIS ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.182608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168277 restraints weight = 111780.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.168435 restraints weight = 113656.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.168382 restraints weight = 67524.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168482 restraints weight = 56433.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168525 restraints weight = 41554.808| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 50135 Z= 0.279 Angle : 1.261 16.779 73349 Z= 0.516 Chirality : 0.095 1.190 9186 Planarity : 0.006 0.083 5036 Dihedral : 19.162 179.069 16959 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.41 % Favored : 86.70 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.14), residues: 2781 helix: -0.67 (0.20), residues: 628 sheet: -2.61 (0.26), residues: 297 loop : -3.27 (0.12), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG G 56 TYR 0.037 0.003 TYR F 17 PHE 0.055 0.003 PHE B 116 TRP 0.069 0.004 TRP F 171 HIS 0.009 0.002 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.28 (50134) covalent geometry : angle 1.26120 / 0.52 (73347) SS BOND : bond 0.00585 / 0.31 ( 1) SS BOND : angle 1.77578 / 0.97 ( 2) hydrogen bonds : bond 0.07981 / 5.61 ( 1289) hydrogen bonds : angle 4.60877 / 3.28 ( 2809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.134 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: A 1 MET cc_start: 0.5822 (ptm) cc_final: 0.5349 (ptm) REVERT: A 235 ARG cc_start: 0.9153 (ttt180) cc_final: 0.8370 (ttt180) REVERT: B 19 ASP cc_start: 0.7408 (t0) cc_final: 0.7065 (t0) REVERT: B 69 LYS cc_start: 0.7776 (tptm) cc_final: 0.7478 (tptp) REVERT: C 54 MET cc_start: -0.0837 (ppp) cc_final: -0.1173 (ppp) REVERT: C 159 ILE cc_start: 0.6966 (pt) cc_final: 0.6713 (mt) REVERT: D 82 ILE cc_start: 0.2762 (tp) cc_final: 0.2421 (mt) REVERT: D 97 ASN cc_start: 0.5170 (m110) cc_final: 0.4806 (m110) REVERT: D 166 LYS cc_start: 0.3072 (tptt) cc_final: 0.2854 (tptp) REVERT: E 70 ARG cc_start: 0.8667 (mtt180) cc_final: 0.8334 (mtt-85) REVERT: E 102 MET cc_start: 0.8523 (tpt) cc_final: 0.8304 (tpt) REVERT: G 1 MET cc_start: 0.5362 (ttt) cc_final: 0.3873 (ttt) REVERT: J 21 LYS cc_start: 0.6563 (mtmt) cc_final: 0.5807 (ptpp) REVERT: J 67 LYS cc_start: 0.8054 (mttt) cc_final: 0.7504 (mttm) REVERT: J 194 ILE cc_start: 0.6496 (pt) cc_final: 0.6118 (pt) REVERT: K 1 MET cc_start: 0.3390 (ptt) cc_final: 0.2342 (mmp) REVERT: K 189 ARG cc_start: 0.5277 (tpm170) cc_final: 0.4156 (ptp-170) REVERT: K 275 MET cc_start: -0.2390 (mtp) cc_final: -0.2801 (mtm) REVERT: K 444 ARG cc_start: 0.6651 (mmp80) cc_final: 0.6249 (mmp-170) REVERT: K 447 GLN cc_start: 0.4655 (pt0) cc_final: 0.4102 (tp40) REVERT: K 564 TYR cc_start: 0.1884 (p90) cc_final: 0.0856 (p90) REVERT: K 751 LEU cc_start: 0.3549 (pp) cc_final: 0.2757 (pp) REVERT: K 791 MET cc_start: 0.2472 (mmp) cc_final: 0.1838 (mpp) REVERT: K 862 TYR cc_start: 0.2766 (m-80) cc_final: 0.2196 (m-80) REVERT: K 888 MET cc_start: 0.3958 (tpt) cc_final: 0.3303 (tpt) REVERT: K 1015 MET cc_start: 0.0587 (mtt) cc_final: -0.1418 (tpt) REVERT: K 1021 MET cc_start: 0.3736 (mmt) cc_final: 0.3324 (ptt) REVERT: K 1091 MET cc_start: 0.6014 (mpp) cc_final: 0.5624 (mpp) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.2731 time to fit residues: 179.6138 Evaluate side-chains 330 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 312 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 2 optimal weight: 0.0670 chunk 130 optimal weight: 0.9990 chunk 343 optimal weight: 10.0000 chunk 374 optimal weight: 7.9990 chunk 259 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 307 optimal weight: 8.9990 chunk 241 optimal weight: 40.0000 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 HIS E 10 ASN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 ASN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN K 342 ASN K 844 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.184850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.170300 restraints weight = 111003.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.167731 restraints weight = 99659.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.164292 restraints weight = 71184.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.164941 restraints weight = 59341.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.165160 restraints weight = 44270.173| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 50135 Z= 0.218 Angle : 1.177 16.889 73349 Z= 0.482 Chirality : 0.090 1.114 9186 Planarity : 0.006 0.084 5036 Dihedral : 19.033 178.467 16959 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.93 % Allowed : 12.26 % Favored : 86.80 % Rotamer: Outliers : 0.04 % Allowed : 2.11 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.14), residues: 2781 helix: -0.59 (0.20), residues: 629 sheet: -2.54 (0.25), residues: 317 loop : -3.16 (0.13), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 693 TYR 0.026 0.002 TYR K 573 PHE 0.025 0.002 PHE B 116 TRP 0.054 0.004 TRP K 135 HIS 0.007 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.22 (50134) covalent geometry : angle 1.17748 / 0.48 (73347) SS BOND : bond 0.00476 / 0.25 ( 1) SS BOND : angle 1.56211 / 0.86 ( 2) hydrogen bonds : bond 0.07368 / 5.21 ( 1289) hydrogen bonds : angle 4.46272 / 3.18 ( 2809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 399 time to evaluate : 1.133 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: A 1 MET cc_start: 0.5683 (ptm) cc_final: 0.5380 (ptp) REVERT: A 235 ARG cc_start: 0.9104 (ttt180) cc_final: 0.8535 (ttt180) REVERT: A 348 LYS cc_start: 0.8546 (mttm) cc_final: 0.7634 (mtpt) REVERT: B 12 ILE cc_start: 0.7315 (pt) cc_final: 0.7068 (pt) REVERT: B 30 PRO cc_start: 0.7295 (Cg_endo) cc_final: 0.6963 (Cg_exo) REVERT: B 69 LYS cc_start: 0.7713 (tptm) cc_final: 0.7445 (tptp) REVERT: B 93 VAL cc_start: 0.7592 (p) cc_final: 0.7381 (p) REVERT: B 155 SER cc_start: 0.9136 (m) cc_final: 0.8750 (p) REVERT: C 33 PHE cc_start: 0.6475 (p90) cc_final: 0.6199 (p90) REVERT: C 159 ILE cc_start: 0.6948 (pt) cc_final: 0.6516 (mt) REVERT: D 82 ILE cc_start: 0.2635 (tp) cc_final: 0.2322 (mt) REVERT: D 166 LYS cc_start: 0.2857 (tptt) cc_final: 0.2647 (tptp) REVERT: E 37 ILE cc_start: 0.8122 (mm) cc_final: 0.7646 (mt) REVERT: E 70 ARG cc_start: 0.8639 (mtt180) cc_final: 0.7926 (ttm-80) REVERT: F 66 GLU cc_start: 0.7726 (tp30) cc_final: 0.7412 (tp30) REVERT: G 1 MET cc_start: 0.4995 (ttt) cc_final: 0.3999 (ttt) REVERT: H 14 CYS cc_start: 0.7167 (m) cc_final: 0.6952 (m) REVERT: J 21 LYS cc_start: 0.6317 (mtmt) cc_final: 0.5569 (ptpp) REVERT: J 67 LYS cc_start: 0.7901 (mttt) cc_final: 0.7275 (mttm) REVERT: J 194 ILE cc_start: 0.6135 (pt) cc_final: 0.5740 (pt) REVERT: K 1 MET cc_start: 0.3756 (ptt) cc_final: 0.2335 (mmp) REVERT: K 275 MET cc_start: -0.2635 (mtp) cc_final: -0.2911 (mtm) REVERT: K 289 LYS cc_start: 0.5433 (tptt) cc_final: 0.5082 (tmtt) REVERT: K 444 ARG cc_start: 0.6780 (mmp80) cc_final: 0.6214 (mmp-170) REVERT: K 447 GLN cc_start: 0.4524 (pt0) cc_final: 0.3837 (tp40) REVERT: K 791 MET cc_start: 0.2377 (mmp) cc_final: 0.1825 (mpp) REVERT: K 1002 VAL cc_start: 0.6118 (t) cc_final: 0.5895 (t) REVERT: K 1015 MET cc_start: 0.0211 (mtt) cc_final: -0.1631 (tpt) REVERT: K 1021 MET cc_start: 0.3739 (mmt) cc_final: 0.2913 (ptt) REVERT: K 1091 MET cc_start: 0.5705 (mpp) cc_final: 0.5252 (mpp) outliers start: 1 outliers final: 0 residues processed: 400 average time/residue: 0.2831 time to fit residues: 188.1511 Evaluate side-chains 336 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 387 optimal weight: 10.0000 chunk 201 optimal weight: 0.0870 chunk 42 optimal weight: 20.0000 chunk 194 optimal weight: 0.9980 chunk 375 optimal weight: 8.9990 chunk 316 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 142 optimal weight: 0.0570 chunk 362 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 315 optimal weight: 10.0000 overall best weight: 4.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 51 GLN D 100 HIS ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 ASN F 182 GLN G 61 ASN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.184191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.169028 restraints weight = 113838.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.168987 restraints weight = 112806.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.167995 restraints weight = 61447.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.167962 restraints weight = 53628.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.168053 restraints weight = 42125.417| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 50135 Z= 0.241 Angle : 1.213 16.390 73349 Z= 0.496 Chirality : 0.091 1.245 9186 Planarity : 0.006 0.077 5036 Dihedral : 19.065 179.187 16959 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.73 % Favored : 86.37 % Rotamer: Outliers : 0.04 % Allowed : 1.69 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.14), residues: 2781 helix: -0.71 (0.20), residues: 641 sheet: -2.47 (0.26), residues: 300 loop : -3.13 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 278 TYR 0.028 0.003 TYR K 573 PHE 0.022 0.002 PHE B 116 TRP 0.062 0.004 TRP A 106 HIS 0.008 0.002 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.24 (50134) covalent geometry : angle 1.21275 / 0.50 (73347) SS BOND : bond 0.00355 / 0.19 ( 1) SS BOND : angle 1.35791 / 0.73 ( 2) hydrogen bonds : bond 0.07580 / 5.36 ( 1289) hydrogen bonds : angle 4.47099 / 3.19 ( 2809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 393 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 LYS cc_start: 0.8615 (mttm) cc_final: 0.7657 (mtpt) REVERT: A 356 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.8045 (mtp85) REVERT: B 30 PRO cc_start: 0.7142 (Cg_endo) cc_final: 0.6837 (Cg_exo) REVERT: B 69 LYS cc_start: 0.7755 (tptm) cc_final: 0.7453 (tptp) REVERT: B 93 VAL cc_start: 0.7885 (p) cc_final: 0.7460 (p) REVERT: B 155 SER cc_start: 0.9118 (m) cc_final: 0.8746 (p) REVERT: C 33 PHE cc_start: 0.5967 (p90) cc_final: 0.5699 (p90) REVERT: C 159 ILE cc_start: 0.6997 (pt) cc_final: 0.6605 (mt) REVERT: D 82 ILE cc_start: 0.2575 (tp) cc_final: 0.2182 (mt) REVERT: H 26 LEU cc_start: 0.8213 (mm) cc_final: 0.8006 (mm) REVERT: J 21 LYS cc_start: 0.6403 (mtmt) cc_final: 0.5701 (ptpp) REVERT: J 67 LYS cc_start: 0.8072 (mttt) cc_final: 0.7396 (mttm) REVERT: J 103 GLN cc_start: 0.5973 (mm-40) cc_final: 0.5157 (mm-40) REVERT: J 131 ILE cc_start: 0.8188 (tt) cc_final: 0.7916 (mp) REVERT: K 9 MET cc_start: -0.0509 (mtt) cc_final: -0.2121 (tpp) REVERT: K 85 GLU cc_start: 0.0099 (mm-30) cc_final: -0.0234 (mm-30) REVERT: K 275 MET cc_start: -0.2042 (mtp) cc_final: -0.2546 (mtm) REVERT: K 444 ARG cc_start: 0.6730 (mmp80) cc_final: 0.6240 (mmp-170) REVERT: K 447 GLN cc_start: 0.4762 (pt0) cc_final: 0.4035 (tp40) REVERT: K 625 LYS cc_start: 0.3486 (mtmt) cc_final: 0.2559 (mmmt) REVERT: K 888 MET cc_start: 0.3471 (tpt) cc_final: 0.2845 (tpt) REVERT: K 1015 MET cc_start: 0.0521 (mtt) cc_final: -0.1442 (tpt) REVERT: K 1021 MET cc_start: 0.3945 (mmt) cc_final: 0.3398 (ptt) REVERT: K 1039 GLU cc_start: 0.3397 (tp30) cc_final: 0.2518 (mt-10) REVERT: K 1091 MET cc_start: 0.5989 (mpp) cc_final: 0.5489 (mpp) REVERT: K 1117 SER cc_start: 0.6261 (m) cc_final: 0.5000 (p) REVERT: K 1118 LYS cc_start: 0.6136 (pttt) cc_final: 0.3907 (mmpt) outliers start: 1 outliers final: 0 residues processed: 394 average time/residue: 0.2427 time to fit residues: 159.1796 Evaluate side-chains 320 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 131 optimal weight: 3.9990 chunk 222 optimal weight: 40.0000 chunk 212 optimal weight: 4.9990 chunk 210 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 290 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 274 optimal weight: 0.3980 chunk 134 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 ASN C 147 ASN ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN E 10 ASN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN J 54 HIS ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN K 466 GLN ** K 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.182222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.167038 restraints weight = 113372.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.167244 restraints weight = 109595.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.166518 restraints weight = 61363.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.166299 restraints weight = 52643.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.166488 restraints weight = 40988.838| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 50135 Z= 0.281 Angle : 1.280 16.464 73349 Z= 0.522 Chirality : 0.094 1.403 9186 Planarity : 0.006 0.086 5036 Dihedral : 19.226 179.607 16959 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.90 % Allowed : 13.81 % Favored : 85.29 % Rotamer: Outliers : 0.04 % Allowed : 1.07 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.14), residues: 2781 helix: -0.86 (0.20), residues: 641 sheet: -2.51 (0.26), residues: 303 loop : -3.17 (0.13), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 278 TYR 0.035 0.003 TYR E 11 PHE 0.023 0.002 PHE B 116 TRP 0.070 0.005 TRP A 106 HIS 0.009 0.002 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.28 (50134) covalent geometry : angle 1.27958 / 0.52 (73347) SS BOND : bond 0.00536 / 0.28 ( 1) SS BOND : angle 1.38663 / 0.75 ( 2) hydrogen bonds : bond 0.08087 / 5.68 ( 1289) hydrogen bonds : angle 4.59034 / 3.26 ( 2809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 384 time to evaluate : 0.856 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: A 348 LYS cc_start: 0.8657 (mttm) cc_final: 0.7722 (mtpt) REVERT: A 356 ARG cc_start: 0.8340 (mmm-85) cc_final: 0.8087 (mtp85) REVERT: B 12 ILE cc_start: 0.7150 (pt) cc_final: 0.6864 (pt) REVERT: B 30 PRO cc_start: 0.7272 (Cg_endo) cc_final: 0.6979 (Cg_exo) REVERT: B 69 LYS cc_start: 0.7809 (tptm) cc_final: 0.7380 (tptp) REVERT: B 155 SER cc_start: 0.9086 (m) cc_final: 0.8726 (p) REVERT: C 33 PHE cc_start: 0.5828 (p90) cc_final: 0.5542 (p90) REVERT: C 159 ILE cc_start: 0.6995 (pt) cc_final: 0.6617 (mt) REVERT: D 82 ILE cc_start: 0.2244 (tp) cc_final: 0.1901 (mt) REVERT: J 21 LYS cc_start: 0.6604 (mtmt) cc_final: 0.5842 (ptpp) REVERT: J 67 LYS cc_start: 0.8202 (mttt) cc_final: 0.7500 (mttm) REVERT: J 97 ASP cc_start: 0.5918 (t70) cc_final: 0.5700 (t70) REVERT: J 103 GLN cc_start: 0.6239 (mm-40) cc_final: 0.5327 (mm-40) REVERT: J 131 ILE cc_start: 0.8200 (tt) cc_final: 0.7919 (mp) REVERT: J 194 ILE cc_start: 0.6392 (pt) cc_final: 0.5976 (pt) REVERT: K 275 MET cc_start: -0.1687 (mtp) cc_final: -0.2199 (mtm) REVERT: K 289 LYS cc_start: 0.5421 (tptt) cc_final: 0.5213 (tttp) REVERT: K 447 GLN cc_start: 0.4862 (pt0) cc_final: 0.4097 (tp40) REVERT: K 520 LYS cc_start: 0.2533 (ttpp) cc_final: 0.0957 (tptt) REVERT: K 562 ASN cc_start: 0.2224 (t0) cc_final: 0.1903 (t0) REVERT: K 776 MET cc_start: 0.2507 (tpt) cc_final: 0.2298 (tpp) REVERT: K 965 MET cc_start: 0.4967 (mmt) cc_final: 0.4200 (mmt) REVERT: K 981 MET cc_start: 0.5881 (tmm) cc_final: 0.4664 (tmm) REVERT: K 1014 GLU cc_start: 0.0804 (mm-30) cc_final: 0.0545 (mm-30) REVERT: K 1015 MET cc_start: 0.0631 (mtt) cc_final: -0.1576 (tpt) REVERT: K 1021 MET cc_start: 0.3542 (mmt) cc_final: 0.2798 (ptt) REVERT: K 1091 MET cc_start: 0.6143 (mpp) cc_final: 0.5827 (mpp) REVERT: K 1117 SER cc_start: 0.6530 (m) cc_final: 0.5521 (p) outliers start: 1 outliers final: 1 residues processed: 385 average time/residue: 0.2439 time to fit residues: 157.6096 Evaluate side-chains 324 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 356 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 265 optimal weight: 9.9990 chunk 337 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 266 optimal weight: 7.9990 chunk 243 optimal weight: 0.7980 chunk 27 optimal weight: 0.0060 chunk 326 optimal weight: 10.0000 chunk 272 optimal weight: 8.9990 overall best weight: 3.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 HIS D 137 HIS E 10 ASN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN K 611 ASN K 632 GLN K 712 GLN K 845 ASN ** K 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.185199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.165245 restraints weight = 113827.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.163325 restraints weight = 82464.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.164092 restraints weight = 71641.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.164461 restraints weight = 52589.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.164598 restraints weight = 44041.575| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 50135 Z= 0.218 Angle : 1.176 16.102 73349 Z= 0.482 Chirality : 0.089 1.163 9186 Planarity : 0.005 0.083 5036 Dihedral : 19.077 179.768 16959 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.83 % Allowed : 12.19 % Favored : 86.98 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.14), residues: 2781 helix: -0.81 (0.20), residues: 651 sheet: -2.27 (0.27), residues: 284 loop : -3.13 (0.13), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 278 TYR 0.041 0.002 TYR K 573 PHE 0.021 0.002 PHE B 116 TRP 0.079 0.004 TRP K1057 HIS 0.011 0.002 HIS K 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.22 (50134) covalent geometry : angle 1.17574 / 0.48 (73347) SS BOND : bond 0.00450 / 0.24 ( 1) SS BOND : angle 1.47758 / 0.80 ( 2) hydrogen bonds : bond 0.07314 / 5.18 ( 1289) hydrogen bonds : angle 4.45627 / 3.17 ( 2809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 1.112 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: A 47 MET cc_start: 0.7740 (mmm) cc_final: 0.7014 (mmm) REVERT: A 348 LYS cc_start: 0.8659 (mttm) cc_final: 0.7721 (mtpt) REVERT: B 12 ILE cc_start: 0.7040 (pt) cc_final: 0.6793 (pt) REVERT: B 30 PRO cc_start: 0.7343 (Cg_endo) cc_final: 0.7072 (Cg_exo) REVERT: B 69 LYS cc_start: 0.7743 (tptm) cc_final: 0.7415 (tptp) REVERT: B 155 SER cc_start: 0.9161 (m) cc_final: 0.8810 (p) REVERT: C 33 PHE cc_start: 0.6959 (p90) cc_final: 0.6646 (p90) REVERT: C 159 ILE cc_start: 0.7054 (pt) cc_final: 0.6482 (mt) REVERT: D 64 ILE cc_start: 0.7136 (mt) cc_final: 0.6865 (mt) REVERT: D 82 ILE cc_start: 0.1621 (tp) cc_final: 0.1303 (mt) REVERT: E 81 GLN cc_start: 0.8223 (mp10) cc_final: 0.7510 (mp10) REVERT: F 19 LYS cc_start: 0.5554 (mttt) cc_final: 0.5111 (mttt) REVERT: F 43 THR cc_start: 0.7186 (t) cc_final: 0.6958 (m) REVERT: J 21 LYS cc_start: 0.6217 (mtmt) cc_final: 0.5651 (ptpp) REVERT: J 67 LYS cc_start: 0.7952 (mttt) cc_final: 0.7305 (mttm) REVERT: J 103 GLN cc_start: 0.6066 (mm-40) cc_final: 0.5203 (mt0) REVERT: K 9 MET cc_start: -0.2136 (mtt) cc_final: -0.2647 (mtt) REVERT: K 251 ILE cc_start: 0.3805 (mt) cc_final: 0.3590 (mt) REVERT: K 254 GLN cc_start: 0.7770 (tp40) cc_final: 0.6231 (mt0) REVERT: K 275 MET cc_start: -0.1857 (mtp) cc_final: -0.2127 (mtm) REVERT: K 326 LYS cc_start: 0.5061 (mmmt) cc_final: 0.4851 (mmmt) REVERT: K 393 GLN cc_start: 0.6706 (tm-30) cc_final: 0.6482 (tm-30) REVERT: K 625 LYS cc_start: 0.3453 (ptpt) cc_final: 0.3094 (tptp) REVERT: K 708 GLU cc_start: 0.5724 (pp20) cc_final: 0.4843 (pp20) REVERT: K 981 MET cc_start: 0.6386 (tmm) cc_final: 0.5491 (tmm) REVERT: K 1005 LYS cc_start: 0.4808 (tttp) cc_final: 0.3293 (mmtt) REVERT: K 1015 MET cc_start: 0.0189 (mtt) cc_final: -0.1740 (tpt) REVERT: K 1021 MET cc_start: 0.3291 (mmt) cc_final: 0.2296 (ptm) REVERT: K 1039 GLU cc_start: 0.3499 (tp30) cc_final: 0.2475 (mt-10) REVERT: K 1091 MET cc_start: 0.5539 (mpp) cc_final: 0.5134 (mpp) REVERT: K 1117 SER cc_start: 0.6286 (m) cc_final: 0.5415 (p) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.2310 time to fit residues: 149.1580 Evaluate side-chains 315 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 358 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 chunk 233 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 197 optimal weight: 20.0000 chunk 219 optimal weight: 9.9990 chunk 312 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 318 optimal weight: 20.0000 chunk 187 optimal weight: 3.9990 chunk 294 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 ASN ** E 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 ASN J 171 HIS ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN K 295 GLN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 712 GLN ** K 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.180637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.164428 restraints weight = 114186.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.162957 restraints weight = 107128.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.164073 restraints weight = 71199.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.164121 restraints weight = 43375.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.164118 restraints weight = 41328.665| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 50135 Z= 0.319 Angle : 1.344 15.402 73349 Z= 0.548 Chirality : 0.097 1.564 9186 Planarity : 0.006 0.084 5036 Dihedral : 19.345 179.397 16959 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.79 % Allowed : 15.17 % Favored : 84.03 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.14), residues: 2781 helix: -0.98 (0.20), residues: 638 sheet: -2.33 (0.27), residues: 286 loop : -3.24 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 278 TYR 0.032 0.003 TYR E 11 PHE 0.023 0.003 PHE B 116 TRP 0.081 0.005 TRP K1057 HIS 0.012 0.002 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.32 (50134) covalent geometry : angle 1.34356 / 0.55 (73347) SS BOND : bond 0.00538 / 0.28 ( 1) SS BOND : angle 1.63679 / 0.88 ( 2) hydrogen bonds : bond 0.08538 / 5.97 ( 1289) hydrogen bonds : angle 4.67798 / 3.31 ( 2809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6416.55 seconds wall clock time: 112 minutes 48.99 seconds (6768.99 seconds total)