Starting phenix.real_space_refine on Wed Aug 27 02:41:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5anc_3147/08_2025/5anc_3147.cif Found real_map, /net/cci-nas-00/data/ceres_data/5anc_3147/08_2025/5anc_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 { model { file = "/net/cci-nas-00/data/ceres_data/5anc_3147/08_2025/5anc_3147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5anc_3147/08_2025/5anc_3147.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5anc_3147/08_2025/5anc_3147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5anc_3147/08_2025/5anc_3147.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 Inner-chain residues flagged as termini: ['pdbres=" C N1356 "', 'pdbres=" A N2392 "', 'pdbres=" A N2925 "'] Classifications: {'RNA': 1162} Modifications used: {'5*END': 4, 'rna2p_pur': 109, 'rna2p_pyr': 57, 'rna3p_pur': 515, 'rna3p_pyr': 481} Link IDs: {'rna2p': 166, 'rna3p': 995} Time building chain proxies: 7.69, per 1000 atoms: 0.16 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: 3.17 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 6.83 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: 20.63 Time building geometry restraints manager: 4.51 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=" 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=" CA PRO A 82 " pdb=" C PRO A 82 " ideal model delta sigma weight residual 1.517 1.556 -0.039 9.30e-03 1.16e+04 1.72e+01 bond pdb=" CA LYS A 178 " pdb=" C LYS A 178 " ideal model delta sigma weight residual 1.523 1.575 -0.052 1.28e-02 6.10e+03 1.65e+01 bond pdb=" O3' A N2405 " pdb=" P A N2406 " ideal model delta sigma weight residual 1.607 1.668 -0.061 1.50e-02 4.44e+03 1.64e+01 bond pdb=" O3' U N1550 " pdb=" P A N1551 " ideal model delta sigma weight residual 1.607 1.668 -0.061 1.50e-02 4.44e+03 1.64e+01 ... (remaining 50129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 70809 3.36 - 6.72: 2380 6.72 - 10.08: 139 10.08 - 13.44: 14 13.44 - 16.80: 5 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 113.70 96.90 16.80 1.50e+00 4.44e-01 1.25e+02 angle pdb=" O3' C N2625 " pdb=" C3' C N2625 " pdb=" C2' C N2625 " ideal model delta sigma weight residual 109.50 125.10 -15.60 1.50e+00 4.44e-01 1.08e+02 angle pdb=" C4' G N3231 " pdb=" C3' G N3231 " pdb=" O3' G N3231 " ideal model delta sigma weight residual 113.00 98.82 14.18 1.50e+00 4.44e-01 8.94e+01 angle pdb=" O3' U N1550 " pdb=" C3' U N1550 " pdb=" C2' U N1550 " ideal model delta sigma weight residual 109.50 123.46 -13.96 1.50e+00 4.44e-01 8.66e+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 ... (remaining 73342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 28305 35.66 - 71.32: 2983 71.32 - 106.98: 328 106.98 - 142.64: 14 142.64 - 178.30: 41 Dihedral angle restraints: 31671 sinusoidal: 23596 harmonic: 8075 Sorted by residual: dihedral pdb=" C5' C N2625 " pdb=" C4' C N2625 " pdb=" C3' C N2625 " pdb=" O3' C N2625 " ideal model delta sinusoidal sigma weight residual 147.00 69.66 77.34 1 8.00e+00 1.56e-02 1.17e+02 dihedral pdb=" C5' C N3328 " pdb=" C4' C N3328 " pdb=" C3' C N3328 " pdb=" O3' C N3328 " ideal model delta sinusoidal sigma weight residual 147.00 70.14 76.86 1 8.00e+00 1.56e-02 1.16e+02 dihedral pdb=" C4' C N3328 " pdb=" C3' C N3328 " pdb=" C2' C N3328 " pdb=" C1' C N3328 " ideal model delta sinusoidal sigma weight residual -35.00 34.86 -69.86 1 8.00e+00 1.56e-02 9.83e+01 ... (remaining 31668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.226: 8809 0.226 - 0.453: 371 0.453 - 0.679: 5 0.679 - 0.905: 0 0.905 - 1.132: 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 -2.50 -1.36 -1.13 2.00e-01 2.50e+01 3.20e+01 chirality pdb=" C3' C N3328 " pdb=" C4' C N3328 " pdb=" O3' C N3328 " pdb=" C2' C N3328 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.56 2.00e-01 2.50e+01 7.84e+00 chirality pdb=" C3' U N1550 " pdb=" C4' U N1550 " pdb=" O3' U N1550 " pdb=" C2' U N1550 " both_signs ideal model delta sigma weight residual False -2.74 -2.24 -0.50 2.00e-01 2.50e+01 6.31e+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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 52.550 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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= 0.589 Angle : 1.355 16.797 73349 Z= 0.902 Chirality : 0.103 1.132 9186 Planarity : 0.007 0.075 5036 Dihedral : 23.789 178.303 26452 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 aren 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 covalent geometry : bond 0.00812 (50134) covalent geometry : angle 1.35459 (73347) SS BOND : bond 0.91078 ( 1) SS BOND : angle 0.98689 ( 2) hydrogen bonds : bond 0.16873 ( 1289) hydrogen bonds : angle 9.56154 ( 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 : 0.874 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: 0.6852 (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: -0.0764 (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: 0.2697 time to fit residues: 286.4460 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 : 1.062 ------------------------------------------------------------------------------- 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: 9.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 246 HIS 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 47 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 K1076 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.185262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.168278 restraints weight = 110249.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.169125 restraints weight = 105700.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.167375 restraints weight = 57754.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.167225 restraints weight = 54231.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.167391 restraints weight = 40303.132| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2528 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= 0.197 Angle : 0.799 12.152 73349 Z= 0.412 Chirality : 0.045 0.319 9186 Planarity : 0.006 0.073 5036 Dihedral : 23.906 179.676 20801 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 1.19 % Allowed : 11.15 % Favored : 87.67 % Rotamer: Outliers : 0.08 % Allowed : 4.92 % Favored : 95.00 % 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 aren not related in a simple way. whole: -3.61 (0.14), residues: 2781 helix: 0.19 (0.22), residues: 635 sheet: -3.10 (0.24), residues: 303 loop : -3.49 (0.12), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 278 TYR 0.024 0.002 TYR F 17 PHE 0.029 0.002 PHE C 33 TRP 0.039 0.003 TRP K 135 HIS 0.010 0.002 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00379 (50134) covalent geometry : angle 0.79904 (73347) SS BOND : bond 0.00261 ( 1) SS BOND : angle 1.82475 ( 2) hydrogen bonds : bond 0.06930 ( 1289) hydrogen bonds : angle 4.79355 ( 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 485 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 483 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 PRO cc_start: 0.6509 (Cg_endo) cc_final: 0.6168 (Cg_exo) REVERT: A 62 LYS cc_start: 0.7596 (tttt) cc_final: 0.7358 (ttpt) REVERT: A 154 ILE cc_start: 0.8619 (pt) cc_final: 0.8125 (mt) REVERT: A 340 ARG cc_start: 0.6635 (mtt180) cc_final: 0.6263 (mtt90) REVERT: A 348 LYS cc_start: 0.8571 (mttm) cc_final: 0.7869 (mtpt) REVERT: B 15 ASN cc_start: 0.7867 (p0) cc_final: 0.7291 (p0) REVERT: B 55 VAL cc_start: 0.9340 (t) cc_final: 0.9131 (t) REVERT: B 69 LYS cc_start: 0.7904 (tttt) cc_final: 0.7632 (tppp) REVERT: B 155 SER cc_start: 0.9081 (m) cc_final: 0.8744 (p) REVERT: C 54 MET cc_start: -0.0771 (ppp) cc_final: -0.0980 (ppp) REVERT: C 159 ILE cc_start: 0.6962 (pt) cc_final: 0.6581 (mt) REVERT: D 82 ILE cc_start: 0.2918 (tp) cc_final: 0.2649 (mt) REVERT: E 59 MET cc_start: 0.7766 (mmm) cc_final: 0.7284 (mmm) REVERT: E 120 GLU cc_start: 0.6402 (mp0) cc_final: 0.6114 (mp0) REVERT: F 19 LYS cc_start: 0.6411 (mttm) cc_final: 0.5462 (mttm) REVERT: F 39 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8450 (mtmm) REVERT: F 125 THR cc_start: 0.8630 (m) cc_final: 0.8333 (p) REVERT: F 154 ARG cc_start: 0.8153 (mtp180) cc_final: 0.7828 (mtp85) REVERT: F 157 TYR cc_start: 0.8230 (m-80) cc_final: 0.7763 (m-10) REVERT: G 1 MET cc_start: 0.3758 (mmm) cc_final: 0.3383 (mtp) REVERT: H 14 CYS cc_start: 0.7015 (m) cc_final: 0.6807 (m) REVERT: H 20 ARG cc_start: 0.8338 (mtt-85) cc_final: 0.8123 (mtt-85) REVERT: J 1 MET cc_start: 0.3863 (mmp) cc_final: 0.3580 (mmt) REVERT: J 21 LYS cc_start: 0.6648 (mtmt) cc_final: 0.5889 (ptpp) REVERT: J 45 LYS cc_start: 0.5621 (mtpt) cc_final: 0.5313 (mptt) REVERT: J 67 LYS cc_start: 0.7602 (mttt) cc_final: 0.7260 (mttm) REVERT: J 164 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8228 (ttpp) REVERT: K 221 SER cc_start: 0.6109 (m) cc_final: 0.5532 (p) REVERT: K 378 MET cc_start: 0.2130 (mtp) cc_final: 0.1498 (mmm) REVERT: K 536 ARG cc_start: 0.0959 (ptp-170) cc_final: 0.0558 (ptp90) REVERT: K 555 MET cc_start: 0.1833 (mmt) cc_final: 0.1143 (mmt) REVERT: K 564 TYR cc_start: 0.1902 (p90) cc_final: 0.0989 (p90) REVERT: K 705 VAL cc_start: 0.5053 (m) cc_final: 0.4767 (p) REVERT: K 791 MET cc_start: 0.1061 (mmp) cc_final: -0.1194 (ttt) REVERT: K 849 THR cc_start: 0.5160 (m) cc_final: 0.4786 (p) REVERT: K 1015 MET cc_start: 0.1547 (mtt) cc_final: -0.1117 (tpt) REVERT: K 1021 MET cc_start: 0.3301 (mmt) cc_final: 0.2880 (ptm) outliers start: 2 outliers final: 0 residues processed: 485 average time/residue: 0.2566 time to fit residues: 201.1880 Evaluate side-chains 362 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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: 9.9990 chunk 380 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 206 optimal weight: 0.9990 chunk 171 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN A 215 ASN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN F 51 HIS F 177 ASN K 4 ASN ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 818 ASN K 844 GLN K1109 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.186121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.170056 restraints weight = 111970.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.170433 restraints weight = 111968.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.169343 restraints weight = 62673.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.169435 restraints weight = 56892.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.169592 restraints weight = 41542.294| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 50135 Z= 0.168 Angle : 0.709 10.050 73349 Z= 0.366 Chirality : 0.041 0.282 9186 Planarity : 0.005 0.083 5036 Dihedral : 23.600 179.861 20801 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 1.11 % Allowed : 11.22 % Favored : 87.67 % Rotamer: Outliers : 0.12 % Allowed : 4.46 % Favored : 95.41 % 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 aren not related in a simple way. whole: -3.42 (0.14), residues: 2781 helix: 0.04 (0.21), residues: 641 sheet: -2.74 (0.25), residues: 308 loop : -3.29 (0.12), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 693 TYR 0.027 0.002 TYR B 133 PHE 0.020 0.002 PHE K 512 TRP 0.042 0.003 TRP F 171 HIS 0.009 0.002 HIS A 3 Details of bonding type rmsd covalent geometry : bond 0.00327 (50134) covalent geometry : angle 0.70944 (73347) SS BOND : bond 0.00075 ( 1) SS BOND : angle 1.67840 ( 2) hydrogen bonds : bond 0.05986 ( 1289) hydrogen bonds : angle 4.40590 ( 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 455 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 452 time to evaluate : 1.027 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: A 59 ASP cc_start: 0.7845 (m-30) cc_final: 0.7432 (m-30) REVERT: A 62 LYS cc_start: 0.7659 (tttt) cc_final: 0.7285 (ttpt) REVERT: A 154 ILE cc_start: 0.8642 (pt) cc_final: 0.8121 (mt) REVERT: A 183 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7848 (mm-30) REVERT: A 348 LYS cc_start: 0.8496 (mttm) cc_final: 0.7986 (mtpt) REVERT: B 1 MET cc_start: 0.2191 (mmt) cc_final: 0.1893 (mmt) REVERT: B 15 ASN cc_start: 0.7842 (p0) cc_final: 0.7492 (p0) REVERT: B 69 LYS cc_start: 0.7943 (tttt) cc_final: 0.7632 (tppp) REVERT: B 88 TYR cc_start: 0.7780 (m-10) cc_final: 0.7430 (m-10) REVERT: B 93 VAL cc_start: 0.7823 (p) cc_final: 0.7535 (p) REVERT: B 155 SER cc_start: 0.9042 (m) cc_final: 0.8716 (p) REVERT: C 159 ILE cc_start: 0.6844 (pt) cc_final: 0.6553 (mt) REVERT: D 82 ILE cc_start: 0.2158 (tp) cc_final: 0.1805 (mt) REVERT: H 14 CYS cc_start: 0.6952 (m) cc_final: 0.6656 (m) REVERT: J 21 LYS cc_start: 0.6408 (mtmt) cc_final: 0.5880 (ptpp) REVERT: J 44 GLU cc_start: 0.4957 (mm-30) cc_final: 0.4610 (tm-30) REVERT: J 50 VAL cc_start: 0.8551 (m) cc_final: 0.8319 (p) REVERT: J 51 LEU cc_start: 0.7967 (mp) cc_final: 0.7624 (pp) REVERT: J 67 LYS cc_start: 0.7665 (mttt) cc_final: 0.7235 (mttm) REVERT: J 164 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8074 (ttpp) REVERT: K 189 ARG cc_start: 0.5363 (tpm170) cc_final: 0.4409 (ptm160) REVERT: K 349 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.5269 (mt) REVERT: K 378 MET cc_start: 0.1317 (mtp) cc_final: 0.0897 (mmm) REVERT: K 536 ARG cc_start: 0.1280 (ptp-170) cc_final: 0.0893 (ttm170) REVERT: K 555 MET cc_start: 0.2277 (mmt) cc_final: 0.1700 (mmt) REVERT: K 564 TYR cc_start: 0.1577 (p90) cc_final: 0.0814 (p90) REVERT: K 630 MET cc_start: 0.4484 (mmm) cc_final: 0.4056 (mmm) REVERT: K 776 MET cc_start: 0.3732 (tpp) cc_final: 0.3365 (tpp) REVERT: K 791 MET cc_start: 0.1146 (mmp) cc_final: -0.0220 (tpp) REVERT: K 888 MET cc_start: 0.4197 (tmm) cc_final: 0.3981 (tpt) REVERT: K 1015 MET cc_start: 0.1581 (mtt) cc_final: -0.1127 (tpt) REVERT: K 1021 MET cc_start: 0.3293 (mmt) cc_final: 0.2973 (ptm) REVERT: K 1091 MET cc_start: 0.5777 (mpp) cc_final: 0.5370 (mpp) outliers start: 3 outliers final: 0 residues processed: 455 average time/residue: 0.2556 time to fit residues: 189.5829 Evaluate side-chains 363 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 362 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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: 0.4980 chunk 74 optimal weight: 20.0000 chunk 36 optimal weight: 0.0980 chunk 33 optimal weight: 0.0980 chunk 153 optimal weight: 5.9990 chunk 109 optimal weight: 0.3980 chunk 210 optimal weight: 0.0270 chunk 296 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 overall best weight: 0.2238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 215 ASN E 10 ASN E 33 ASN F 51 HIS H 32 ASN K 15 ASN ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN K 440 GLN K 844 GLN ** K1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1085 ASN K1092 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.192538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.177570 restraints weight = 111478.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.178258 restraints weight = 114264.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.176445 restraints weight = 59171.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.176515 restraints weight = 50568.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.176495 restraints weight = 41122.035| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 50135 Z= 0.121 Angle : 0.643 11.623 73349 Z= 0.327 Chirality : 0.037 0.279 9186 Planarity : 0.005 0.077 5036 Dihedral : 23.376 179.760 20801 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.97 % Allowed : 9.17 % Favored : 89.86 % Rotamer: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.07 % 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 aren not related in a simple way. whole: -3.28 (0.14), residues: 2781 helix: -0.01 (0.21), residues: 650 sheet: -2.48 (0.24), residues: 332 loop : -3.17 (0.12), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 24 TYR 0.028 0.002 TYR F 17 PHE 0.034 0.002 PHE B 38 TRP 0.046 0.002 TRP A 106 HIS 0.007 0.001 HIS A 3 Details of bonding type rmsd covalent geometry : bond 0.00241 (50134) covalent geometry : angle 0.64300 (73347) SS BOND : bond 0.01565 ( 1) SS BOND : angle 1.52951 ( 2) hydrogen bonds : bond 0.05359 ( 1289) hydrogen bonds : angle 4.17894 ( 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 461 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 460 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7494 (tttt) cc_final: 0.7271 (ttpt) REVERT: A 87 VAL cc_start: 0.8691 (p) cc_final: 0.8483 (m) REVERT: A 183 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 348 LYS cc_start: 0.8584 (mttm) cc_final: 0.7898 (mtpt) REVERT: B 12 ILE cc_start: 0.7001 (pt) cc_final: 0.6527 (pt) REVERT: B 55 VAL cc_start: 0.9261 (t) cc_final: 0.9041 (t) REVERT: B 93 VAL cc_start: 0.7363 (p) cc_final: 0.7080 (p) REVERT: B 155 SER cc_start: 0.9048 (m) cc_final: 0.8753 (p) REVERT: C 59 MET cc_start: 0.7042 (ptm) cc_final: 0.6570 (ptm) REVERT: C 159 ILE cc_start: 0.6765 (pt) cc_final: 0.6468 (mt) REVERT: D 82 ILE cc_start: 0.2248 (tp) cc_final: 0.1863 (mt) REVERT: E 35 TYR cc_start: 0.8191 (t80) cc_final: 0.7948 (t80) REVERT: F 191 MET cc_start: 0.5265 (mpp) cc_final: 0.4239 (mtm) REVERT: G 1 MET cc_start: 0.4162 (ttt) cc_final: 0.3313 (ttp) REVERT: H 14 CYS cc_start: 0.6951 (m) cc_final: 0.6623 (m) REVERT: J 21 LYS cc_start: 0.6500 (mtmt) cc_final: 0.5781 (ptpp) REVERT: J 67 LYS cc_start: 0.7419 (mttt) cc_final: 0.7041 (mttm) REVERT: K 9 MET cc_start: -0.1762 (mtt) cc_final: -0.1990 (mtt) REVERT: K 378 MET cc_start: 0.1617 (mtp) cc_final: 0.1375 (mmm) REVERT: K 447 GLN cc_start: 0.3876 (pt0) cc_final: 0.3560 (tp40) REVERT: K 555 MET cc_start: 0.1951 (mmt) cc_final: 0.1419 (mmt) REVERT: K 564 TYR cc_start: 0.1389 (p90) cc_final: 0.0815 (p90) REVERT: K 630 MET cc_start: 0.3957 (mmm) cc_final: 0.3704 (mmm) REVERT: K 751 LEU cc_start: 0.3800 (pp) cc_final: 0.3024 (pp) REVERT: K 776 MET cc_start: 0.3749 (tpp) cc_final: 0.3265 (tpp) REVERT: K 791 MET cc_start: 0.1737 (mmp) cc_final: 0.0260 (tpp) REVERT: K 1015 MET cc_start: 0.0913 (mtt) cc_final: -0.1130 (tpt) REVERT: K 1021 MET cc_start: 0.3923 (mmt) cc_final: 0.3402 (ptm) REVERT: K 1091 MET cc_start: 0.5681 (mpp) cc_final: 0.5022 (mpp) outliers start: 1 outliers final: 0 residues processed: 461 average time/residue: 0.3056 time to fit residues: 228.4510 Evaluate side-chains 357 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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: 0.0770 chunk 335 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 chunk 149 optimal weight: 30.0000 chunk 180 optimal weight: 8.9990 chunk 377 optimal weight: 10.0000 chunk 329 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 chunk 201 optimal weight: 30.0000 chunk 68 optimal weight: 0.4980 chunk 91 optimal weight: 20.0000 overall best weight: 5.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN C 138 GLN E 10 ASN E 104 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 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 466 GLN K 554 HIS ** K 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 915 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.182039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.165951 restraints weight = 112792.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.166121 restraints weight = 111833.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.165604 restraints weight = 65128.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.165611 restraints weight = 60257.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.165809 restraints weight = 42265.966| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 50135 Z= 0.285 Angle : 0.840 9.756 73349 Z= 0.422 Chirality : 0.045 0.301 9186 Planarity : 0.006 0.078 5036 Dihedral : 23.464 179.176 20801 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.73 % Favored : 86.37 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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 aren not related in a simple way. whole: -3.38 (0.14), residues: 2781 helix: -0.36 (0.20), residues: 650 sheet: -2.26 (0.26), residues: 297 loop : -3.19 (0.12), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG F 38 TYR 0.037 0.003 TYR F 17 PHE 0.024 0.003 PHE A 229 TRP 0.078 0.006 TRP F 171 HIS 0.010 0.002 HIS K 27 Details of bonding type rmsd covalent geometry : bond 0.00554 (50134) covalent geometry : angle 0.83947 (73347) SS BOND : bond 0.00280 ( 1) SS BOND : angle 2.19678 ( 2) hydrogen bonds : bond 0.07185 ( 1289) hydrogen bonds : angle 4.45306 ( 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 408 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.164 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: A 47 MET cc_start: 0.7518 (mmt) cc_final: 0.7163 (mmm) REVERT: A 62 LYS cc_start: 0.8064 (tttt) cc_final: 0.7758 (ttpt) REVERT: A 106 TRP cc_start: 0.7209 (m-90) cc_final: 0.6972 (m-90) REVERT: A 235 ARG cc_start: 0.9159 (ttt180) cc_final: 0.8371 (ttt180) REVERT: A 348 LYS cc_start: 0.8698 (mttm) cc_final: 0.7972 (mtpt) REVERT: B 155 SER cc_start: 0.8988 (m) cc_final: 0.8660 (p) REVERT: C 26 MET cc_start: 0.3786 (ptm) cc_final: 0.3578 (ptm) REVERT: C 159 ILE cc_start: 0.6877 (pt) cc_final: 0.6627 (mt) REVERT: D 82 ILE cc_start: 0.2467 (tp) cc_final: 0.1957 (mt) REVERT: E 35 TYR cc_start: 0.8241 (t80) cc_final: 0.8017 (t80) REVERT: F 191 MET cc_start: 0.5927 (mpp) cc_final: 0.5222 (mtm) REVERT: F 200 ILE cc_start: 0.7949 (mt) cc_final: 0.7709 (mt) REVERT: G 1 MET cc_start: 0.5654 (ttt) cc_final: 0.4254 (ttt) REVERT: G 53 MET cc_start: 0.3846 (tpt) cc_final: 0.3400 (tmm) REVERT: H 14 CYS cc_start: 0.7455 (m) cc_final: 0.7134 (m) REVERT: J 21 LYS cc_start: 0.6393 (mtmt) cc_final: 0.5777 (ptpp) REVERT: J 44 GLU cc_start: 0.5456 (mm-30) cc_final: 0.5061 (tm-30) REVERT: J 67 LYS cc_start: 0.7899 (mttt) cc_final: 0.7184 (mttm) REVERT: K 189 ARG cc_start: 0.4978 (tpm170) cc_final: 0.4327 (ptm160) REVERT: K 207 GLN cc_start: 0.4382 (mm-40) cc_final: 0.4006 (mm-40) REVERT: K 358 MET cc_start: 0.4683 (mmt) cc_final: 0.4261 (mmt) REVERT: K 378 MET cc_start: 0.1558 (mtp) cc_final: 0.1064 (mmm) REVERT: K 447 GLN cc_start: 0.4660 (pt0) cc_final: 0.4113 (tp40) REVERT: K 520 LYS cc_start: 0.2696 (ttpp) cc_final: 0.1389 (tptt) REVERT: K 555 MET cc_start: 0.2649 (mmt) cc_final: 0.1927 (mmt) REVERT: K 564 TYR cc_start: 0.2238 (p90) cc_final: 0.1422 (p90) REVERT: K 630 MET cc_start: 0.3748 (mmm) cc_final: 0.3386 (mmm) REVERT: K 708 GLU cc_start: 0.6872 (pp20) cc_final: 0.6666 (pp20) REVERT: K 776 MET cc_start: 0.3759 (tpp) cc_final: 0.3075 (tpp) REVERT: K 791 MET cc_start: 0.1385 (mmp) cc_final: 0.0323 (mpp) REVERT: K 1015 MET cc_start: 0.0928 (mtt) cc_final: -0.1082 (tpt) REVERT: K 1021 MET cc_start: 0.3724 (mmt) cc_final: 0.3044 (ptm) REVERT: K 1091 MET cc_start: 0.5871 (mpp) cc_final: 0.5426 (mpp) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.3055 time to fit residues: 202.5884 Evaluate side-chains 335 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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: 4.9990 chunk 69 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 282 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 255 optimal weight: 30.0000 chunk 16 optimal weight: 6.9990 chunk 256 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 343 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** E 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 ASN J 171 HIS ** 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 435 GLN ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 844 GLN K1092 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.181736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.166748 restraints weight = 112892.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.167357 restraints weight = 112948.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.166230 restraints weight = 63047.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.166249 restraints weight = 54716.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.166275 restraints weight = 41323.128| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 50135 Z= 0.254 Angle : 0.807 10.554 73349 Z= 0.409 Chirality : 0.044 0.325 9186 Planarity : 0.006 0.077 5036 Dihedral : 23.567 178.995 20801 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.83 % Allowed : 12.33 % Favored : 86.84 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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 aren not related in a simple way. whole: -3.46 (0.14), residues: 2781 helix: -0.54 (0.20), residues: 633 sheet: -2.39 (0.26), residues: 270 loop : -3.16 (0.12), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 278 TYR 0.035 0.003 TYR F 17 PHE 0.058 0.002 PHE B 116 TRP 0.069 0.004 TRP F 171 HIS 0.012 0.002 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00497 (50134) covalent geometry : angle 0.80715 (73347) SS BOND : bond 0.00208 ( 1) SS BOND : angle 1.42378 ( 2) hydrogen bonds : bond 0.07159 ( 1289) hydrogen bonds : angle 4.51829 ( 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 405 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.195 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: A 60 LEU cc_start: 0.7338 (tp) cc_final: 0.7100 (tp) REVERT: A 62 LYS cc_start: 0.8031 (tttt) cc_final: 0.7728 (ttpt) REVERT: A 106 TRP cc_start: 0.7298 (m-90) cc_final: 0.7021 (m-90) REVERT: A 235 ARG cc_start: 0.9063 (ttt180) cc_final: 0.8299 (ttt180) REVERT: B 19 ASP cc_start: 0.7301 (t0) cc_final: 0.7028 (t0) REVERT: B 97 PHE cc_start: 0.5582 (m-80) cc_final: 0.5322 (m-80) REVERT: B 155 SER cc_start: 0.9017 (m) cc_final: 0.8667 (p) REVERT: C 59 MET cc_start: 0.7219 (ptm) cc_final: 0.6969 (ptt) REVERT: E 35 TYR cc_start: 0.8204 (t80) cc_final: 0.7996 (t80) REVERT: F 43 THR cc_start: 0.7161 (t) cc_final: 0.6901 (m) REVERT: F 191 MET cc_start: 0.6085 (mpp) cc_final: 0.5441 (mtm) REVERT: G 1 MET cc_start: 0.5499 (ttt) cc_final: 0.3446 (ttt) REVERT: H 14 CYS cc_start: 0.7570 (m) cc_final: 0.7241 (m) REVERT: J 21 LYS cc_start: 0.6366 (mtmt) cc_final: 0.5740 (ptpp) REVERT: J 67 LYS cc_start: 0.8030 (mttt) cc_final: 0.7365 (mttm) REVERT: J 164 LYS cc_start: 0.8061 (ttmm) cc_final: 0.7765 (ttpt) REVERT: J 169 ARG cc_start: 0.4853 (mtt90) cc_final: 0.3932 (ptp-110) REVERT: K 447 GLN cc_start: 0.4797 (pt0) cc_final: 0.4128 (tp40) REVERT: K 564 TYR cc_start: 0.2076 (p90) cc_final: 0.1177 (p90) REVERT: K 630 MET cc_start: 0.3799 (mmm) cc_final: 0.3360 (mmm) REVERT: K 776 MET cc_start: 0.3840 (tpp) cc_final: 0.2997 (tpp) REVERT: K 791 MET cc_start: 0.2127 (mmp) cc_final: 0.1447 (mpp) REVERT: K 1015 MET cc_start: 0.0792 (mtt) cc_final: -0.1505 (tpt) REVERT: K 1021 MET cc_start: 0.3877 (mmt) cc_final: 0.3149 (ptt) REVERT: K 1091 MET cc_start: 0.5993 (mpp) cc_final: 0.5654 (mpp) REVERT: K 1118 LYS cc_start: 0.5803 (pttt) cc_final: 0.5116 (pttp) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.2987 time to fit residues: 197.7639 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 : 1.144 ------------------------------------------------------------------------------- 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: 10.0000 chunk 162 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 343 optimal weight: 10.0000 chunk 374 optimal weight: 10.0000 chunk 259 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 218 optimal weight: 0.0970 chunk 307 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 overall best weight: 6.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** 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 295 GLN K 334 HIS K 342 ASN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.178186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.163557 restraints weight = 113220.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.163859 restraints weight = 116179.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.163328 restraints weight = 66381.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.163291 restraints weight = 52432.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.163499 restraints weight = 40313.224| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 50135 Z= 0.326 Angle : 0.929 10.941 73349 Z= 0.466 Chirality : 0.049 0.322 9186 Planarity : 0.007 0.076 5036 Dihedral : 23.737 179.923 20801 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.93 % Allowed : 13.95 % Favored : 85.11 % Rotamer: Outliers : 0.04 % Allowed : 2.52 % Favored : 97.44 % 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 aren not related in a simple way. whole: -3.73 (0.14), residues: 2781 helix: -0.90 (0.20), residues: 627 sheet: -2.60 (0.25), residues: 302 loop : -3.26 (0.12), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG K 693 TYR 0.038 0.003 TYR F 17 PHE 0.059 0.003 PHE B 116 TRP 0.068 0.004 TRP F 171 HIS 0.012 0.003 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00634 (50134) covalent geometry : angle 0.92905 (73347) SS BOND : bond 0.00175 ( 1) SS BOND : angle 1.74587 ( 2) hydrogen bonds : bond 0.08413 ( 1289) hydrogen bonds : angle 4.80626 ( 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 : 1.123 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 47 MET cc_start: 0.7622 (mmm) cc_final: 0.6920 (mmm) REVERT: A 62 LYS cc_start: 0.8244 (tttt) cc_final: 0.7957 (ttpt) REVERT: A 235 ARG cc_start: 0.9175 (ttt180) cc_final: 0.8466 (ttt90) REVERT: B 19 ASP cc_start: 0.7685 (t0) cc_final: 0.7417 (t0) REVERT: B 155 SER cc_start: 0.9030 (m) cc_final: 0.8688 (p) REVERT: C 59 MET cc_start: 0.7133 (ptm) cc_final: 0.6860 (ptt) REVERT: F 66 GLU cc_start: 0.7769 (tp30) cc_final: 0.7564 (tp30) REVERT: F 70 ILE cc_start: 0.9015 (pt) cc_final: 0.8781 (pt) REVERT: F 191 MET cc_start: 0.6142 (mpp) cc_final: 0.5266 (mtm) REVERT: G 1 MET cc_start: 0.5307 (ttt) cc_final: 0.3444 (ttt) REVERT: G 53 MET cc_start: 0.5104 (tpt) cc_final: 0.4712 (mmm) REVERT: H 14 CYS cc_start: 0.7553 (m) cc_final: 0.7339 (m) REVERT: H 26 LEU cc_start: 0.8341 (mm) cc_final: 0.8101 (mm) REVERT: H 29 ARG cc_start: 0.7086 (ttp-110) cc_final: 0.6732 (mtm110) REVERT: J 21 LYS cc_start: 0.6464 (mtmt) cc_final: 0.5874 (ptpp) REVERT: J 54 HIS cc_start: 0.7175 (t-170) cc_final: 0.6640 (t-90) REVERT: J 67 LYS cc_start: 0.8263 (mttt) cc_final: 0.7530 (mttm) REVERT: K 207 GLN cc_start: 0.4151 (mm-40) cc_final: 0.3796 (mm-40) REVERT: K 447 GLN cc_start: 0.4993 (pt0) cc_final: 0.4175 (tp40) REVERT: K 637 MET cc_start: 0.3131 (tpt) cc_final: 0.2733 (tpt) REVERT: K 776 MET cc_start: 0.3861 (tpp) cc_final: 0.3628 (tpp) REVERT: K 790 HIS cc_start: 0.1075 (m-70) cc_final: 0.0830 (m-70) REVERT: K 888 MET cc_start: 0.3578 (ttt) cc_final: 0.3110 (ttt) REVERT: K 1015 MET cc_start: 0.0320 (mtt) cc_final: -0.1471 (tpt) REVERT: K 1091 MET cc_start: 0.6337 (mpp) cc_final: 0.5968 (mpp) REVERT: K 1117 SER cc_start: 0.5918 (m) cc_final: 0.4779 (p) outliers start: 1 outliers final: 0 residues processed: 400 average time/residue: 0.2944 time to fit residues: 194.3965 Evaluate side-chains 325 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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: 7.9990 chunk 42 optimal weight: 6.9990 chunk 194 optimal weight: 0.0040 chunk 375 optimal weight: 8.9990 chunk 316 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 362 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 315 optimal weight: 10.0000 overall best weight: 6.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 ASN ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 HIS ** 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 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN ** K 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.179284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.165583 restraints weight = 113337.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.163282 restraints weight = 104211.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.159468 restraints weight = 80209.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.160264 restraints weight = 68731.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.160353 restraints weight = 55640.729| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 50135 Z= 0.289 Angle : 0.873 12.431 73349 Z= 0.441 Chirality : 0.047 0.335 9186 Planarity : 0.006 0.082 5036 Dihedral : 23.756 179.864 20801 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.83 % Allowed : 12.94 % Favored : 86.23 % Rotamer: Outliers : 0.04 % Allowed : 1.40 % Favored : 98.55 % 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 aren not related in a simple way. whole: -3.80 (0.14), residues: 2781 helix: -1.04 (0.19), residues: 637 sheet: -2.57 (0.26), residues: 287 loop : -3.29 (0.12), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 278 TYR 0.035 0.003 TYR E 11 PHE 0.027 0.003 PHE B 116 TRP 0.057 0.004 TRP F 171 HIS 0.011 0.002 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00561 (50134) covalent geometry : angle 0.87295 (73347) SS BOND : bond 0.00411 ( 1) SS BOND : angle 1.19386 ( 2) hydrogen bonds : bond 0.07970 ( 1289) hydrogen bonds : angle 4.79451 ( 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 392 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 391 time to evaluate : 1.180 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 62 LYS cc_start: 0.8256 (tttt) cc_final: 0.8030 (ttpt) REVERT: A 110 LEU cc_start: 0.6307 (tt) cc_final: 0.6037 (tt) REVERT: A 183 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8296 (mm-30) REVERT: A 235 ARG cc_start: 0.9073 (ttt180) cc_final: 0.8579 (ttt180) REVERT: B 12 ILE cc_start: 0.7623 (pt) cc_final: 0.7401 (pt) REVERT: B 15 ASN cc_start: 0.7927 (p0) cc_final: 0.7701 (p0) REVERT: B 19 ASP cc_start: 0.7683 (t0) cc_final: 0.7449 (t0) REVERT: B 93 VAL cc_start: 0.8137 (p) cc_final: 0.7711 (m) REVERT: B 155 SER cc_start: 0.9049 (m) cc_final: 0.8685 (p) REVERT: C 30 GLU cc_start: 0.6021 (tp30) cc_final: 0.5774 (tp30) REVERT: C 33 PHE cc_start: 0.6234 (p90) cc_final: 0.5933 (p90) REVERT: D 166 LYS cc_start: 0.3089 (tptt) cc_final: 0.2887 (tptp) REVERT: E 56 ASP cc_start: 0.8347 (p0) cc_final: 0.7969 (p0) REVERT: E 81 GLN cc_start: 0.8463 (mp10) cc_final: 0.7636 (mp10) REVERT: F 191 MET cc_start: 0.6038 (mpp) cc_final: 0.5002 (mtm) REVERT: G 1 MET cc_start: 0.4888 (ttt) cc_final: 0.3356 (ttt) REVERT: G 53 MET cc_start: 0.4856 (tpt) cc_final: 0.4566 (mmm) REVERT: H 14 CYS cc_start: 0.7498 (m) cc_final: 0.7200 (m) REVERT: J 21 LYS cc_start: 0.6181 (mtmt) cc_final: 0.5799 (ptpp) REVERT: J 67 LYS cc_start: 0.8213 (mttt) cc_final: 0.7464 (mttm) REVERT: J 103 GLN cc_start: 0.6056 (mm-40) cc_final: 0.5113 (mm-40) REVERT: J 131 ILE cc_start: 0.8202 (tt) cc_final: 0.7782 (mp) REVERT: J 194 ILE cc_start: 0.6330 (pt) cc_final: 0.5897 (pt) REVERT: K 207 GLN cc_start: 0.4101 (mm-40) cc_final: 0.3785 (mm-40) REVERT: K 447 GLN cc_start: 0.4815 (pt0) cc_final: 0.3813 (tp40) REVERT: K 1015 MET cc_start: -0.0130 (mtt) cc_final: -0.1872 (tpt) REVERT: K 1091 MET cc_start: 0.6063 (mpp) cc_final: 0.5684 (mpp) REVERT: K 1118 LYS cc_start: 0.5295 (pttt) cc_final: 0.4844 (pttp) outliers start: 1 outliers final: 0 residues processed: 392 average time/residue: 0.2933 time to fit residues: 189.3317 Evaluate side-chains 327 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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: 4.9990 chunk 222 optimal weight: 30.0000 chunk 212 optimal weight: 7.9990 chunk 210 optimal weight: 0.0570 chunk 75 optimal weight: 10.0000 chunk 290 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 274 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 overall best weight: 5.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 ASN ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 ASN ** H 42 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 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN K 466 GLN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 611 ASN ** K 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 810 HIS ** K 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1109 HIS ** 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 = 0.4210 r_free = 0.4210 target = 0.180191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.164103 restraints weight = 113348.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.164538 restraints weight = 100798.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.164050 restraints weight = 53481.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.163899 restraints weight = 46649.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.163999 restraints weight = 38274.335| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 50135 Z= 0.253 Angle : 0.840 11.654 73349 Z= 0.425 Chirality : 0.045 0.319 9186 Planarity : 0.006 0.093 5036 Dihedral : 23.720 179.926 20801 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.79 % Allowed : 13.99 % Favored : 85.22 % Rotamer: Outliers : 0.04 % Allowed : 0.79 % Favored : 99.17 % 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 aren not related in a simple way. whole: -3.73 (0.14), residues: 2781 helix: -0.99 (0.19), residues: 620 sheet: -2.39 (0.27), residues: 278 loop : -3.26 (0.12), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 56 TYR 0.035 0.003 TYR B 94 PHE 0.073 0.003 PHE B 116 TRP 0.064 0.004 TRP K 135 HIS 0.012 0.002 HIS K 682 Details of bonding type rmsd covalent geometry : bond 0.00494 (50134) covalent geometry : angle 0.83961 (73347) SS BOND : bond 0.00373 ( 1) SS BOND : angle 1.39835 ( 2) hydrogen bonds : bond 0.07689 ( 1289) hydrogen bonds : angle 4.74500 ( 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 378 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 1.073 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 60 LEU cc_start: 0.7248 (tp) cc_final: 0.7016 (tp) REVERT: A 62 LYS cc_start: 0.8142 (tttt) cc_final: 0.7753 (ttpt) REVERT: A 183 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8333 (mm-30) REVERT: A 235 ARG cc_start: 0.9090 (ttt180) cc_final: 0.8514 (ttt180) REVERT: B 155 SER cc_start: 0.9053 (m) cc_final: 0.8704 (p) REVERT: B 175 ASP cc_start: 0.7971 (t0) cc_final: 0.7170 (t0) REVERT: C 33 PHE cc_start: 0.5864 (p90) cc_final: 0.5582 (p90) REVERT: E 81 GLN cc_start: 0.8306 (mp10) cc_final: 0.7575 (mp10) REVERT: F 191 MET cc_start: 0.5988 (mpp) cc_final: 0.4911 (mtm) REVERT: G 1 MET cc_start: 0.5209 (ttt) cc_final: 0.3901 (ttt) REVERT: H 14 CYS cc_start: 0.7482 (m) cc_final: 0.7205 (m) REVERT: J 21 LYS cc_start: 0.6123 (mtmt) cc_final: 0.5715 (ptpp) REVERT: J 67 LYS cc_start: 0.8232 (mttt) cc_final: 0.7455 (mttm) REVERT: J 103 GLN cc_start: 0.6076 (mm-40) cc_final: 0.5158 (mm-40) REVERT: J 131 ILE cc_start: 0.8247 (tt) cc_final: 0.7765 (mp) REVERT: K 207 GLN cc_start: 0.4117 (mm-40) cc_final: 0.3894 (mm-40) REVERT: K 625 LYS cc_start: 0.3354 (ptpt) cc_final: 0.2632 (tttm) REVERT: K 708 GLU cc_start: 0.6281 (pp20) cc_final: 0.5881 (pp20) REVERT: K 888 MET cc_start: 0.3255 (ttt) cc_final: 0.3034 (ttt) REVERT: K 965 MET cc_start: 0.4944 (mmt) cc_final: 0.3743 (mmt) REVERT: K 1015 MET cc_start: 0.0146 (mtt) cc_final: -0.1781 (tpt) REVERT: K 1091 MET cc_start: 0.6164 (mpp) cc_final: 0.5896 (mpp) REVERT: K 1118 LYS cc_start: 0.5222 (pttt) cc_final: 0.2970 (mptt) outliers start: 1 outliers final: 1 residues processed: 378 average time/residue: 0.2572 time to fit residues: 161.4050 Evaluate side-chains 314 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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: 10.0000 chunk 106 optimal weight: 7.9990 chunk 265 optimal weight: 7.9990 chunk 337 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 243 optimal weight: 6.9990 chunk 27 optimal weight: 0.0670 chunk 326 optimal weight: 9.9990 chunk 272 optimal weight: 9.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN F 147 ASN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 712 GLN K 720 GLN ** K 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 809 GLN ** K 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1056 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 = 0.4227 r_free = 0.4227 target = 0.181685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.165456 restraints weight = 113845.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.165583 restraints weight = 108807.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.165818 restraints weight = 58143.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.165633 restraints weight = 40892.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.165823 restraints weight = 35359.086| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 50135 Z= 0.216 Angle : 0.792 10.981 73349 Z= 0.403 Chirality : 0.043 0.357 9186 Planarity : 0.006 0.089 5036 Dihedral : 23.666 179.813 20801 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.79 % Allowed : 12.62 % Favored : 86.59 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.62 (0.14), residues: 2781 helix: -0.85 (0.20), residues: 615 sheet: -2.28 (0.28), residues: 264 loop : -3.21 (0.12), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 278 TYR 0.029 0.003 TYR F 9 PHE 0.065 0.002 PHE B 116 TRP 0.057 0.004 TRP K 135 HIS 0.015 0.002 HIS K 78 Details of bonding type rmsd covalent geometry : bond 0.00422 (50134) covalent geometry : angle 0.79157 (73347) SS BOND : bond 0.00392 ( 1) SS BOND : angle 1.24383 ( 2) hydrogen bonds : bond 0.07222 ( 1289) hydrogen bonds : angle 4.63322 ( 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 386 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.787 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 47 MET cc_start: 0.7713 (mmm) cc_final: 0.7432 (mmm) REVERT: A 60 LEU cc_start: 0.7153 (tp) cc_final: 0.6920 (tp) REVERT: A 62 LYS cc_start: 0.8022 (tttt) cc_final: 0.7710 (ttpt) REVERT: A 235 ARG cc_start: 0.9091 (ttt180) cc_final: 0.8497 (ttt180) REVERT: A 348 LYS cc_start: 0.8569 (mttm) cc_final: 0.7572 (mtpt) REVERT: B 155 SER cc_start: 0.9031 (m) cc_final: 0.8691 (p) REVERT: B 175 ASP cc_start: 0.7740 (t0) cc_final: 0.7278 (t0) REVERT: C 33 PHE cc_start: 0.5906 (p90) cc_final: 0.5613 (p90) REVERT: E 81 GLN cc_start: 0.8264 (mp10) cc_final: 0.7610 (mp10) REVERT: F 19 LYS cc_start: 0.5842 (mttt) cc_final: 0.5414 (mttt) REVERT: F 191 MET cc_start: 0.5933 (mpp) cc_final: 0.4821 (mtm) REVERT: G 1 MET cc_start: 0.5181 (ttt) cc_final: 0.3869 (ttt) REVERT: J 21 LYS cc_start: 0.6192 (mtmt) cc_final: 0.5722 (ptpp) REVERT: J 67 LYS cc_start: 0.8117 (mttt) cc_final: 0.7413 (mttm) REVERT: J 103 GLN cc_start: 0.6049 (mm-40) cc_final: 0.5121 (mt0) REVERT: J 131 ILE cc_start: 0.8156 (tt) cc_final: 0.7814 (mp) REVERT: K 207 GLN cc_start: 0.3671 (mm-40) cc_final: 0.3466 (mm-40) REVERT: K 254 GLN cc_start: 0.7475 (tp40) cc_final: 0.6297 (mt0) REVERT: K 625 LYS cc_start: 0.3123 (ptpt) cc_final: 0.2330 (tttm) REVERT: K 708 GLU cc_start: 0.5843 (pp20) cc_final: 0.5026 (pp20) REVERT: K 763 THR cc_start: 0.3680 (m) cc_final: 0.3455 (m) REVERT: K 888 MET cc_start: 0.3382 (ttt) cc_final: 0.3148 (ttt) REVERT: K 965 MET cc_start: 0.4958 (mmt) cc_final: 0.3746 (mmt) REVERT: K 1015 MET cc_start: 0.0085 (mtt) cc_final: -0.1788 (tpt) REVERT: K 1039 GLU cc_start: 0.3378 (tp30) cc_final: 0.2604 (mt-10) REVERT: K 1091 MET cc_start: 0.6318 (mpp) cc_final: 0.5834 (mpp) REVERT: K 1117 SER cc_start: 0.6023 (m) cc_final: 0.4742 (p) REVERT: K 1118 LYS cc_start: 0.5294 (pttt) cc_final: 0.3022 (mptt) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.2231 time to fit residues: 143.3730 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 : 1.049 ------------------------------------------------------------------------------- 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: 10.0000 chunk 220 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 312 optimal weight: 10.0000 chunk 203 optimal weight: 0.0570 chunk 318 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 chunk 294 optimal weight: 30.0000 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 HIS E 10 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN ** K 27 HIS ** 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 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 632 GLN ** K 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 927 ASN ** K1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.183384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.167589 restraints weight = 112444.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.167371 restraints weight = 108347.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.167713 restraints weight = 54052.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.167586 restraints weight = 36965.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.167747 restraints weight = 34461.124| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 50135 Z= 0.185 Angle : 0.745 10.335 73349 Z= 0.380 Chirality : 0.041 0.354 9186 Planarity : 0.006 0.083 5036 Dihedral : 23.560 179.609 20801 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.68 % Allowed : 12.37 % Favored : 86.95 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.71 % 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 aren not related in a simple way. whole: -3.54 (0.14), residues: 2781 helix: -0.80 (0.20), residues: 625 sheet: -2.16 (0.28), residues: 267 loop : -3.17 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 278 TYR 0.029 0.002 TYR F 9 PHE 0.041 0.002 PHE A 114 TRP 0.055 0.004 TRP K 135 HIS 0.007 0.002 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00361 (50134) covalent geometry : angle 0.74450 (73347) SS BOND : bond 0.00111 ( 1) SS BOND : angle 1.80619 ( 2) hydrogen bonds : bond 0.06666 ( 1289) hydrogen bonds : angle 4.51919 ( 2809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6050.27 seconds wall clock time: 106 minutes 37.43 seconds (6397.43 seconds total)