Starting phenix.real_space_refine on Mon Jul 6 10:24:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h40_34476/07_2026/8h40_34476.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h40_34476/07_2026/8h40_34476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h40_34476/07_2026/8h40_34476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h40_34476/07_2026/8h40_34476.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h40_34476/07_2026/8h40_34476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h40_34476/07_2026/8h40_34476.map" } resolution = 3.6 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= 0.000 sd= 0.002 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 120 5.49 5 S 109 5.16 5 C 21516 2.51 5 N 6193 2.21 5 O 6895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34833 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1358 Classifications: {'DNA': 66} Link IDs: {'rna3p': 65} Chain: "2" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1109 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain breaks: 1 Chain: "A" Number of atoms: 8473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8473 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 61, 'TRANS': 1015} Chain: "B" Number of atoms: 9292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1217, 9292 Classifications: {'peptide': 1217} Link IDs: {'PTRANS': 52, 'TRANS': 1164} Chain breaks: 3 Chain: "C" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1762 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1762 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "E" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4923 Classifications: {'peptide': 620} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 586} Chain: "F" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 474 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "G" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2600 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "X" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1540 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "Y" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1540 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Time building chain proxies: 6.53, per 1000 atoms: 0.19 Number of scatterers: 34833 At special positions: 0 Unit cell: (156.22, 193.67, 146.59, 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 109 16.00 P 120 15.00 O 6895 8.00 N 6193 7.00 C 21516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 73 " distance=1.94 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 86 " distance=2.12 Simple disulfide: pdb=" SG CYS E 73 " - pdb=" SG CYS E 86 " distance=2.05 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7636 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 49 sheets defined 31.5% alpha, 7.1% beta 41 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'A' and resid 31 through 44 removed outlier: 3.823A pdb=" N ARG A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 249 through 263 removed outlier: 3.630A pdb=" N ASP A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 293 through 309 removed outlier: 4.171A pdb=" N ILE A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 327 through 352 Processing helix chain 'A' and resid 368 through 380 Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.802A pdb=" N ASP A 486 " --> pdb=" O ASP A 483 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASP A 487 " --> pdb=" O GLU A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 483 through 487' Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 549 through 561 removed outlier: 3.591A pdb=" N ALA A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 587 removed outlier: 4.147A pdb=" N GLY A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 619 Processing helix chain 'A' and resid 706 through 711 Processing helix chain 'A' and resid 782 through 793 Processing helix chain 'A' and resid 867 through 871 removed outlier: 3.771A pdb=" N MET A 871 " --> pdb=" O ILE A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 910 Processing helix chain 'A' and resid 927 through 941 removed outlier: 4.242A pdb=" N ASP A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 990 removed outlier: 3.593A pdb=" N ILE A 990 " --> pdb=" O ASP A 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 987 through 990' Processing helix chain 'A' and resid 1018 through 1023 Processing helix chain 'A' and resid 1031 through 1039 Processing helix chain 'A' and resid 1044 through 1058 removed outlier: 3.513A pdb=" N GLY A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1079 removed outlier: 3.938A pdb=" N LYS A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 24 Processing helix chain 'B' and resid 27 through 48 Processing helix chain 'B' and resid 61 through 82 Processing helix chain 'B' and resid 86 through 95 removed outlier: 3.809A pdb=" N LYS B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 115 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.739A pdb=" N GLN B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 204 removed outlier: 5.267A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.595A pdb=" N ARG B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 274 Processing helix chain 'B' and resid 295 through 300 removed outlier: 3.819A pdb=" N GLY B 300 " --> pdb=" O GLN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 328 Proline residue: B 326 - end of helix Processing helix chain 'B' and resid 697 through 703 Processing helix chain 'B' and resid 1009 through 1020 removed outlier: 3.538A pdb=" N ARG B1013 " --> pdb=" O GLN B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1100 Processing helix chain 'B' and resid 1105 through 1133 Processing helix chain 'B' and resid 1137 through 1149 removed outlier: 3.562A pdb=" N ILE B1141 " --> pdb=" O ALA B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1170 through 1184 Processing helix chain 'B' and resid 1206 through 1214 removed outlier: 3.776A pdb=" N ALA B1210 " --> pdb=" O SER B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1226 removed outlier: 3.566A pdb=" N GLU B1222 " --> pdb=" O ARG B1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 1237 through 1242 Processing helix chain 'B' and resid 1247 through 1251 Processing helix chain 'C' and resid 31 through 45 removed outlier: 4.000A pdb=" N LEU C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 removed outlier: 4.211A pdb=" N GLU C 84 " --> pdb=" O MET C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 205 through 222 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 74 through 84 removed outlier: 4.212A pdb=" N GLU D 84 " --> pdb=" O MET D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 155 Processing helix chain 'D' and resid 205 through 222 Processing helix chain 'E' and resid 18 through 24 Processing helix chain 'E' and resid 115 through 118 Processing helix chain 'E' and resid 123 through 130 Processing helix chain 'E' and resid 164 through 172 Processing helix chain 'E' and resid 189 through 200 removed outlier: 3.606A pdb=" N LEU E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 215 removed outlier: 3.977A pdb=" N ILE E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 209 through 215' Processing helix chain 'E' and resid 221 through 237 Processing helix chain 'E' and resid 240 through 243 Processing helix chain 'E' and resid 253 through 257 Processing helix chain 'E' and resid 270 through 292 Processing helix chain 'E' and resid 295 through 315 removed outlier: 3.561A pdb=" N VAL E 299 " --> pdb=" O PRO E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 349 Processing helix chain 'E' and resid 376 through 396 removed outlier: 3.728A pdb=" N GLU E 382 " --> pdb=" O GLU E 378 " (cutoff:3.500A) Proline residue: E 386 - end of helix Processing helix chain 'E' and resid 400 through 411 Processing helix chain 'E' and resid 412 through 417 Processing helix chain 'E' and resid 418 through 424 removed outlier: 4.355A pdb=" N GLU E 424 " --> pdb=" O GLU E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 465 Processing helix chain 'E' and resid 480 through 492 removed outlier: 3.710A pdb=" N LEU E 492 " --> pdb=" O ARG E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 496 removed outlier: 3.969A pdb=" N ASN E 496 " --> pdb=" O ALA E 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 493 through 496' Processing helix chain 'E' and resid 512 through 522 Processing helix chain 'E' and resid 539 through 547 Processing helix chain 'E' and resid 609 through 624 removed outlier: 3.711A pdb=" N ILE E 614 " --> pdb=" O PRO E 610 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 24 Processing helix chain 'F' and resid 27 through 45 Processing helix chain 'F' and resid 56 through 67 Processing helix chain 'G' and resid 81 through 91 removed outlier: 4.170A pdb=" N GLU G 88 " --> pdb=" O LEU G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 124 removed outlier: 3.997A pdb=" N LEU G 103 " --> pdb=" O GLU G 99 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU G 113 " --> pdb=" O ASP G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 163 removed outlier: 3.529A pdb=" N ARG G 145 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS G 155 " --> pdb=" O GLY G 151 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER G 161 " --> pdb=" O LYS G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 177 removed outlier: 3.880A pdb=" N LYS G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR G 173 " --> pdb=" O ILE G 169 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN G 175 " --> pdb=" O LYS G 171 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG G 176 " --> pdb=" O LYS G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 197 Processing helix chain 'G' and resid 205 through 208 Processing helix chain 'G' and resid 209 through 223 removed outlier: 4.217A pdb=" N ALA G 221 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE G 222 " --> pdb=" O ILE G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 253 removed outlier: 3.704A pdb=" N GLU G 237 " --> pdb=" O VAL G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 264 Processing helix chain 'G' and resid 269 through 280 removed outlier: 3.564A pdb=" N LEU G 273 " --> pdb=" O THR G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 327 Processing helix chain 'G' and resid 330 through 340 removed outlier: 3.595A pdb=" N VAL G 336 " --> pdb=" O ARG G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 360 removed outlier: 3.744A pdb=" N GLN G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN G 359 " --> pdb=" O GLY G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 377 removed outlier: 4.043A pdb=" N ILE G 368 " --> pdb=" O ARG G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 385 Processing helix chain 'X' and resid 82 through 86 removed outlier: 3.789A pdb=" N SER X 86 " --> pdb=" O GLY X 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 104 through 108 Processing helix chain 'X' and resid 109 through 114 Processing helix chain 'X' and resid 115 through 140 removed outlier: 3.672A pdb=" N SER X 119 " --> pdb=" O ASN X 115 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU X 138 " --> pdb=" O GLU X 134 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR X 139 " --> pdb=" O MET X 135 " (cutoff:3.500A) Processing helix chain 'X' and resid 146 through 152 Processing helix chain 'X' and resid 152 through 158 Processing helix chain 'X' and resid 177 through 184 Processing helix chain 'X' and resid 187 through 198 removed outlier: 3.823A pdb=" N LEU X 193 " --> pdb=" O THR X 189 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU X 194 " --> pdb=" O VAL X 190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP X 196 " --> pdb=" O ARG X 192 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 114 Processing helix chain 'Y' and resid 116 through 118 No H-bonds generated for 'chain 'Y' and resid 116 through 118' Processing helix chain 'Y' and resid 119 through 141 removed outlier: 3.514A pdb=" N GLU Y 134 " --> pdb=" O ILE Y 130 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N MET Y 136 " --> pdb=" O GLN Y 132 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N THR Y 139 " --> pdb=" O MET Y 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 146 through 159 Processing helix chain 'Y' and resid 175 through 180 Processing helix chain 'Y' and resid 187 through 198 removed outlier: 3.815A pdb=" N LEU Y 194 " --> pdb=" O VAL Y 190 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP Y 196 " --> pdb=" O ARG Y 192 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU Y 197 " --> pdb=" O LEU Y 193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 98 removed outlier: 6.607A pdb=" N MET A 95 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 326 removed outlier: 4.002A pdb=" N ASN A 139 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER A 446 " --> pdb=" O CYS A 431 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA8, first strand: chain 'A' and resid 574 through 575 Processing sheet with id=AA9, first strand: chain 'A' and resid 590 through 591 removed outlier: 6.239A pdb=" N ILE A 590 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB2, first strand: chain 'A' and resid 850 through 853 removed outlier: 4.942A pdb=" N LYS A 851 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 982 " --> pdb=" O LYS A 851 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N THR A 973 " --> pdb=" O TYR A 690 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 690 " --> pdb=" O THR A 973 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU A 884 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA A 689 " --> pdb=" O LEU A 884 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 850 through 853 removed outlier: 4.942A pdb=" N LYS A 851 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 982 " --> pdb=" O LYS A 851 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 8.106A pdb=" N ILE A 704 " --> pdb=" O SER A 863 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 865 " --> pdb=" O ILE A 704 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 716 Processing sheet with id=AB6, first strand: chain 'A' and resid 724 through 727 removed outlier: 6.330A pdb=" N ILE A 724 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL A 835 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA A 726 " --> pdb=" O ASN A 833 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 768 through 770 removed outlier: 5.980A pdb=" N LEU A 804 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 774 through 775 Processing sheet with id=AB9, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AC1, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AC2, first strand: chain 'B' and resid 438 through 439 Processing sheet with id=AC3, first strand: chain 'B' and resid 502 through 503 Processing sheet with id=AC4, first strand: chain 'B' and resid 538 through 540 Processing sheet with id=AC5, first strand: chain 'B' and resid 572 through 574 removed outlier: 4.557A pdb=" N THR B 793 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 602 through 603 Processing sheet with id=AC7, first strand: chain 'B' and resid 641 through 642 Processing sheet with id=AC8, first strand: chain 'B' and resid 660 through 661 Processing sheet with id=AC9, first strand: chain 'B' and resid 670 through 673 Processing sheet with id=AD1, first strand: chain 'B' and resid 765 through 766 Processing sheet with id=AD2, first strand: chain 'B' and resid 940 through 942 removed outlier: 6.684A pdb=" N THR B 965 " --> pdb=" O VAL B 941 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1167 through 1169 removed outlier: 3.655A pdb=" N LYS B1151 " --> pdb=" O VAL B1193 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 10 through 11 removed outlier: 4.038A pdb=" N GLU C 10 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C 21 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 198 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU C 197 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL C 176 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TRP C 199 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 10 through 11 removed outlier: 4.038A pdb=" N GLU C 10 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C 21 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 198 " --> pdb=" O SER C 21 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 56 through 57 removed outlier: 3.571A pdb=" N GLY C 97 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.632A pdb=" N LYS C 88 " --> pdb=" O GLU C 119 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 6 through 8 removed outlier: 4.338A pdb=" N LEU D 194 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU D 197 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL D 176 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TRP D 199 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 6 through 8 removed outlier: 4.338A pdb=" N LEU D 194 " --> pdb=" O LEU D 25 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AE2, first strand: chain 'D' and resid 56 through 57 removed outlier: 3.572A pdb=" N GLY D 97 " --> pdb=" O PHE D 140 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.557A pdb=" N LYS D 88 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 106 through 108 Processing sheet with id=AE5, first strand: chain 'E' and resid 104 through 113 removed outlier: 6.786A pdb=" N THR E 247 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 10.914A pdb=" N ALA E 110 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 9.881A pdb=" N VAL E 245 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 260 through 261 Processing sheet with id=AE7, first strand: chain 'E' and resid 357 through 360 removed outlier: 3.619A pdb=" N GLN E 442 " --> pdb=" O LEU E 430 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 363 through 364 removed outlier: 6.221A pdb=" N VAL E 363 " --> pdb=" O LEU E 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 586 through 587 removed outlier: 3.557A pdb=" N VAL E 586 " --> pdb=" O VAL E 593 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 45 through 46 Processing sheet with id=AF2, first strand: chain 'X' and resid 161 through 163 Processing sheet with id=AF3, first strand: chain 'Y' and resid 53 through 55 Processing sheet with id=AF4, first strand: chain 'Y' and resid 162 through 163 962 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 88 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 7.74 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.16: 90 1.16 - 1.34: 13392 1.34 - 1.53: 18181 1.53 - 1.71: 3826 1.71 - 1.90: 153 Bond restraints: 35642 Sorted by residual: bond pdb=" CA SER A1079 " pdb=" C SER A1079 " ideal model delta sigma weight residual 1.526 1.044 0.482 1.23e-02 6.61e+03 1.53e+03 bond pdb=" CA LEU D 45 " pdb=" C LEU D 45 " ideal model delta sigma weight residual 1.523 0.981 0.542 1.41e-02 5.03e+03 1.47e+03 bond pdb=" CA LEU C 45 " pdb=" C LEU C 45 " ideal model delta sigma weight residual 1.523 0.981 0.541 1.41e-02 5.03e+03 1.47e+03 bond pdb=" CA TYR E 117 " pdb=" C TYR E 117 " ideal model delta sigma weight residual 1.524 0.971 0.554 1.66e-02 3.63e+03 1.11e+03 bond pdb=" CA ARG E 61 " pdb=" C ARG E 61 " ideal model delta sigma weight residual 1.523 1.030 0.493 1.48e-02 4.57e+03 1.11e+03 ... (remaining 35637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.30: 47367 9.30 - 18.59: 1186 18.59 - 27.89: 149 27.89 - 37.19: 24 37.19 - 46.48: 6 Bond angle restraints: 48732 Sorted by residual: angle pdb=" N MET C 80 " pdb=" CA MET C 80 " pdb=" C MET C 80 " ideal model delta sigma weight residual 112.23 86.51 25.72 1.26e+00 6.30e-01 4.17e+02 angle pdb=" N MET D 80 " pdb=" CA MET D 80 " pdb=" C MET D 80 " ideal model delta sigma weight residual 112.23 86.52 25.71 1.26e+00 6.30e-01 4.16e+02 angle pdb=" C LEU E 538 " pdb=" N ASP E 539 " pdb=" CA ASP E 539 " ideal model delta sigma weight residual 121.54 85.16 36.38 1.91e+00 2.74e-01 3.63e+02 angle pdb=" C ASP X 39 " pdb=" N PRO X 40 " pdb=" CA PRO X 40 " ideal model delta sigma weight residual 119.84 142.94 -23.10 1.25e+00 6.40e-01 3.41e+02 angle pdb=" N ASP C 219 " pdb=" CA ASP C 219 " pdb=" C ASP C 219 " ideal model delta sigma weight residual 111.24 87.71 23.53 1.29e+00 6.01e-01 3.33e+02 ... (remaining 48727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 20355 35.31 - 70.63: 1122 70.63 - 105.94: 110 105.94 - 141.26: 16 141.26 - 176.57: 10 Dihedral angle restraints: 21613 sinusoidal: 9748 harmonic: 11865 Sorted by residual: dihedral pdb=" CA GLN B 854 " pdb=" C GLN B 854 " pdb=" N THR B 855 " pdb=" CA THR B 855 " ideal model delta harmonic sigma weight residual -180.00 -118.98 -61.02 0 5.00e+00 4.00e-02 1.49e+02 dihedral pdb=" C MET Y 120 " pdb=" N MET Y 120 " pdb=" CA MET Y 120 " pdb=" CB MET Y 120 " ideal model delta harmonic sigma weight residual -122.60 -92.99 -29.61 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" CA GLU A 735 " pdb=" C GLU A 735 " pdb=" N ILE A 736 " pdb=" CA ILE A 736 " ideal model delta harmonic sigma weight residual -180.00 -122.71 -57.29 0 5.00e+00 4.00e-02 1.31e+02 ... (remaining 21610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 4688 0.224 - 0.448: 739 0.448 - 0.672: 129 0.672 - 0.896: 20 0.896 - 1.120: 6 Chirality restraints: 5582 Sorted by residual: chirality pdb=" CB THR A 222 " pdb=" CA THR A 222 " pdb=" OG1 THR A 222 " pdb=" CG2 THR A 222 " both_signs ideal model delta sigma weight residual False 2.55 1.43 1.12 2.00e-01 2.50e+01 3.14e+01 chirality pdb=" CB THR A 616 " pdb=" CA THR A 616 " pdb=" OG1 THR A 616 " pdb=" CG2 THR A 616 " both_signs ideal model delta sigma weight residual False 2.55 1.48 1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CA TYR E 117 " pdb=" N TYR E 117 " pdb=" C TYR E 117 " pdb=" CB TYR E 117 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.69e+01 ... (remaining 5579 not shown) Planarity restraints: 5940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA 1 100 " -0.069 2.00e-02 2.50e+03 6.94e-02 1.32e+02 pdb=" N9 DA 1 100 " -0.065 2.00e-02 2.50e+03 pdb=" C8 DA 1 100 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA 1 100 " 0.015 2.00e-02 2.50e+03 pdb=" C5 DA 1 100 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DA 1 100 " -0.029 2.00e-02 2.50e+03 pdb=" N6 DA 1 100 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DA 1 100 " -0.069 2.00e-02 2.50e+03 pdb=" C2 DA 1 100 " -0.046 2.00e-02 2.50e+03 pdb=" N3 DA 1 100 " 0.090 2.00e-02 2.50e+03 pdb=" C4 DA 1 100 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA 2 67 " -0.046 2.00e-02 2.50e+03 6.49e-02 1.16e+02 pdb=" N9 DA 2 67 " -0.069 2.00e-02 2.50e+03 pdb=" C8 DA 2 67 " -0.009 2.00e-02 2.50e+03 pdb=" N7 DA 2 67 " 0.031 2.00e-02 2.50e+03 pdb=" C5 DA 2 67 " 0.138 2.00e-02 2.50e+03 pdb=" C6 DA 2 67 " -0.014 2.00e-02 2.50e+03 pdb=" N6 DA 2 67 " -0.089 2.00e-02 2.50e+03 pdb=" N1 DA 2 67 " -0.037 2.00e-02 2.50e+03 pdb=" C2 DA 2 67 " 0.063 2.00e-02 2.50e+03 pdb=" N3 DA 2 67 " -0.037 2.00e-02 2.50e+03 pdb=" C4 DA 2 67 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 653 " 0.031 2.00e-02 2.50e+03 6.70e-02 8.97e+01 pdb=" CG TYR B 653 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR B 653 " -0.111 2.00e-02 2.50e+03 pdb=" CD2 TYR B 653 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR B 653 " 0.119 2.00e-02 2.50e+03 pdb=" CE2 TYR B 653 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 653 " -0.085 2.00e-02 2.50e+03 pdb=" OH TYR B 653 " 0.030 2.00e-02 2.50e+03 ... (remaining 5937 not shown) Histogram of nonbonded interaction distances: 0.73 - 1.56: 13 1.56 - 2.40: 2073 2.40 - 3.23: 54789 3.23 - 4.07: 107850 4.07 - 4.90: 171403 Warning: very small nonbonded interaction distances. Nonbonded interactions: 336128 Sorted by model distance: nonbonded pdb=" N6 DA 1 75 " pdb=" O4 DT 2 51 " model vdw 0.727 3.120 nonbonded pdb=" OP2 DA 2 26 " pdb=" N3 DA 2 26 " model vdw 1.064 3.120 nonbonded pdb=" N6 DA 1 79 " pdb=" O4 DT 2 47 " model vdw 1.188 3.120 nonbonded pdb=" O6 DG 1 85 " pdb=" N4 DC 2 41 " model vdw 1.240 3.120 nonbonded pdb=" C6 DA 1 75 " pdb=" O4 DT 2 51 " model vdw 1.293 3.260 ... (remaining 336123 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.10 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 33.480 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.059 0.554 35648 Z= 3.185 Angle : 3.515 46.482 48740 Z= 1.984 Chirality : 0.180 1.120 5582 Planarity : 0.023 0.356 5940 Dihedral : 20.656 176.570 13965 Min Nonbonded Distance : 0.727 Molprobity Statistics. All-atom Clashscore : 175.61 Ramachandran Plot: Outliers : 3.82 % Allowed : 35.75 % Favored : 60.42 % Rotamer: Outliers : 4.55 % Allowed : 8.91 % Favored : 86.54 % Cbeta Deviations : 4.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 4.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.43 (0.08), residues: 4106 helix: -4.92 (0.07), residues: 1098 sheet: -4.54 (0.22), residues: 342 loop : -5.38 (0.08), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.070 0.003 ARG A 662 TYR 0.139 0.008 TYR F 29 PHE 0.084 0.007 PHE A 38 TRP 0.108 0.011 TRP A 905 HIS 0.038 0.005 HIS A1087 Details of bonding type rmsd/Z covalent geometry : bond 0.05850 / 3.18 (35642) covalent geometry : angle 3.51324 / 1.98 (48732) SS BOND : bond 0.06717 / 5.27 ( 4) SS BOND : angle 10.31960 / 20.51 ( 8) hydrogen bonds : bond 0.30932 / 34.59 ( 1040) hydrogen bonds : angle 13.70942 / 17.83 ( 2848) Misc. bond : bond 0.31297 / 15.65 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 462 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.4704 (tm-30) REVERT: A 559 MET cc_start: 0.8992 (mpp) cc_final: 0.8705 (mpp) REVERT: A 614 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7182 (mp) REVERT: A 891 SER cc_start: 0.5739 (OUTLIER) cc_final: 0.5518 (t) REVERT: A 1023 TRP cc_start: 0.8343 (m-10) cc_final: 0.7913 (m-10) REVERT: A 1082 LEU cc_start: 0.4665 (mt) cc_final: 0.4157 (tp) REVERT: B 1 MET cc_start: 0.9305 (mtm) cc_final: 0.9071 (mtm) REVERT: B 204 SER cc_start: 0.8361 (t) cc_final: 0.7974 (t) REVERT: B 822 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5334 (mp) REVERT: B 1029 LEU cc_start: 0.6527 (tp) cc_final: 0.6090 (mp) REVERT: C 171 MET cc_start: 0.8741 (tmm) cc_final: 0.8386 (tmm) REVERT: D 28 LEU cc_start: 0.7860 (mt) cc_final: 0.7531 (mt) REVERT: D 228 SER cc_start: 0.1083 (OUTLIER) cc_final: 0.0774 (t) REVERT: E 435 THR cc_start: 0.4066 (OUTLIER) cc_final: 0.3241 (p) REVERT: E 447 ILE cc_start: 0.8812 (mp) cc_final: 0.8552 (mt) REVERT: Y 132 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8197 (mt0) outliers start: 161 outliers final: 34 residues processed: 580 average time/residue: 0.2249 time to fit residues: 205.0962 Evaluate side-chains 251 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 389 PRO Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 1025 GLU Chi-restraints excluded: chain B residue 1217 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 203 ILE Chi-restraints excluded: chain Y residue 132 GLN Chi-restraints excluded: chain Y residue 150 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 0.0470 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 140 GLN A 196 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN A 643 GLN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 ASN A1078 GLN ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 347 GLN B 382 ASN B 573 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1118 GLN B1126 GLN ** B1172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1214 GLN ** B1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS E 166 GLN E 180 GLN E 442 GLN E 549 GLN E 616 ASN G 149 HIS G 312 GLN G 380 ASN ** X 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.077739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.055663 restraints weight = 205334.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.057207 restraints weight = 106039.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.058235 restraints weight = 71771.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.058752 restraints weight = 57041.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.059103 restraints weight = 50415.648| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.121 35648 Z= 0.435 Angle : 1.490 19.753 48740 Z= 0.772 Chirality : 0.074 0.520 5582 Planarity : 0.012 0.176 5940 Dihedral : 23.108 176.871 5967 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 47.96 Ramachandran Plot: Outliers : 1.05 % Allowed : 19.75 % Favored : 79.20 % Rotamer: Outliers : 5.77 % Allowed : 17.67 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 2.01 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.01 (0.10), residues: 4106 helix: -3.51 (0.10), residues: 1208 sheet: -3.68 (0.24), residues: 358 loop : -4.57 (0.09), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG D 193 TYR 0.046 0.004 TYR F 29 PHE 0.042 0.004 PHE C 112 TRP 0.036 0.004 TRP E 416 HIS 0.024 0.004 HIS X 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00952 / 0.44 (35642) covalent geometry : angle 1.48864 / 0.77 (48732) SS BOND : bond 0.01050 / 0.52 ( 4) SS BOND : angle 5.29774 / 10.21 ( 8) hydrogen bonds : bond 0.13411 / 15.10 ( 1040) hydrogen bonds : angle 8.86383 / 11.57 ( 2848) Misc. bond : bond 0.00310 / 0.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 241 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.8295 (ppp) cc_final: 0.7870 (ppp) REVERT: A 700 ASP cc_start: 0.7146 (m-30) cc_final: 0.6583 (t0) REVERT: A 891 SER cc_start: 0.6396 (OUTLIER) cc_final: 0.6110 (t) REVERT: A 979 MET cc_start: 0.8948 (mmm) cc_final: 0.8558 (mmm) REVERT: A 1076 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8043 (pm20) REVERT: B 51 ILE cc_start: 0.8750 (tt) cc_final: 0.8525 (tp) REVERT: B 204 SER cc_start: 0.8854 (t) cc_final: 0.8432 (p) REVERT: B 305 HIS cc_start: 0.5506 (OUTLIER) cc_final: 0.4361 (p90) REVERT: B 1029 LEU cc_start: 0.6290 (tp) cc_final: 0.5827 (mp) REVERT: C 171 MET cc_start: 0.7533 (tmm) cc_final: 0.7215 (tmm) REVERT: E 86 CYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7065 (t) REVERT: E 308 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8577 (pm20) REVERT: E 435 THR cc_start: 0.4308 (OUTLIER) cc_final: 0.3938 (p) REVERT: E 555 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: E 580 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: F 15 MET cc_start: 0.8319 (mmm) cc_final: 0.7988 (tpp) REVERT: F 29 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.5185 (m-80) REVERT: G 266 MET cc_start: 0.8276 (mmm) cc_final: 0.7798 (mmm) REVERT: G 339 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9152 (mt) REVERT: Y 59 GLU cc_start: 0.4974 (OUTLIER) cc_final: 0.4682 (pt0) outliers start: 204 outliers final: 89 residues processed: 418 average time/residue: 0.1819 time to fit residues: 128.9390 Evaluate side-chains 275 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 175 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 968 PHE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1025 GLU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1217 THR Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 47 TYR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 86 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 397 MET Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 442 GLN Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain E residue 555 TYR Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 579 ASN Chi-restraints excluded: chain E residue 580 GLU Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 29 TYR Chi-restraints excluded: chain F residue 44 TYR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 378 HIS Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 142 HIS Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain Y residue 58 TYR Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Y residue 144 ASP Chi-restraints excluded: chain Y residue 150 VAL Chi-restraints excluded: chain Y residue 152 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 231 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 321 optimal weight: 0.9990 chunk 277 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 413 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 83 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 HIS B1140 HIS ** B1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 177 ASN E 46 ASN E 180 GLN ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 380 ASN ** X 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.077873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.055509 restraints weight = 201075.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.057041 restraints weight = 103213.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.058070 restraints weight = 69570.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.058658 restraints weight = 55304.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.058987 restraints weight = 48545.106| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 35648 Z= 0.267 Angle : 1.147 20.331 48740 Z= 0.592 Chirality : 0.060 0.376 5582 Planarity : 0.008 0.102 5940 Dihedral : 22.477 173.540 5929 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 34.81 Ramachandran Plot: Outliers : 0.78 % Allowed : 18.17 % Favored : 81.05 % Rotamer: Outliers : 5.91 % Allowed : 20.70 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.89 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.80 (0.11), residues: 4106 helix: -2.27 (0.13), residues: 1223 sheet: -2.99 (0.27), residues: 303 loop : -3.94 (0.10), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 42 TYR 0.036 0.003 TYR B1107 PHE 0.041 0.003 PHE C 112 TRP 0.042 0.003 TRP E 416 HIS 0.019 0.002 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.27 (35642) covalent geometry : angle 1.14584 / 0.59 (48732) SS BOND : bond 0.01982 / 0.87 ( 4) SS BOND : angle 4.78154 / 9.36 ( 8) hydrogen bonds : bond 0.10483 / 12.08 ( 1040) hydrogen bonds : angle 7.61177 / 9.76 ( 2848) Misc. bond : bond 0.00098 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 215 time to evaluate : 1.160 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 236 MET cc_start: 0.9000 (tpp) cc_final: 0.8765 (tpp) REVERT: A 330 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7877 (pp20) REVERT: A 351 MET cc_start: 0.8271 (ppp) cc_final: 0.7881 (ppp) REVERT: A 855 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8904 (mtm180) REVERT: B 37 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8811 (pptt) REVERT: B 204 SER cc_start: 0.9017 (t) cc_final: 0.8676 (p) REVERT: B 268 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9162 (tt) REVERT: B 305 HIS cc_start: 0.5470 (OUTLIER) cc_final: 0.4229 (p90) REVERT: B 622 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7162 (pp20) REVERT: B 1029 LEU cc_start: 0.6181 (tp) cc_final: 0.5594 (mt) REVERT: B 1148 MET cc_start: 0.9042 (ttp) cc_final: 0.8678 (ttm) REVERT: C 148 TYR cc_start: 0.6514 (m-80) cc_final: 0.5992 (m-80) REVERT: C 171 MET cc_start: 0.7626 (tmm) cc_final: 0.7371 (tmm) REVERT: D 111 HIS cc_start: 0.8833 (OUTLIER) cc_final: 0.8577 (m170) REVERT: D 136 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7310 (mt) REVERT: E 308 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8542 (pt0) REVERT: F 15 MET cc_start: 0.8560 (mmm) cc_final: 0.8335 (mmt) REVERT: F 29 TYR cc_start: 0.6429 (OUTLIER) cc_final: 0.5065 (m-80) REVERT: F 55 MET cc_start: 0.8098 (mmm) cc_final: 0.7497 (ptt) REVERT: G 125 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6644 (tm-30) REVERT: G 158 MET cc_start: 0.8614 (ttp) cc_final: 0.8251 (ttt) REVERT: G 266 MET cc_start: 0.8480 (mmm) cc_final: 0.7960 (mmm) REVERT: G 340 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8785 (tpm170) REVERT: X 136 MET cc_start: 0.8679 (tmm) cc_final: 0.8449 (ppp) REVERT: Y 58 TYR cc_start: 0.3174 (OUTLIER) cc_final: 0.2517 (m-80) outliers start: 209 outliers final: 94 residues processed: 394 average time/residue: 0.1797 time to fit residues: 120.3072 Evaluate side-chains 283 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 176 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 834 MET Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 968 PHE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 902 HIS Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1217 THR Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 47 TYR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 429 MET Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain E residue 579 ASN Chi-restraints excluded: chain E residue 580 GLU Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 29 TYR Chi-restraints excluded: chain F residue 44 TYR Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 378 HIS Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 96 THR Chi-restraints excluded: chain X residue 142 HIS Chi-restraints excluded: chain X residue 194 LEU Chi-restraints excluded: chain X residue 206 HIS Chi-restraints excluded: chain Y residue 58 TYR Chi-restraints excluded: chain Y residue 68 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 261 optimal weight: 4.9990 chunk 381 optimal weight: 30.0000 chunk 99 optimal weight: 0.9990 chunk 314 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 221 optimal weight: 8.9990 chunk 413 optimal weight: 20.0000 chunk 402 optimal weight: 0.8980 chunk 8 optimal weight: 40.0000 chunk 344 optimal weight: 0.9980 chunk 300 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 HIS ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 HIS B1238 ASN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 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 = 0.3889 r_free = 0.3889 target = 0.077340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.054668 restraints weight = 198720.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.056258 restraints weight = 102137.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.057273 restraints weight = 69166.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.057847 restraints weight = 55083.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 76)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.058161 restraints weight = 48481.397| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 35648 Z= 0.221 Angle : 1.025 16.376 48740 Z= 0.528 Chirality : 0.056 0.401 5582 Planarity : 0.007 0.103 5940 Dihedral : 22.115 175.434 5917 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 29.29 Ramachandran Plot: Outliers : 0.80 % Allowed : 16.39 % Favored : 82.81 % Rotamer: Outliers : 6.05 % Allowed : 21.71 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.18 (0.12), residues: 4106 helix: -1.57 (0.14), residues: 1226 sheet: -3.00 (0.27), residues: 310 loop : -3.60 (0.11), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG G 362 TYR 0.042 0.002 TYR B1190 PHE 0.026 0.002 PHE D 163 TRP 0.039 0.002 TRP E 416 HIS 0.015 0.002 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.22 (35642) covalent geometry : angle 1.02379 / 0.53 (48732) SS BOND : bond 0.00747 / 0.51 ( 4) SS BOND : angle 4.48634 / 8.76 ( 8) hydrogen bonds : bond 0.09667 / 11.08 ( 1040) hydrogen bonds : angle 6.99746 / 8.90 ( 2848) Misc. bond : bond 0.00065 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 187 time to evaluate : 0.849 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 236 MET cc_start: 0.8946 (tpp) cc_final: 0.8411 (mmm) REVERT: A 330 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7873 (pp20) REVERT: A 351 MET cc_start: 0.8199 (ppp) cc_final: 0.7859 (ppp) REVERT: A 700 ASP cc_start: 0.7417 (m-30) cc_final: 0.7058 (t70) REVERT: A 855 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8910 (mtm180) REVERT: B 32 MET cc_start: 0.9287 (ppp) cc_final: 0.9069 (ppp) REVERT: B 37 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8878 (pptt) REVERT: B 204 SER cc_start: 0.8997 (t) cc_final: 0.8590 (p) REVERT: B 268 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9168 (tt) REVERT: B 305 HIS cc_start: 0.5465 (OUTLIER) cc_final: 0.4165 (p90) REVERT: B 380 GLU cc_start: -0.2827 (OUTLIER) cc_final: -0.3104 (mt-10) REVERT: B 622 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7021 (pp20) REVERT: B 1029 LEU cc_start: 0.6008 (tp) cc_final: 0.5517 (mt) REVERT: C 138 MET cc_start: 0.9167 (tpp) cc_final: 0.8823 (ttm) REVERT: C 171 MET cc_start: 0.7603 (tmm) cc_final: 0.7395 (tmm) REVERT: D 95 GLN cc_start: 0.5353 (OUTLIER) cc_final: 0.4926 (mm-40) REVERT: D 136 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7206 (mt) REVERT: D 138 MET cc_start: 0.8651 (tpp) cc_final: 0.8296 (mmm) REVERT: D 228 SER cc_start: 0.2045 (OUTLIER) cc_final: 0.1422 (t) REVERT: E 244 MET cc_start: 0.9143 (mtm) cc_final: 0.8789 (mtp) REVERT: F 15 MET cc_start: 0.8424 (mmm) cc_final: 0.8204 (mmt) REVERT: F 29 TYR cc_start: 0.6339 (OUTLIER) cc_final: 0.4956 (m-80) REVERT: F 65 MET cc_start: 0.8975 (ttm) cc_final: 0.8584 (mtm) REVERT: G 266 MET cc_start: 0.8644 (mmm) cc_final: 0.8227 (mmt) REVERT: G 320 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8363 (pm20) REVERT: G 339 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9291 (tp) REVERT: G 340 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8884 (tpp-160) REVERT: X 145 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7906 (pmm) REVERT: Y 136 MET cc_start: 0.9090 (tmm) cc_final: 0.8327 (ptt) outliers start: 214 outliers final: 106 residues processed: 378 average time/residue: 0.1793 time to fit residues: 115.1160 Evaluate side-chains 283 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 162 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 968 PHE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1026 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 902 HIS Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 943 VAL Chi-restraints excluded: chain B residue 984 ASP Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1081 GLN Chi-restraints excluded: chain B residue 1205 ASP Chi-restraints excluded: chain B residue 1217 THR Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 4 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 397 MET Chi-restraints excluded: chain E residue 437 HIS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 539 ASP Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 579 ASN Chi-restraints excluded: chain E residue 580 GLU Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 29 TYR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 44 TYR Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 320 GLU Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 378 HIS Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 96 THR Chi-restraints excluded: chain X residue 142 HIS Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 194 LEU Chi-restraints excluded: chain X residue 206 HIS Chi-restraints excluded: chain Y residue 144 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 405 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 196 optimal weight: 50.0000 chunk 132 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 413 optimal weight: 6.9990 chunk 306 optimal weight: 4.9990 chunk 295 optimal weight: 0.9980 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN A 333 GLN ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 HIS B1214 GLN B1238 ASN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 HIS ** X 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 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 = 0.3901 r_free = 0.3901 target = 0.077770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.055652 restraints weight = 198382.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.057650 restraints weight = 105542.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.057749 restraints weight = 70253.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.058216 restraints weight = 54614.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.058216 restraints weight = 51446.774| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.6991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35648 Z= 0.184 Angle : 0.962 16.356 48740 Z= 0.493 Chirality : 0.054 0.380 5582 Planarity : 0.006 0.103 5940 Dihedral : 21.874 173.442 5916 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.78 % Allowed : 15.17 % Favored : 84.05 % Rotamer: Outliers : 5.57 % Allowed : 23.07 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.12), residues: 4106 helix: -1.19 (0.14), residues: 1227 sheet: -2.85 (0.26), residues: 331 loop : -3.37 (0.11), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 42 TYR 0.025 0.002 TYR G 85 PHE 0.022 0.002 PHE D 163 TRP 0.036 0.002 TRP E 416 HIS 0.013 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (35642) covalent geometry : angle 0.96034 / 0.49 (48732) SS BOND : bond 0.00358 / 0.15 ( 4) SS BOND : angle 4.38058 / 8.58 ( 8) hydrogen bonds : bond 0.09182 / 10.57 ( 1040) hydrogen bonds : angle 6.61923 / 8.34 ( 2848) Misc. bond : bond 0.00058 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 194 time to evaluate : 1.322 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 205 SER cc_start: 0.7272 (OUTLIER) cc_final: 0.7007 (t) REVERT: A 330 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7833 (pp20) REVERT: A 351 MET cc_start: 0.8344 (ppp) cc_final: 0.8041 (ppp) REVERT: A 546 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7402 (pt0) REVERT: A 555 MET cc_start: 0.8361 (mtm) cc_final: 0.7160 (ptp) REVERT: A 559 MET cc_start: 0.9086 (mpp) cc_final: 0.8295 (mpp) REVERT: A 700 ASP cc_start: 0.7554 (m-30) cc_final: 0.7057 (t70) REVERT: A 1037 LEU cc_start: 0.9654 (tt) cc_final: 0.9360 (tp) REVERT: B 32 MET cc_start: 0.9378 (ppp) cc_final: 0.9150 (ppp) REVERT: B 57 MET cc_start: 0.9115 (mtm) cc_final: 0.8849 (mtm) REVERT: B 147 MET cc_start: 0.8111 (mmp) cc_final: 0.7819 (mmp) REVERT: B 204 SER cc_start: 0.8934 (t) cc_final: 0.8545 (p) REVERT: B 305 HIS cc_start: 0.5813 (OUTLIER) cc_final: 0.4414 (p90) REVERT: B 538 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6565 (pm20) REVERT: B 622 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6600 (pp20) REVERT: B 1029 LEU cc_start: 0.5890 (tp) cc_final: 0.5405 (mt) REVERT: B 1180 MET cc_start: 0.6317 (mtp) cc_final: 0.5589 (ttp) REVERT: B 1217 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8197 (t) REVERT: D 136 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7015 (mt) REVERT: D 228 SER cc_start: 0.2213 (OUTLIER) cc_final: 0.1639 (t) REVERT: E 103 MET cc_start: 0.8705 (mtt) cc_final: 0.8224 (mtt) REVERT: E 244 MET cc_start: 0.9242 (mtm) cc_final: 0.8951 (mtp) REVERT: E 486 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7608 (pm20) REVERT: F 15 MET cc_start: 0.8488 (mmm) cc_final: 0.8242 (mmt) REVERT: F 29 TYR cc_start: 0.6148 (OUTLIER) cc_final: 0.4798 (m-80) REVERT: F 55 MET cc_start: 0.7994 (tpp) cc_final: 0.7546 (pmm) REVERT: F 65 MET cc_start: 0.9017 (ttm) cc_final: 0.8691 (mtt) REVERT: G 133 TRP cc_start: 0.8651 (t-100) cc_final: 0.8187 (t-100) REVERT: G 158 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8318 (ttt) REVERT: G 174 MET cc_start: 0.8003 (ppp) cc_final: 0.7698 (ppp) REVERT: G 266 MET cc_start: 0.8867 (mmm) cc_final: 0.8456 (mmt) REVERT: G 320 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8395 (pm20) REVERT: G 339 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9281 (tp) REVERT: G 340 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.8785 (tpm170) REVERT: X 145 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8031 (pmm) REVERT: Y 58 TYR cc_start: 0.2920 (OUTLIER) cc_final: 0.2327 (m-80) REVERT: Y 120 MET cc_start: 0.4574 (tpp) cc_final: 0.4150 (tpp) REVERT: Y 136 MET cc_start: 0.9140 (tmm) cc_final: 0.8924 (tmm) outliers start: 197 outliers final: 107 residues processed: 372 average time/residue: 0.1908 time to fit residues: 121.3057 Evaluate side-chains 290 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 166 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 968 PHE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 538 GLU Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 943 VAL Chi-restraints excluded: chain B residue 984 ASP Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1081 GLN Chi-restraints excluded: chain B residue 1205 ASP Chi-restraints excluded: chain B residue 1217 THR Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 437 HIS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain E residue 539 ASP Chi-restraints excluded: chain E residue 580 GLU Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain F residue 29 TYR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 44 TYR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 320 GLU Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 351 LEU Chi-restraints excluded: chain X residue 64 ILE Chi-restraints excluded: chain X residue 142 HIS Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 194 LEU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 58 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 175 optimal weight: 8.9990 chunk 7 optimal weight: 40.0000 chunk 232 optimal weight: 10.0000 chunk 370 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 265 optimal weight: 7.9990 chunk 337 optimal weight: 0.6980 chunk 144 optimal weight: 9.9990 chunk 288 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1140 HIS ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 476 HIS F 27 ASN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 GLN ** X 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 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 = 0.3890 r_free = 0.3890 target = 0.077150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.054527 restraints weight = 196525.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.056032 restraints weight = 100259.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.057014 restraints weight = 67492.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.057452 restraints weight = 53814.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.057892 restraints weight = 48043.965| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.7399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 35648 Z= 0.182 Angle : 0.915 11.463 48740 Z= 0.469 Chirality : 0.052 0.388 5582 Planarity : 0.006 0.103 5940 Dihedral : 21.664 174.343 5915 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.34 % Favored : 84.90 % Rotamer: Outliers : 5.26 % Allowed : 23.49 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.12), residues: 4106 helix: -0.98 (0.14), residues: 1243 sheet: -2.70 (0.26), residues: 334 loop : -3.22 (0.11), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 17 TYR 0.021 0.002 TYR G 85 PHE 0.026 0.002 PHE D 163 TRP 0.036 0.002 TRP E 416 HIS 0.011 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (35642) covalent geometry : angle 0.91298 / 0.47 (48732) SS BOND : bond 0.01046 / 0.69 ( 4) SS BOND : angle 5.16677 / 10.18 ( 8) hydrogen bonds : bond 0.08702 / 9.98 ( 1040) hydrogen bonds : angle 6.35885 / 7.98 ( 2848) Misc. bond : bond 0.00041 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 182 time to evaluate : 1.001 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: A 95 MET cc_start: 0.8703 (pmm) cc_final: 0.8406 (pmm) REVERT: A 205 SER cc_start: 0.7288 (OUTLIER) cc_final: 0.6994 (t) REVERT: A 236 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8284 (mmm) REVERT: A 330 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7810 (pp20) REVERT: A 351 MET cc_start: 0.8333 (ppp) cc_final: 0.8115 (ppp) REVERT: A 541 MET cc_start: 0.8768 (mmm) cc_final: 0.8485 (mtt) REVERT: A 546 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7509 (pt0) REVERT: A 609 ARG cc_start: 0.5896 (OUTLIER) cc_final: 0.5331 (ptp-110) REVERT: A 1037 LEU cc_start: 0.9643 (tt) cc_final: 0.9383 (tp) REVERT: B 37 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8797 (pptt) REVERT: B 57 MET cc_start: 0.9110 (mtm) cc_final: 0.8859 (mtm) REVERT: B 147 MET cc_start: 0.7871 (mmp) cc_final: 0.7629 (mmp) REVERT: B 204 SER cc_start: 0.8956 (t) cc_final: 0.8553 (p) REVERT: B 305 HIS cc_start: 0.6104 (OUTLIER) cc_final: 0.5417 (p90) REVERT: B 457 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6547 (pm20) REVERT: B 538 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6359 (pm20) REVERT: B 622 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6867 (pp20) REVERT: B 922 ILE cc_start: 0.6192 (OUTLIER) cc_final: 0.5940 (tt) REVERT: B 1029 LEU cc_start: 0.5973 (tp) cc_final: 0.5634 (mt) REVERT: B 1071 MET cc_start: 0.2654 (OUTLIER) cc_final: 0.1846 (ttt) REVERT: B 1180 MET cc_start: 0.5916 (mtp) cc_final: 0.5551 (ttm) REVERT: D 228 SER cc_start: 0.2452 (OUTLIER) cc_final: 0.1013 (p) REVERT: E 244 MET cc_start: 0.9240 (mtm) cc_final: 0.8963 (mtp) REVERT: E 486 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: F 29 TYR cc_start: 0.6104 (OUTLIER) cc_final: 0.4646 (m-80) REVERT: F 55 MET cc_start: 0.7745 (tpp) cc_final: 0.7383 (pmm) REVERT: F 65 MET cc_start: 0.8991 (ttm) cc_final: 0.8666 (mtm) REVERT: G 133 TRP cc_start: 0.8528 (t-100) cc_final: 0.8171 (t-100) REVERT: G 174 MET cc_start: 0.8082 (ppp) cc_final: 0.7822 (ppp) REVERT: G 222 ILE cc_start: 0.9339 (pt) cc_final: 0.9058 (mm) REVERT: G 266 MET cc_start: 0.8842 (mmm) cc_final: 0.8270 (mmm) REVERT: G 332 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8180 (ptm-80) REVERT: G 340 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8717 (tpm170) REVERT: X 145 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8115 (pmm) REVERT: X 198 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8569 (ptp-170) REVERT: Y 58 TYR cc_start: 0.2753 (OUTLIER) cc_final: 0.2224 (m-80) REVERT: Y 120 MET cc_start: 0.5054 (tpp) cc_final: 0.4732 (tpp) outliers start: 186 outliers final: 106 residues processed: 349 average time/residue: 0.1797 time to fit residues: 107.5472 Evaluate side-chains 288 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 162 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 968 PHE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 538 GLU Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1205 ASP Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 397 MET Chi-restraints excluded: chain E residue 437 HIS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 539 ASP Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 580 GLU Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain F residue 29 TYR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 351 LEU Chi-restraints excluded: chain G residue 378 HIS Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 64 ILE Chi-restraints excluded: chain X residue 142 HIS Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 194 LEU Chi-restraints excluded: chain X residue 198 ARG Chi-restraints excluded: chain X residue 206 HIS Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 58 TYR Chi-restraints excluded: chain Y residue 68 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 349 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 174 optimal weight: 40.0000 chunk 206 optimal weight: 30.0000 chunk 62 optimal weight: 0.8980 chunk 384 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 319 HIS ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 GLN B1132 GLN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN E 549 GLN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.075545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.052546 restraints weight = 197077.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.053994 restraints weight = 100623.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.054937 restraints weight = 68116.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.055490 restraints weight = 54595.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.055762 restraints weight = 48358.419| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.7648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 35648 Z= 0.223 Angle : 0.911 13.011 48740 Z= 0.467 Chirality : 0.053 0.431 5582 Planarity : 0.006 0.101 5940 Dihedral : 21.541 175.926 5913 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 24.14 Ramachandran Plot: Outliers : 0.71 % Allowed : 14.47 % Favored : 84.83 % Rotamer: Outliers : 4.98 % Allowed : 24.40 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.12), residues: 4106 helix: -0.83 (0.14), residues: 1251 sheet: -2.59 (0.28), residues: 327 loop : -3.18 (0.11), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 42 TYR 0.024 0.002 TYR F 29 PHE 0.022 0.002 PHE D 163 TRP 0.029 0.002 TRP E 416 HIS 0.012 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 (35642) covalent geometry : angle 0.90927 / 0.47 (48732) SS BOND : bond 0.00687 / 0.35 ( 4) SS BOND : angle 4.61772 / 9.04 ( 8) hydrogen bonds : bond 0.08409 / 9.57 ( 1040) hydrogen bonds : angle 6.27012 / 7.90 ( 2848) Misc. bond : bond 0.00048 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 169 time to evaluate : 1.333 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: A 205 SER cc_start: 0.7369 (OUTLIER) cc_final: 0.7071 (t) REVERT: A 236 MET cc_start: 0.8816 (tpt) cc_final: 0.8602 (tpp) REVERT: A 351 MET cc_start: 0.8503 (ppp) cc_final: 0.8274 (ppp) REVERT: A 546 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7635 (pt0) REVERT: B 37 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8851 (pptt) REVERT: B 57 MET cc_start: 0.9197 (mtm) cc_final: 0.8933 (mtm) REVERT: B 167 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9041 (mt) REVERT: B 204 SER cc_start: 0.9114 (t) cc_final: 0.8673 (p) REVERT: B 268 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9175 (tt) REVERT: B 457 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6324 (pm20) REVERT: B 538 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6144 (pm20) REVERT: B 622 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6548 (pp20) REVERT: B 922 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.6107 (tt) REVERT: B 1029 LEU cc_start: 0.5970 (tp) cc_final: 0.5671 (mt) REVERT: B 1071 MET cc_start: 0.2681 (OUTLIER) cc_final: 0.1943 (ttt) REVERT: B 1127 MET cc_start: 0.9021 (mmm) cc_final: 0.8686 (mmm) REVERT: B 1180 MET cc_start: 0.6109 (mtp) cc_final: 0.5266 (ttp) REVERT: D 95 GLN cc_start: 0.6110 (OUTLIER) cc_final: 0.5787 (mm-40) REVERT: D 228 SER cc_start: 0.3053 (OUTLIER) cc_final: 0.2631 (t) REVERT: E 244 MET cc_start: 0.9284 (mtm) cc_final: 0.8968 (mtp) REVERT: E 486 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: F 29 TYR cc_start: 0.6152 (OUTLIER) cc_final: 0.4569 (m-80) REVERT: F 65 MET cc_start: 0.9080 (ttm) cc_final: 0.8763 (mtt) REVERT: G 165 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7810 (tp) REVERT: G 174 MET cc_start: 0.8165 (ppp) cc_final: 0.7915 (ppp) REVERT: G 222 ILE cc_start: 0.9371 (pt) cc_final: 0.9104 (mm) REVERT: G 339 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9278 (tp) REVERT: G 340 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8699 (tpm170) REVERT: G 348 MET cc_start: 0.8759 (pmm) cc_final: 0.8059 (pmm) REVERT: X 135 MET cc_start: 0.8955 (mpp) cc_final: 0.8486 (pmm) REVERT: X 136 MET cc_start: 0.8607 (tmm) cc_final: 0.8296 (mmm) REVERT: X 145 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8185 (pmm) REVERT: Y 58 TYR cc_start: 0.2790 (OUTLIER) cc_final: 0.2289 (m-80) REVERT: Y 120 MET cc_start: 0.5108 (tpp) cc_final: 0.4840 (tpp) REVERT: Y 135 MET cc_start: 0.8861 (ppp) cc_final: 0.8612 (ppp) outliers start: 176 outliers final: 111 residues processed: 326 average time/residue: 0.1835 time to fit residues: 103.0835 Evaluate side-chains 288 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 158 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 968 PHE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 538 GLU Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 903 SER Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 984 ASP Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1081 GLN Chi-restraints excluded: chain B residue 1205 ASP Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 4 PHE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 437 HIS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain E residue 539 ASP Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 580 GLU Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 29 TYR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 341 TYR Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 378 HIS Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 142 HIS Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 194 LEU Chi-restraints excluded: chain X residue 206 HIS Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 58 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 24 optimal weight: 6.9990 chunk 44 optimal weight: 0.0270 chunk 26 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 335 optimal weight: 5.9990 chunk 316 optimal weight: 0.3980 chunk 405 optimal weight: 0.1980 chunk 417 optimal weight: 4.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN C 111 HIS D 63 HIS D 111 HIS E 180 GLN E 390 ASN E 484 GLN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN X 142 HIS X 176 HIS X 177 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.077232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.054406 restraints weight = 195863.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.055956 restraints weight = 99320.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.056945 restraints weight = 66649.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.057531 restraints weight = 53081.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.057843 restraints weight = 46723.305| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.8033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 35648 Z= 0.158 Angle : 0.882 17.667 48740 Z= 0.446 Chirality : 0.051 0.397 5582 Planarity : 0.006 0.100 5940 Dihedral : 21.383 179.466 5913 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.71 % Allowed : 13.37 % Favored : 85.92 % Rotamer: Outliers : 4.01 % Allowed : 25.70 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.12), residues: 4106 helix: -0.72 (0.14), residues: 1237 sheet: -2.32 (0.29), residues: 325 loop : -3.06 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 764 TYR 0.022 0.002 TYR G 388 PHE 0.024 0.001 PHE D 163 TRP 0.020 0.001 TRP E 416 HIS 0.009 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (35642) covalent geometry : angle 0.87899 / 0.44 (48732) SS BOND : bond 0.00832 / 0.38 ( 4) SS BOND : angle 5.28246 / 10.43 ( 8) hydrogen bonds : bond 0.08339 / 9.60 ( 1040) hydrogen bonds : angle 6.05513 / 7.63 ( 2848) Misc. bond : bond 0.00019 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 194 time to evaluate : 1.161 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: A 236 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8592 (tpp) REVERT: A 546 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7382 (pt0) REVERT: B 57 MET cc_start: 0.9186 (mtm) cc_final: 0.8925 (mtm) REVERT: B 143 MET cc_start: 0.6868 (tmm) cc_final: 0.6615 (tmm) REVERT: B 167 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8953 (mt) REVERT: B 204 SER cc_start: 0.8912 (t) cc_final: 0.8486 (p) REVERT: B 212 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7928 (pp) REVERT: B 268 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9152 (tt) REVERT: B 363 LEU cc_start: 0.2768 (OUTLIER) cc_final: 0.2329 (tp) REVERT: B 457 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6275 (pm20) REVERT: B 538 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6194 (pm20) REVERT: B 622 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6731 (pp20) REVERT: B 922 ILE cc_start: 0.6013 (OUTLIER) cc_final: 0.5802 (tt) REVERT: B 984 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: B 1029 LEU cc_start: 0.5919 (tp) cc_final: 0.5644 (mt) REVERT: B 1035 GLU cc_start: 0.4151 (OUTLIER) cc_final: 0.3911 (pm20) REVERT: B 1071 MET cc_start: 0.2919 (OUTLIER) cc_final: 0.2236 (ttt) REVERT: B 1180 MET cc_start: 0.6057 (mtp) cc_final: 0.5814 (ttm) REVERT: E 54 MET cc_start: 0.7136 (tpp) cc_final: 0.6929 (tpp) REVERT: E 244 MET cc_start: 0.9207 (mtm) cc_final: 0.8880 (mtp) REVERT: E 259 MET cc_start: 0.8578 (tpp) cc_final: 0.8355 (tpt) REVERT: E 486 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7740 (pm20) REVERT: F 65 MET cc_start: 0.9009 (ttm) cc_final: 0.8649 (mtm) REVERT: G 174 MET cc_start: 0.8116 (ppp) cc_final: 0.7891 (ppp) REVERT: G 266 MET cc_start: 0.8961 (mmt) cc_final: 0.8592 (mmm) REVERT: G 332 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8034 (ptm-80) REVERT: G 339 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9288 (tp) REVERT: G 340 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8717 (tpm170) REVERT: X 145 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8199 (pmm) REVERT: Y 58 TYR cc_start: 0.2460 (OUTLIER) cc_final: 0.1980 (m-80) REVERT: Y 120 MET cc_start: 0.5026 (tpp) cc_final: 0.4701 (tpp) REVERT: Y 135 MET cc_start: 0.8791 (ppp) cc_final: 0.8538 (ppp) outliers start: 142 outliers final: 95 residues processed: 320 average time/residue: 0.1833 time to fit residues: 100.4615 Evaluate side-chains 278 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 164 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 968 PHE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 538 GLU Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 903 SER Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 984 ASP Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1035 GLU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1205 ASP Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 397 MET Chi-restraints excluded: chain E residue 437 HIS Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 539 ASP Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 580 GLU Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 341 TYR Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 378 HIS Chi-restraints excluded: chain X residue 142 HIS Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 194 LEU Chi-restraints excluded: chain X residue 206 HIS Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 58 TYR Chi-restraints excluded: chain Y residue 68 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 224 optimal weight: 6.9990 chunk 312 optimal weight: 0.9990 chunk 377 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 301 optimal weight: 9.9990 chunk 407 optimal weight: 7.9990 chunk 361 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 GLN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.076408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.053769 restraints weight = 195011.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.055419 restraints weight = 104604.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.055993 restraints weight = 67462.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.056110 restraints weight = 51706.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.056288 restraints weight = 55739.767| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.8158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35648 Z= 0.173 Angle : 0.871 15.557 48740 Z= 0.442 Chirality : 0.051 0.402 5582 Planarity : 0.005 0.099 5940 Dihedral : 21.281 174.989 5913 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.66 % Allowed : 13.15 % Favored : 86.19 % Rotamer: Outliers : 3.82 % Allowed : 26.27 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.12), residues: 4106 helix: -0.59 (0.15), residues: 1237 sheet: -2.37 (0.28), residues: 331 loop : -2.99 (0.11), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D 174 TYR 0.019 0.002 TYR G 388 PHE 0.025 0.001 PHE D 163 TRP 0.024 0.001 TRP E 416 HIS 0.026 0.001 HIS X 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (35642) covalent geometry : angle 0.86852 / 0.44 (48732) SS BOND : bond 0.00632 / 0.31 ( 4) SS BOND : angle 4.78757 / 9.46 ( 8) hydrogen bonds : bond 0.08116 / 9.30 ( 1040) hydrogen bonds : angle 5.97160 / 7.52 ( 2848) Misc. bond : bond 0.00029 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 171 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 MET cc_start: 0.8856 (mmm) cc_final: 0.8289 (tpp) REVERT: A 546 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7504 (pt0) REVERT: B 57 MET cc_start: 0.9236 (mtm) cc_final: 0.8925 (mtm) REVERT: B 167 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8901 (mt) REVERT: B 185 ASP cc_start: 0.8238 (m-30) cc_final: 0.7976 (m-30) REVERT: B 204 SER cc_start: 0.8974 (t) cc_final: 0.8512 (p) REVERT: B 212 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7995 (pp) REVERT: B 268 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9189 (tt) REVERT: B 363 LEU cc_start: 0.3570 (OUTLIER) cc_final: 0.3025 (tp) REVERT: B 532 LYS cc_start: 0.4151 (OUTLIER) cc_final: 0.3923 (pttp) REVERT: B 538 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6198 (pm20) REVERT: B 622 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6292 (pp20) REVERT: B 922 ILE cc_start: 0.6013 (OUTLIER) cc_final: 0.5807 (tt) REVERT: B 1029 LEU cc_start: 0.5809 (tp) cc_final: 0.5582 (mt) REVERT: B 1071 MET cc_start: 0.2852 (OUTLIER) cc_final: 0.2279 (ttt) REVERT: B 1127 MET cc_start: 0.8852 (mmm) cc_final: 0.8431 (mmm) REVERT: E 92 GLU cc_start: 0.7896 (mt-10) cc_final: 0.6826 (pt0) REVERT: E 244 MET cc_start: 0.9211 (mtm) cc_final: 0.8878 (mtp) REVERT: E 259 MET cc_start: 0.8561 (tpp) cc_final: 0.8342 (tpt) REVERT: E 486 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7801 (pm20) REVERT: F 29 TYR cc_start: 0.5825 (OUTLIER) cc_final: 0.4284 (m-80) REVERT: F 65 MET cc_start: 0.9111 (ttm) cc_final: 0.8733 (mtm) REVERT: G 133 TRP cc_start: 0.8463 (t-100) cc_final: 0.8241 (t60) REVERT: G 174 MET cc_start: 0.8159 (ppp) cc_final: 0.7940 (ppp) REVERT: G 266 MET cc_start: 0.9041 (mmt) cc_final: 0.8654 (mmm) REVERT: G 332 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8042 (ptm-80) REVERT: G 339 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9320 (tp) REVERT: G 340 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8672 (tpm170) REVERT: X 135 MET cc_start: 0.9071 (mpp) cc_final: 0.8523 (pmm) REVERT: X 145 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8149 (pmm) REVERT: Y 58 TYR cc_start: 0.2555 (OUTLIER) cc_final: 0.2095 (m-80) REVERT: Y 120 MET cc_start: 0.5229 (tpp) cc_final: 0.4896 (tpp) REVERT: Y 135 MET cc_start: 0.8810 (ppp) cc_final: 0.8533 (ppp) outliers start: 135 outliers final: 97 residues processed: 290 average time/residue: 0.1802 time to fit residues: 90.9832 Evaluate side-chains 275 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 161 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 968 PHE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 538 GLU Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 903 SER Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1081 GLN Chi-restraints excluded: chain B residue 1205 ASP Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 397 MET Chi-restraints excluded: chain E residue 437 HIS Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 539 ASP Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 580 GLU Chi-restraints excluded: chain E residue 593 VAL Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain F residue 29 TYR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 378 HIS Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 142 HIS Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 206 HIS Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 58 TYR Chi-restraints excluded: chain Y residue 68 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 32 optimal weight: 7.9990 chunk 168 optimal weight: 40.0000 chunk 299 optimal weight: 6.9990 chunk 283 optimal weight: 3.9990 chunk 328 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 5 optimal weight: 50.0000 chunk 353 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.076367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.053429 restraints weight = 196858.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.054981 restraints weight = 99816.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.055964 restraints weight = 67286.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.056503 restraints weight = 53719.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.056808 restraints weight = 47579.849| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.8160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 35648 Z= 0.203 Angle : 0.945 59.200 48740 Z= 0.492 Chirality : 0.051 0.402 5582 Planarity : 0.005 0.100 5940 Dihedral : 21.277 175.006 5913 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.63 % Allowed : 13.37 % Favored : 86.00 % Rotamer: Outliers : 3.48 % Allowed : 26.52 % Favored : 70.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.12), residues: 4106 helix: -0.58 (0.15), residues: 1237 sheet: -2.36 (0.28), residues: 331 loop : -3.01 (0.11), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1075 TYR 0.016 0.002 TYR B 43 PHE 0.025 0.001 PHE D 163 TRP 0.024 0.001 TRP E 416 HIS 0.022 0.001 HIS X 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (35642) covalent geometry : angle 0.94298 / 0.49 (48732) SS BOND : bond 0.00706 / 0.35 ( 4) SS BOND : angle 4.67492 / 9.23 ( 8) hydrogen bonds : bond 0.08116 / 9.30 ( 1040) hydrogen bonds : angle 5.96770 / 7.51 ( 2848) Misc. bond : bond 0.00026 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 163 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 MET cc_start: 0.8867 (mmm) cc_final: 0.8297 (tpp) REVERT: A 546 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7522 (pt0) REVERT: A 871 MET cc_start: 0.8246 (mtt) cc_final: 0.8040 (mtm) REVERT: B 57 MET cc_start: 0.9126 (mtm) cc_final: 0.8854 (mtm) REVERT: B 167 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8937 (mt) REVERT: B 185 ASP cc_start: 0.8220 (m-30) cc_final: 0.7951 (m-30) REVERT: B 204 SER cc_start: 0.8988 (t) cc_final: 0.8532 (p) REVERT: B 212 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8011 (pp) REVERT: B 268 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9187 (tt) REVERT: B 363 LEU cc_start: 0.2670 (OUTLIER) cc_final: 0.2237 (tp) REVERT: B 532 LYS cc_start: 0.4221 (OUTLIER) cc_final: 0.3997 (pttp) REVERT: B 538 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6290 (pm20) REVERT: B 922 ILE cc_start: 0.6046 (OUTLIER) cc_final: 0.5840 (tt) REVERT: B 1071 MET cc_start: 0.2918 (OUTLIER) cc_final: 0.2259 (ttt) REVERT: B 1127 MET cc_start: 0.8811 (mmm) cc_final: 0.8355 (mmm) REVERT: E 92 GLU cc_start: 0.7891 (mt-10) cc_final: 0.6835 (pt0) REVERT: E 244 MET cc_start: 0.9218 (mtm) cc_final: 0.8886 (mtp) REVERT: E 259 MET cc_start: 0.8583 (tpp) cc_final: 0.8359 (tpt) REVERT: E 486 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7770 (pm20) REVERT: F 29 TYR cc_start: 0.5819 (OUTLIER) cc_final: 0.4278 (m-80) REVERT: F 65 MET cc_start: 0.9067 (ttm) cc_final: 0.8705 (mtm) REVERT: G 174 MET cc_start: 0.8155 (ppp) cc_final: 0.7933 (ppp) REVERT: G 266 MET cc_start: 0.8964 (mmt) cc_final: 0.8597 (mmm) REVERT: G 332 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8028 (ptm-80) REVERT: G 339 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9302 (tp) REVERT: G 340 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8638 (tpp-160) REVERT: X 135 MET cc_start: 0.9054 (mpp) cc_final: 0.8518 (pmm) REVERT: X 145 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8137 (pmm) REVERT: Y 58 TYR cc_start: 0.2456 (OUTLIER) cc_final: 0.1983 (m-80) REVERT: Y 120 MET cc_start: 0.5085 (tpp) cc_final: 0.4778 (tpp) REVERT: Y 135 MET cc_start: 0.8769 (ppp) cc_final: 0.8456 (ppp) outliers start: 123 outliers final: 102 residues processed: 271 average time/residue: 0.1921 time to fit residues: 90.5405 Evaluate side-chains 278 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 160 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 968 PHE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 538 GLU Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 903 SER Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1081 GLN Chi-restraints excluded: chain B residue 1205 ASP Chi-restraints excluded: chain B residue 1206 SER Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 397 MET Chi-restraints excluded: chain E residue 437 HIS Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 539 ASP Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 580 GLU Chi-restraints excluded: chain E residue 593 VAL Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain F residue 29 TYR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 378 HIS Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 142 HIS Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 206 HIS Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 58 TYR Chi-restraints excluded: chain Y residue 68 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 30 optimal weight: 0.1980 chunk 320 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 300 optimal weight: 1.9990 chunk 336 optimal weight: 0.9990 chunk 394 optimal weight: 6.9990 chunk 401 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.076317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.053301 restraints weight = 193734.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.054767 restraints weight = 98569.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.055667 restraints weight = 66723.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.056141 restraints weight = 53471.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.056526 restraints weight = 47687.969| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.8173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 35648 Z= 0.203 Angle : 0.945 59.198 48740 Z= 0.492 Chirality : 0.051 0.402 5582 Planarity : 0.005 0.100 5940 Dihedral : 21.277 175.006 5913 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.63 % Allowed : 13.37 % Favored : 86.00 % Rotamer: Outliers : 3.34 % Allowed : 26.63 % Favored : 70.03 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.12), residues: 4106 helix: -0.58 (0.15), residues: 1237 sheet: -2.36 (0.28), residues: 331 loop : -3.01 (0.11), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1075 TYR 0.016 0.002 TYR B 43 PHE 0.025 0.001 PHE D 163 TRP 0.024 0.001 TRP E 416 HIS 0.022 0.001 HIS X 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (35642) covalent geometry : angle 0.94297 / 0.49 (48732) SS BOND : bond 0.00706 / 0.35 ( 4) SS BOND : angle 4.67488 / 9.23 ( 8) hydrogen bonds : bond 0.08116 / 9.30 ( 1040) hydrogen bonds : angle 5.96770 / 7.51 ( 2848) Misc. bond : bond 0.00026 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7784.28 seconds wall clock time: 134 minutes 47.64 seconds (8087.64 seconds total)