Starting phenix.real_space_refine on Sun Jun 29 19:03:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h40_34476/06_2025/8h40_34476.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h40_34476/06_2025/8h40_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h40_34476/06_2025/8h40_34476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h40_34476/06_2025/8h40_34476.map" model { file = "/net/cci-nas-00/data/ceres_data/8h40_34476/06_2025/8h40_34476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h40_34476/06_2025/8h40_34476.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.81, per 1000 atoms: 0.57 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: 12.08 Conformation dependent library (CDL) restraints added in 4.2 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: 13.36 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: 14.15 Time building geometry restraints manager: 13.64 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: 47370 9.30 - 18.59: 1183 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: 4705 0.224 - 0.448: 730 0.448 - 0.672: 121 0.672 - 0.896: 19 0.896 - 1.120: 7 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: 1.100 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: 1.550 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 90.080 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.020 ------------------------------------------------------------------------------- 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= 2.747 Angle : 3.510 46.482 48740 Z= 1.904 Chirality : 0.179 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 : 175.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.108 0.011 TRP A 905 HIS 0.038 0.005 HIS A1087 PHE 0.084 0.007 PHE A 38 TYR 0.139 0.008 TYR F 29 ARG 0.070 0.003 ARG A 662 Details of bonding type rmsd hydrogen bonds : bond 0.30932 ( 1040) hydrogen bonds : angle 13.70942 ( 2848) SS BOND : bond 0.06717 ( 4) SS BOND : angle 10.31960 ( 8) covalent geometry : bond 0.05856 (35642) covalent geometry : angle 3.50773 (48732) Misc. bond : bond 0.31297 ( 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 : 4.111 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 64 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.4706 (tm-30) REVERT: A 559 MET cc_start: 0.8992 (mpp) cc_final: 0.8707 (mpp) REVERT: A 614 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7181 (mp) REVERT: A 891 SER cc_start: 0.5739 (OUTLIER) cc_final: 0.5516 (t) REVERT: A 1023 TRP cc_start: 0.8343 (m-10) cc_final: 0.7917 (m-10) REVERT: B 1 MET cc_start: 0.9305 (mtm) cc_final: 0.9072 (mtm) REVERT: B 122 VAL cc_start: 0.7049 (OUTLIER) cc_final: 0.6831 (t) 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: 0.5335 (mp) REVERT: B 1029 LEU cc_start: 0.6527 (tp) cc_final: 0.6092 (mp) REVERT: C 171 MET cc_start: 0.8741 (tmm) cc_final: 0.8389 (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: 0.0778 (t) REVERT: E 435 THR cc_start: 0.4066 (OUTLIER) cc_final: 0.3216 (p) REVERT: E 447 ILE cc_start: 0.8812 (mp) cc_final: 0.8583 (mt) REVERT: G 98 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7062 (p0) REVERT: Y 132 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8196 (mt0) outliers start: 161 outliers final: 34 residues processed: 580 average time/residue: 0.5350 time to fit residues: 484.2613 Evaluate side-chains 258 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 4.355 ------------------------------------------------------------------------------- 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 122 VAL 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 1214 GLN 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 98 ASP 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 353 optimal weight: 6.9990 chunk 317 optimal weight: 2.9990 chunk 176 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 328 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 199 optimal weight: 30.0000 chunk 244 optimal weight: 8.9990 chunk 380 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 70 HIS A 140 GLN A 196 GLN A 278 ASN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 HIS ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 ASN A 523 GLN A 643 GLN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN B 382 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** ** B 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 181 GLN ** G 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 GLN ** G 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.076541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.054071 restraints weight = 201291.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.055615 restraints weight = 104242.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.056580 restraints weight = 70975.562| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.134 35648 Z= 0.402 Angle : 1.324 17.553 48740 Z= 0.689 Chirality : 0.065 0.447 5582 Planarity : 0.010 0.120 5940 Dihedral : 22.773 179.015 5970 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 41.37 Ramachandran Plot: Outliers : 0.90 % Allowed : 19.09 % Favored : 80.00 % Rotamer: Outliers : 5.60 % Allowed : 16.79 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.65 % Twisted General : 1.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.91 (0.10), residues: 4106 helix: -3.41 (0.10), residues: 1225 sheet: -3.72 (0.22), residues: 380 loop : -4.50 (0.09), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP E 416 HIS 0.021 0.003 HIS B 372 PHE 0.030 0.003 PHE C 112 TYR 0.034 0.004 TYR B 488 ARG 0.020 0.001 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.11209 ( 1040) hydrogen bonds : angle 8.30655 ( 2848) SS BOND : bond 0.01272 ( 4) SS BOND : angle 5.33208 ( 8) covalent geometry : bond 0.00897 (35642) covalent geometry : angle 1.32249 (48732) Misc. bond : bond 0.00115 ( 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 439 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 241 time to evaluate : 3.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9003 (ptm) cc_final: 0.8713 (ppp) REVERT: A 351 MET cc_start: 0.8221 (ppp) cc_final: 0.7915 (ppp) REVERT: A 700 ASP cc_start: 0.7387 (m-30) cc_final: 0.6834 (t70) REVERT: A 1076 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: B 122 VAL cc_start: 0.7588 (OUTLIER) cc_final: 0.7379 (t) REVERT: B 204 SER cc_start: 0.9009 (t) cc_final: 0.8664 (p) REVERT: B 305 HIS cc_start: 0.6470 (OUTLIER) cc_final: 0.5349 (p90) REVERT: B 479 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7237 (mp) REVERT: B 746 VAL cc_start: 0.6088 (OUTLIER) cc_final: 0.5878 (p) REVERT: B 1029 LEU cc_start: 0.6104 (tp) cc_final: 0.5543 (mt) REVERT: C 171 MET cc_start: 0.7706 (tmm) cc_final: 0.7336 (tmm) REVERT: D 95 GLN cc_start: 0.5362 (OUTLIER) cc_final: 0.5014 (mm-40) REVERT: D 136 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7288 (mt) REVERT: E 86 CYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7132 (t) REVERT: E 257 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.9022 (ptt90) REVERT: E 452 ARG cc_start: 0.8570 (mtt180) cc_final: 0.8308 (mtp85) REVERT: F 15 MET cc_start: 0.8450 (mmm) cc_final: 0.8148 (tpp) REVERT: F 29 TYR cc_start: 0.6032 (OUTLIER) cc_final: 0.5060 (m-80) REVERT: G 266 MET cc_start: 0.8433 (mmm) cc_final: 0.7906 (mmm) REVERT: G 339 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9121 (tp) REVERT: Y 58 TYR cc_start: 0.3308 (OUTLIER) cc_final: 0.2685 (m-80) outliers start: 198 outliers final: 77 residues processed: 417 average time/residue: 0.4752 time to fit residues: 333.3554 Evaluate side-chains 268 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 179 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR 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 255 GLN Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 696 TYR 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 53 VAL Chi-restraints excluded: chain B residue 122 VAL 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 453 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain B residue 746 VAL 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 916 VAL Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1214 GLN Chi-restraints excluded: chain B residue 1217 THR Chi-restraints excluded: chain C residue 34 THR 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 9 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 36 VAL 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 160 SER Chi-restraints excluded: chain D residue 186 ASP 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 127 ILE Chi-restraints excluded: chain E residue 155 THR 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 257 ARG Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 397 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 514 VAL 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 233 VAL Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 381 ARG Chi-restraints excluded: chain X residue 74 VAL 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 X residue 157 CYS Chi-restraints excluded: chain Y residue 58 TYR 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 266 optimal weight: 1.9990 chunk 392 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 399 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 297 optimal weight: 8.9990 chunk 412 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 396 optimal weight: 40.0000 chunk 328 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 454 ASN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 HIS A 858 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 573 ASN ** B 637 HIS ** 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 902 HIS B1123 ASN B1238 ASN ** B1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 177 ASN E 46 ASN ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 GLN E 476 HIS E 620 GLN ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 HIS ** G 378 HIS ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.075052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.051936 restraints weight = 198746.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.053431 restraints weight = 102397.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.054383 restraints weight = 69656.429| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.6659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.175 35648 Z= 0.313 Angle : 1.052 17.033 48740 Z= 0.544 Chirality : 0.055 0.310 5582 Planarity : 0.007 0.104 5940 Dihedral : 22.100 179.889 5927 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 29.79 Ramachandran Plot: Outliers : 0.83 % Allowed : 16.71 % Favored : 82.46 % Rotamer: Outliers : 5.43 % Allowed : 21.49 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.11), residues: 4106 helix: -2.03 (0.13), residues: 1250 sheet: -3.08 (0.26), residues: 340 loop : -3.84 (0.10), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP E 416 HIS 0.013 0.002 HIS G 378 PHE 0.028 0.002 PHE Y 75 TYR 0.041 0.003 TYR B1190 ARG 0.008 0.001 ARG G 115 Details of bonding type rmsd hydrogen bonds : bond 0.09253 ( 1040) hydrogen bonds : angle 6.95465 ( 2848) SS BOND : bond 0.02017 ( 4) SS BOND : angle 4.63310 ( 8) covalent geometry : bond 0.00673 (35642) covalent geometry : angle 1.05020 (48732) Misc. bond : bond 0.00128 ( 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 392 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 200 time to evaluate : 3.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9097 (ptm) cc_final: 0.8723 (ppp) REVERT: A 205 SER cc_start: 0.7349 (OUTLIER) cc_final: 0.7108 (t) REVERT: A 236 MET cc_start: 0.8871 (tpp) cc_final: 0.8648 (tpp) REVERT: A 351 MET cc_start: 0.8327 (ppp) cc_final: 0.7997 (ppp) REVERT: A 387 MET cc_start: 0.8896 (mmm) cc_final: 0.8225 (tpp) REVERT: A 437 GLU cc_start: 0.8614 (pm20) cc_final: 0.8271 (pm20) REVERT: A 555 MET cc_start: 0.8599 (mtm) cc_final: 0.7666 (ptp) REVERT: A 559 MET cc_start: 0.9103 (mpp) cc_final: 0.8197 (mpp) REVERT: A 871 MET cc_start: 0.8882 (mtp) cc_final: 0.8630 (mtp) REVERT: B 122 VAL cc_start: 0.8107 (t) cc_final: 0.7847 (t) REVERT: B 144 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7869 (mpp80) REVERT: B 204 SER cc_start: 0.9162 (t) cc_final: 0.8787 (p) REVERT: B 212 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8430 (pp) REVERT: B 902 HIS cc_start: 0.9282 (OUTLIER) cc_final: 0.8902 (p90) REVERT: B 1029 LEU cc_start: 0.5825 (tp) cc_final: 0.5439 (mt) REVERT: C 171 MET cc_start: 0.7688 (tmm) cc_final: 0.7429 (tmm) REVERT: D 95 GLN cc_start: 0.5761 (OUTLIER) cc_final: 0.4471 (mm-40) REVERT: D 136 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7362 (mt) REVERT: D 199 TRP cc_start: 0.8424 (OUTLIER) cc_final: 0.8167 (m-90) REVERT: E 257 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.8976 (ptt90) REVERT: E 452 ARG cc_start: 0.8518 (mtt180) cc_final: 0.8274 (mtp85) REVERT: F 15 MET cc_start: 0.8304 (mmm) cc_final: 0.8037 (tpp) REVERT: F 29 TYR cc_start: 0.5453 (OUTLIER) cc_final: 0.4616 (m-80) REVERT: G 125 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6842 (tm-30) REVERT: G 158 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8321 (ttt) REVERT: G 266 MET cc_start: 0.8853 (mmm) cc_final: 0.8214 (mmm) REVERT: G 320 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: G 340 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8781 (tpp-160) REVERT: G 373 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9349 (mt) REVERT: X 145 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7809 (pmm) REVERT: Y 120 MET cc_start: 0.4947 (tpp) cc_final: 0.4684 (tpp) outliers start: 192 outliers final: 97 residues processed: 372 average time/residue: 0.4581 time to fit residues: 287.2863 Evaluate side-chains 274 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 162 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 205 SER 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 410 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 466 VAL 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 663 VAL Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 882 ILE 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 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 96 ASP Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 295 CYS 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 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 871 VAL Chi-restraints excluded: chain B residue 902 HIS 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 1214 GLN Chi-restraints excluded: chain B residue 1217 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 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 95 GLN Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 199 TRP Chi-restraints excluded: chain D residue 200 THR 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 228 LEU Chi-restraints excluded: chain E residue 257 ARG Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 339 GLU Chi-restraints excluded: chain E residue 368 LEU 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 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 G residue 87 GLN Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 158 MET 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 340 ARG Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 96 THR Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 142 HIS Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 144 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 242 optimal weight: 0.7980 chunk 302 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 281 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 229 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 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 ** B1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 ASN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN G 251 GLN ** G 378 HIS ** 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 = 0.3868 r_free = 0.3868 target = 0.076168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.053216 restraints weight = 197706.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.054739 restraints weight = 99877.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.055732 restraints weight = 67308.700| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.7304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 35648 Z= 0.191 Angle : 0.924 13.822 48740 Z= 0.477 Chirality : 0.051 0.282 5582 Planarity : 0.006 0.107 5940 Dihedral : 21.826 177.892 5920 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 24.65 Ramachandran Plot: Outliers : 0.73 % Allowed : 14.49 % Favored : 84.78 % Rotamer: Outliers : 4.89 % Allowed : 23.13 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.12), residues: 4106 helix: -1.22 (0.14), residues: 1243 sheet: -3.00 (0.25), residues: 350 loop : -3.45 (0.11), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 416 HIS 0.017 0.002 HIS B 902 PHE 0.021 0.002 PHE Y 75 TYR 0.032 0.002 TYR B1190 ARG 0.007 0.001 ARG G 362 Details of bonding type rmsd hydrogen bonds : bond 0.08717 ( 1040) hydrogen bonds : angle 6.43392 ( 2848) SS BOND : bond 0.00755 ( 4) SS BOND : angle 4.21775 ( 8) covalent geometry : bond 0.00419 (35642) covalent geometry : angle 0.92240 (48732) Misc. bond : bond 0.00059 ( 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 381 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 208 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.7506 (OUTLIER) cc_final: 0.7230 (t) REVERT: A 236 MET cc_start: 0.8923 (tpp) cc_final: 0.8469 (mmm) REVERT: A 351 MET cc_start: 0.8312 (ppp) cc_final: 0.7992 (ppp) REVERT: A 437 GLU cc_start: 0.8451 (pm20) cc_final: 0.8144 (pm20) REVERT: B 32 MET cc_start: 0.9216 (tmm) cc_final: 0.8891 (ppp) REVERT: B 122 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7839 (t) REVERT: B 147 MET cc_start: 0.7911 (mmp) cc_final: 0.7639 (mmp) REVERT: B 204 SER cc_start: 0.9057 (t) cc_final: 0.8676 (p) REVERT: B 305 HIS cc_start: 0.7087 (OUTLIER) cc_final: 0.6117 (p90) REVERT: B 313 GLU cc_start: 0.8503 (pp20) cc_final: 0.7913 (mt-10) REVERT: B 315 VAL cc_start: 0.9547 (OUTLIER) cc_final: 0.9346 (p) REVERT: B 622 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7142 (pp20) REVERT: B 880 GLU cc_start: 0.5510 (OUTLIER) cc_final: 0.4870 (pp20) REVERT: B 902 HIS cc_start: 0.9228 (OUTLIER) cc_final: 0.8820 (m-70) REVERT: B 1029 LEU cc_start: 0.5717 (tp) cc_final: 0.5412 (mt) REVERT: B 1180 MET cc_start: 0.5953 (mtp) cc_final: 0.5616 (ttm) REVERT: C 138 MET cc_start: 0.9220 (tpp) cc_final: 0.8926 (ttm) REVERT: D 95 GLN cc_start: 0.6024 (OUTLIER) cc_final: 0.5670 (mm-40) REVERT: D 228 SER cc_start: 0.2576 (OUTLIER) cc_final: 0.2045 (t) REVERT: E 452 ARG cc_start: 0.8501 (mtt180) cc_final: 0.8222 (mmm-85) REVERT: F 65 MET cc_start: 0.9058 (ttm) cc_final: 0.8607 (mtm) REVERT: G 133 TRP cc_start: 0.8615 (t-100) cc_final: 0.8196 (t-100) REVERT: G 266 MET cc_start: 0.8954 (mmm) cc_final: 0.8120 (mmt) REVERT: G 320 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8307 (pm20) REVERT: G 340 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8772 (tpp-160) REVERT: G 343 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8437 (mm) REVERT: G 348 MET cc_start: 0.8838 (pmm) cc_final: 0.8193 (pmm) REVERT: X 145 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8061 (pmm) REVERT: Y 58 TYR cc_start: 0.3010 (OUTLIER) cc_final: 0.2434 (m-80) REVERT: Y 120 MET cc_start: 0.5085 (tpp) cc_final: 0.4833 (tpp) outliers start: 173 outliers final: 81 residues processed: 365 average time/residue: 0.4382 time to fit residues: 271.1001 Evaluate side-chains 272 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 177 time to evaluate : 3.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 116 ILE 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 272 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 574 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 891 SER Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 968 PHE 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 95 ILE Chi-restraints excluded: chain B residue 122 VAL 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 305 HIS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 410 ILE 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 755 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 880 GLU 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 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 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 D residue 28 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 184 ARG 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 186 VAL Chi-restraints excluded: chain E residue 228 LEU 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 558 VAL Chi-restraints excluded: chain E residue 576 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 44 TYR Chi-restraints excluded: chain G residue 87 GLN 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 340 ARG Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 134 GLU 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 Chi-restraints excluded: chain Y residue 68 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 70 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 239 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 189 optimal weight: 30.0000 chunk 92 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 385 optimal weight: 10.0000 chunk 409 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 278 ASN A 306 ASN ** 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 321 GLN ** 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** B 902 HIS ** B1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 549 GLN F 27 ASN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** G 378 HIS ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.075493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.052877 restraints weight = 197851.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.055000 restraints weight = 102934.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.055155 restraints weight = 63683.976| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.7705 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= 0.189 Angle : 0.876 15.396 48740 Z= 0.451 Chirality : 0.050 0.400 5582 Planarity : 0.006 0.104 5940 Dihedral : 21.620 177.535 5914 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.71 % Allowed : 13.93 % Favored : 85.36 % Rotamer: Outliers : 5.06 % Allowed : 23.95 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.12), residues: 4106 helix: -0.82 (0.14), residues: 1245 sheet: -2.79 (0.25), residues: 363 loop : -3.25 (0.11), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 416 HIS 0.013 0.001 HIS B 902 PHE 0.024 0.002 PHE D 163 TYR 0.021 0.002 TYR A 873 ARG 0.006 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.08282 ( 1040) hydrogen bonds : angle 6.18949 ( 2848) SS BOND : bond 0.02560 ( 4) SS BOND : angle 4.21933 ( 8) covalent geometry : bond 0.00420 (35642) covalent geometry : angle 0.87469 (48732) Misc. bond : bond 0.00072 ( 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 360 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 181 time to evaluate : 4.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.7519 (OUTLIER) cc_final: 0.7233 (t) REVERT: A 236 MET cc_start: 0.9001 (tpp) cc_final: 0.8540 (mmm) REVERT: A 351 MET cc_start: 0.8340 (ppp) cc_final: 0.8025 (ppp) REVERT: A 1037 LEU cc_start: 0.9653 (tt) cc_final: 0.9417 (tp) REVERT: B 32 MET cc_start: 0.9343 (tmm) cc_final: 0.9097 (ppp) REVERT: B 122 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7957 (t) REVERT: B 204 SER cc_start: 0.9093 (t) cc_final: 0.8629 (p) REVERT: B 212 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8215 (pp) REVERT: B 313 GLU cc_start: 0.8535 (pp20) cc_final: 0.7740 (mm-30) REVERT: B 538 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6257 (pm20) REVERT: B 622 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6571 (pp20) REVERT: B 800 GLU cc_start: 0.9132 (tt0) cc_final: 0.8930 (mp0) REVERT: B 880 GLU cc_start: 0.5516 (OUTLIER) cc_final: 0.4802 (pp20) REVERT: B 1029 LEU cc_start: 0.5771 (tp) cc_final: 0.5505 (mt) REVERT: B 1127 MET cc_start: 0.9018 (mtm) cc_final: 0.8814 (mtt) REVERT: B 1135 ASP cc_start: 0.9016 (t0) cc_final: 0.8792 (t0) REVERT: D 95 GLN cc_start: 0.6075 (OUTLIER) cc_final: 0.5717 (mm-40) REVERT: E 18 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8276 (p) REVERT: E 452 ARG cc_start: 0.8445 (mtt180) cc_final: 0.8194 (mtp85) REVERT: F 65 MET cc_start: 0.9092 (ttm) cc_final: 0.8701 (mtm) REVERT: G 222 ILE cc_start: 0.9362 (pt) cc_final: 0.9134 (mm) REVERT: G 266 MET cc_start: 0.9084 (mmm) cc_final: 0.8498 (mmm) REVERT: G 320 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: G 343 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8351 (mm) REVERT: G 348 MET cc_start: 0.8775 (pmm) cc_final: 0.8480 (pmm) REVERT: X 145 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8082 (pmm) REVERT: Y 58 TYR cc_start: 0.3013 (OUTLIER) cc_final: 0.2478 (m-80) REVERT: Y 120 MET cc_start: 0.5197 (tpp) cc_final: 0.4952 (tpp) REVERT: Y 135 MET cc_start: 0.8871 (ppp) cc_final: 0.8639 (ppp) outliers start: 179 outliers final: 99 residues processed: 343 average time/residue: 0.4499 time to fit residues: 264.8679 Evaluate side-chains 276 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 165 time to evaluate : 3.763 ------------------------------------------------------------------------------- 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 116 ILE 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 238 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 402 LEU 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 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 882 ILE Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 968 PHE 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 95 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 154 ILE 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 410 ILE Chi-restraints excluded: chain B residue 487 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 755 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 865 ILE Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 880 GLU 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 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 C residue 57 ARG Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 136 LEU 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 D residue 28 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 199 TRP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 228 LEU 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 513 MET Chi-restraints excluded: chain E residue 528 THR 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 302 ILE Chi-restraints excluded: chain G residue 320 GLU 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 74 VAL Chi-restraints excluded: chain X residue 134 GLU 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 58 TYR Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Y residue 134 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 244 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 354 optimal weight: 9.9990 chunk 221 optimal weight: 6.9990 chunk 190 optimal weight: 50.0000 chunk 21 optimal weight: 5.9990 chunk 367 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 314 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 ASN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 91 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.074474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.051214 restraints weight = 196712.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.052649 restraints weight = 99889.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.053529 restraints weight = 67822.734| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.8070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 35648 Z= 0.215 Angle : 0.872 14.457 48740 Z= 0.448 Chirality : 0.049 0.346 5582 Planarity : 0.006 0.102 5940 Dihedral : 21.491 178.274 5914 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.68 % Allowed : 13.93 % Favored : 85.39 % Rotamer: Outliers : 5.00 % Allowed : 24.31 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.12), residues: 4106 helix: -0.67 (0.14), residues: 1248 sheet: -2.71 (0.26), residues: 365 loop : -3.16 (0.11), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 905 HIS 0.010 0.001 HIS B 372 PHE 0.025 0.002 PHE X 152 TYR 0.018 0.002 TYR A 873 ARG 0.008 0.001 ARG B 841 Details of bonding type rmsd hydrogen bonds : bond 0.08017 ( 1040) hydrogen bonds : angle 6.07979 ( 2848) SS BOND : bond 0.01125 ( 4) SS BOND : angle 4.97932 ( 8) covalent geometry : bond 0.00484 (35642) covalent geometry : angle 0.86937 (48732) Misc. bond : bond 0.00044 ( 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 350 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 173 time to evaluate : 3.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.7542 (OUTLIER) cc_final: 0.7266 (t) REVERT: A 236 MET cc_start: 0.8920 (tpp) cc_final: 0.8536 (mmm) REVERT: A 351 MET cc_start: 0.8360 (ppp) cc_final: 0.8071 (ppp) REVERT: B 32 MET cc_start: 0.9411 (tmm) cc_final: 0.9190 (ppp) REVERT: B 57 MET cc_start: 0.9250 (mtm) cc_final: 0.8904 (mtm) REVERT: B 147 MET cc_start: 0.7559 (mmp) cc_final: 0.7289 (mmp) REVERT: B 204 SER cc_start: 0.9054 (t) cc_final: 0.8834 (t) REVERT: B 205 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8303 (tm-30) REVERT: B 212 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8239 (pp) REVERT: B 313 GLU cc_start: 0.8597 (pp20) cc_final: 0.7917 (mm-30) REVERT: B 363 LEU cc_start: 0.3002 (OUTLIER) cc_final: 0.2544 (tp) REVERT: B 538 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6374 (pm20) REVERT: B 980 LEU cc_start: 0.4583 (OUTLIER) cc_final: 0.4346 (pt) REVERT: B 1035 GLU cc_start: 0.3941 (OUTLIER) cc_final: 0.3708 (pm20) REVERT: B 1071 MET cc_start: 0.2572 (OUTLIER) cc_final: 0.1928 (ttt) REVERT: C 57 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8062 (mmp80) REVERT: D 95 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.5372 (mm-40) REVERT: D 228 SER cc_start: 0.3829 (OUTLIER) cc_final: 0.3116 (t) REVERT: E 18 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8375 (p) REVERT: E 92 GLU cc_start: 0.7937 (mt-10) cc_final: 0.6958 (pt0) REVERT: E 452 ARG cc_start: 0.8440 (mtt180) cc_final: 0.8188 (mtp85) REVERT: G 340 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8706 (tpp-160) REVERT: G 343 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8485 (mm) REVERT: X 145 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8238 (pmm) REVERT: Y 36 PHE cc_start: 0.8435 (m-80) cc_final: 0.8152 (t80) REVERT: Y 58 TYR cc_start: 0.2983 (OUTLIER) cc_final: 0.2419 (m-80) REVERT: Y 120 MET cc_start: 0.5194 (tpp) cc_final: 0.4856 (tpp) REVERT: Y 135 MET cc_start: 0.8738 (ppp) cc_final: 0.8390 (ppp) outliers start: 177 outliers final: 104 residues processed: 331 average time/residue: 0.4370 time to fit residues: 249.2241 Evaluate side-chains 284 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 164 time to evaluate : 4.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 LEU 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 238 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 402 LEU 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 703 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 968 PHE 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 122 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 205 GLN 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 311 LEU 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 384 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 487 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 691 LEU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 865 ILE Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1008 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 1194 LEU Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 136 LEU 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 D residue 4 PHE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 160 SER 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 18 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 397 MET Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 528 THR 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 27 ASN 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 302 ILE Chi-restraints excluded: chain G residue 320 GLU 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 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 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 190 optimal weight: 40.0000 chunk 131 optimal weight: 7.9990 chunk 275 optimal weight: 20.0000 chunk 299 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 397 optimal weight: 8.9990 chunk 253 optimal weight: 8.9990 chunk 143 optimal weight: 0.7980 chunk 388 optimal weight: 8.9990 chunk 383 optimal weight: 6.9990 chunk 214 optimal weight: 0.3980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 GLN ** 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** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 HIS ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 ASN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 142 HIS ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 177 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.074612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.051287 restraints weight = 194778.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.052734 restraints weight = 99062.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.053600 restraints weight = 66421.506| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.8372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35648 Z= 0.193 Angle : 0.848 14.142 48740 Z= 0.434 Chirality : 0.048 0.319 5582 Planarity : 0.005 0.099 5940 Dihedral : 21.357 177.166 5913 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.68 % Allowed : 13.57 % Favored : 85.75 % Rotamer: Outliers : 4.38 % Allowed : 24.77 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.12), residues: 4106 helix: -0.52 (0.15), residues: 1244 sheet: -2.49 (0.26), residues: 348 loop : -3.06 (0.11), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 416 HIS 0.010 0.001 HIS B 372 PHE 0.019 0.001 PHE D 163 TYR 0.017 0.002 TYR A 873 ARG 0.005 0.000 ARG D 174 Details of bonding type rmsd hydrogen bonds : bond 0.07846 ( 1040) hydrogen bonds : angle 5.94661 ( 2848) SS BOND : bond 0.00641 ( 4) SS BOND : angle 4.19577 ( 8) covalent geometry : bond 0.00436 (35642) covalent geometry : angle 0.84615 (48732) Misc. bond : bond 0.00031 ( 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 326 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 171 time to evaluate : 4.153 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: 0.7459 (OUTLIER) cc_final: 0.7173 (t) REVERT: A 236 MET cc_start: 0.8972 (tpp) cc_final: 0.8553 (mmm) REVERT: A 255 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8596 (pm20) REVERT: A 351 MET cc_start: 0.8391 (ppp) cc_final: 0.7899 (ppp) REVERT: A 434 GLU cc_start: 0.8663 (tp30) cc_final: 0.8378 (tp30) REVERT: A 634 GLU cc_start: 0.3308 (OUTLIER) cc_final: 0.3052 (mp0) REVERT: A 1045 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8063 (mmm) REVERT: B 57 MET cc_start: 0.9288 (mtm) cc_final: 0.8963 (mtm) REVERT: B 125 MET cc_start: 0.8406 (ptp) cc_final: 0.8085 (ptp) REVERT: B 204 SER cc_start: 0.9053 (t) cc_final: 0.8840 (t) REVERT: B 212 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8256 (pp) REVERT: B 313 GLU cc_start: 0.8582 (pp20) cc_final: 0.7869 (mm-30) REVERT: B 363 LEU cc_start: 0.2990 (OUTLIER) cc_final: 0.2632 (tp) REVERT: B 538 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6495 (pm20) REVERT: B 1035 GLU cc_start: 0.3747 (OUTLIER) cc_final: 0.3265 (pm20) REVERT: B 1071 MET cc_start: 0.2792 (OUTLIER) cc_final: 0.2137 (ttt) REVERT: B 1127 MET cc_start: 0.9034 (mtm) cc_final: 0.8596 (mtm) REVERT: C 57 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8009 (mmp80) REVERT: D 95 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.5805 (mm-40) REVERT: D 228 SER cc_start: 0.4142 (OUTLIER) cc_final: 0.3372 (t) REVERT: E 18 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.8500 (p) REVERT: E 92 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7019 (pt0) REVERT: E 452 ARG cc_start: 0.8421 (mtt180) cc_final: 0.8170 (mtp85) REVERT: F 65 MET cc_start: 0.9097 (ttm) cc_final: 0.8654 (mtm) REVERT: G 266 MET cc_start: 0.8927 (mmt) cc_final: 0.8711 (mmm) REVERT: G 340 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.9000 (tpt90) REVERT: G 343 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8400 (mm) REVERT: X 145 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8230 (pmm) REVERT: Y 58 TYR cc_start: 0.3197 (OUTLIER) cc_final: 0.2670 (m-80) REVERT: Y 120 MET cc_start: 0.5416 (tpp) cc_final: 0.5087 (tpp) REVERT: Y 135 MET cc_start: 0.8696 (ppp) cc_final: 0.8393 (ppp) outliers start: 155 outliers final: 97 residues processed: 310 average time/residue: 0.4375 time to fit residues: 233.5566 Evaluate side-chains 274 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 160 time to evaluate : 4.041 ------------------------------------------------------------------------------- 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 121 LEU 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 238 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 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 634 GLU Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 968 PHE Chi-restraints excluded: chain A residue 1045 MET 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 122 VAL Chi-restraints excluded: chain B residue 140 LEU 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 305 HIS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 410 ILE 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 700 VAL Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 1008 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 1107 TYR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 136 LEU 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 9 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 95 GLN 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 18 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 228 LEU 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 441 ILE Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 528 THR 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 14 ILE 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 233 VAL Chi-restraints excluded: chain G residue 302 ILE 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 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 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 134 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 371 optimal weight: 0.0000 chunk 271 optimal weight: 10.0000 chunk 398 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 299 optimal weight: 0.9990 chunk 375 optimal weight: 10.0000 overall best weight: 1.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** 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 347 GLN ** 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** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN F 27 ASN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 ASN X 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.075096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.051708 restraints weight = 192621.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.053159 restraints weight = 97336.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.054027 restraints weight = 65879.690| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.8653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35648 Z= 0.169 Angle : 0.831 14.131 48740 Z= 0.424 Chirality : 0.048 0.307 5582 Planarity : 0.005 0.099 5940 Dihedral : 21.247 176.541 5913 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.63 % Allowed : 13.01 % Favored : 86.36 % Rotamer: Outliers : 3.87 % Allowed : 25.50 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.12), residues: 4106 helix: -0.40 (0.15), residues: 1242 sheet: -2.44 (0.26), residues: 353 loop : -2.98 (0.11), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 905 HIS 0.016 0.001 HIS X 176 PHE 0.019 0.001 PHE D 163 TYR 0.016 0.001 TYR B 177 ARG 0.009 0.000 ARG X 143 Details of bonding type rmsd hydrogen bonds : bond 0.07765 ( 1040) hydrogen bonds : angle 5.82123 ( 2848) SS BOND : bond 0.01513 ( 4) SS BOND : angle 4.96267 ( 8) covalent geometry : bond 0.00377 (35642) covalent geometry : angle 0.82818 (48732) Misc. bond : bond 0.00020 ( 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 309 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 172 time to evaluate : 3.784 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 205 SER cc_start: 0.7432 (OUTLIER) cc_final: 0.7148 (t) REVERT: A 236 MET cc_start: 0.8886 (tpp) cc_final: 0.8513 (mmm) REVERT: A 255 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8588 (pm20) REVERT: A 351 MET cc_start: 0.8500 (ppp) cc_final: 0.8016 (ppp) REVERT: A 434 GLU cc_start: 0.8614 (tp30) cc_final: 0.8412 (tp30) REVERT: A 651 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8785 (pp) REVERT: A 1037 LEU cc_start: 0.9626 (tt) cc_final: 0.9396 (tp) REVERT: A 1045 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7978 (mmm) REVERT: B 1 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8360 (ttm) REVERT: B 57 MET cc_start: 0.9230 (mtm) cc_final: 0.8887 (mtm) REVERT: B 125 MET cc_start: 0.8405 (ptp) cc_final: 0.8099 (ptp) REVERT: B 204 SER cc_start: 0.9197 (t) cc_final: 0.8957 (p) REVERT: B 212 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8173 (pp) REVERT: B 313 GLU cc_start: 0.8571 (pp20) cc_final: 0.7813 (mm-30) REVERT: B 363 LEU cc_start: 0.3092 (OUTLIER) cc_final: 0.2741 (tp) REVERT: B 538 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6480 (pm20) REVERT: B 622 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6649 (pm20) REVERT: B 1035 GLU cc_start: 0.3879 (OUTLIER) cc_final: 0.3407 (pm20) REVERT: B 1071 MET cc_start: 0.2659 (OUTLIER) cc_final: 0.2175 (ttt) REVERT: B 1142 GLU cc_start: 0.8796 (tt0) cc_final: 0.8500 (tt0) REVERT: C 57 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8016 (mmp80) REVERT: C 171 MET cc_start: 0.7632 (tmm) cc_final: 0.7354 (ppp) REVERT: D 95 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6056 (mm-40) REVERT: D 228 SER cc_start: 0.3871 (OUTLIER) cc_final: 0.3204 (t) REVERT: E 18 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8522 (p) REVERT: E 92 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7096 (pt0) REVERT: F 65 MET cc_start: 0.9078 (ttm) cc_final: 0.8664 (mtm) REVERT: G 100 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8165 (mm-30) REVERT: G 266 MET cc_start: 0.8903 (mmt) cc_final: 0.8702 (mmm) REVERT: G 340 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8672 (tpp-160) REVERT: X 145 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8283 (pmm) REVERT: Y 58 TYR cc_start: 0.3039 (OUTLIER) cc_final: 0.2514 (m-80) REVERT: Y 120 MET cc_start: 0.5449 (tpp) cc_final: 0.5134 (tpp) REVERT: Y 135 MET cc_start: 0.8610 (ppp) cc_final: 0.8332 (ppp) outliers start: 137 outliers final: 81 residues processed: 292 average time/residue: 0.4319 time to fit residues: 216.3670 Evaluate side-chains 254 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 155 time to evaluate : 4.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 LEU 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 238 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 402 LEU 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 651 LEU Chi-restraints excluded: chain A residue 696 TYR 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 1045 MET 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 122 VAL Chi-restraints excluded: chain B residue 140 LEU 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 305 HIS Chi-restraints excluded: chain B residue 315 VAL 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 410 ILE 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 700 VAL Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 1008 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 1107 TYR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1206 SER Chi-restraints excluded: chain C residue 57 ARG 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 9 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 71 CYS 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 441 ILE Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 513 MET 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 27 ASN Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 341 TYR Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 64 ILE 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 Chi-restraints excluded: chain Y residue 134 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 158 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 175 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 274 optimal weight: 6.9990 chunk 163 optimal weight: 30.0000 chunk 235 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS A 560 GLN ** 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 726 GLN ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1238 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.074143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.050560 restraints weight = 193053.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.051963 restraints weight = 98292.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.052801 restraints weight = 67079.375| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.8804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 35648 Z= 0.201 Angle : 0.851 14.124 48740 Z= 0.432 Chirality : 0.048 0.388 5582 Planarity : 0.006 0.098 5940 Dihedral : 21.212 177.963 5913 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.63 % Allowed : 13.30 % Favored : 86.07 % Rotamer: Outliers : 3.42 % Allowed : 26.18 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.12), residues: 4106 helix: -0.38 (0.15), residues: 1249 sheet: -2.39 (0.26), residues: 349 loop : -2.95 (0.11), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 416 HIS 0.010 0.001 HIS B 372 PHE 0.019 0.001 PHE D 163 TYR 0.019 0.002 TYR A 873 ARG 0.010 0.000 ARG F 28 Details of bonding type rmsd hydrogen bonds : bond 0.07678 ( 1040) hydrogen bonds : angle 5.81766 ( 2848) SS BOND : bond 0.00697 ( 4) SS BOND : angle 4.76278 ( 8) covalent geometry : bond 0.00455 (35642) covalent geometry : angle 0.84843 (48732) Misc. bond : bond 0.00031 ( 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 286 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 165 time to evaluate : 3.718 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: 0.8881 (tpp) cc_final: 0.8517 (mmm) REVERT: A 351 MET cc_start: 0.8550 (ppp) cc_final: 0.8105 (ppp) REVERT: A 434 GLU cc_start: 0.8667 (tp30) cc_final: 0.8444 (tp30) REVERT: A 480 MET cc_start: 0.8312 (ppp) cc_final: 0.7962 (ptm) REVERT: A 634 GLU cc_start: 0.3291 (OUTLIER) cc_final: 0.2731 (tt0) REVERT: A 651 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8834 (pp) REVERT: A 694 GLU cc_start: 0.8705 (pm20) cc_final: 0.8300 (pm20) REVERT: A 1045 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7970 (mmm) REVERT: B 57 MET cc_start: 0.9279 (mtm) cc_final: 0.9010 (mtm) REVERT: B 125 MET cc_start: 0.8544 (ptp) cc_final: 0.8331 (ptp) REVERT: B 204 SER cc_start: 0.9218 (t) cc_final: 0.8876 (p) REVERT: B 212 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8542 (pp) REVERT: B 363 LEU cc_start: 0.3235 (OUTLIER) cc_final: 0.2902 (tp) REVERT: B 538 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6536 (pm20) REVERT: B 800 GLU cc_start: 0.9190 (tt0) cc_final: 0.8985 (mp0) REVERT: B 1029 LEU cc_start: 0.4411 (OUTLIER) cc_final: 0.4069 (mt) REVERT: B 1035 GLU cc_start: 0.3935 (OUTLIER) cc_final: 0.3505 (pm20) REVERT: B 1071 MET cc_start: 0.2654 (OUTLIER) cc_final: 0.2178 (ttt) REVERT: B 1127 MET cc_start: 0.8953 (mtm) cc_final: 0.8664 (mtm) REVERT: B 1142 GLU cc_start: 0.8784 (tt0) cc_final: 0.8423 (tt0) REVERT: C 57 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8037 (mmp80) REVERT: C 171 MET cc_start: 0.7613 (tmm) cc_final: 0.7322 (ppp) REVERT: D 95 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6363 (mm-40) REVERT: D 228 SER cc_start: 0.4451 (OUTLIER) cc_final: 0.3971 (t) REVERT: E 18 SER cc_start: 0.8927 (OUTLIER) cc_final: 0.8615 (p) REVERT: E 92 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7066 (pt0) REVERT: F 65 MET cc_start: 0.9128 (ttm) cc_final: 0.8713 (mtm) REVERT: G 100 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8197 (mm-30) REVERT: G 340 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8705 (tpm170) REVERT: X 145 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8256 (pmm) REVERT: Y 58 TYR cc_start: 0.2802 (OUTLIER) cc_final: 0.2369 (m-80) REVERT: Y 120 MET cc_start: 0.5376 (tpp) cc_final: 0.4941 (tpp) REVERT: Y 135 MET cc_start: 0.8568 (ppp) cc_final: 0.8343 (ppp) outliers start: 121 outliers final: 91 residues processed: 270 average time/residue: 0.4257 time to fit residues: 197.9040 Evaluate side-chains 262 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 155 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE 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 119 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 560 GLN 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 634 GLU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 696 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 968 PHE Chi-restraints excluded: chain A residue 1045 MET 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 122 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 315 VAL 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 410 ILE 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 636 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1029 LEU 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 1107 TYR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1206 SER Chi-restraints excluded: chain C residue 57 ARG 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 D residue 4 PHE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 95 GLN 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 18 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 397 MET Chi-restraints excluded: chain E residue 410 ARG 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 513 MET Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 593 VAL Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 341 TYR Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 64 ILE 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 Chi-restraints excluded: chain Y residue 134 GLU Chi-restraints excluded: chain Y residue 136 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 158 optimal weight: 7.9990 chunk 315 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 313 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 252 optimal weight: 0.3980 chunk 91 optimal weight: 0.0670 chunk 352 optimal weight: 0.2980 chunk 133 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN B 573 ASN ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN E 101 HIS ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.075834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.052323 restraints weight = 190203.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.053792 restraints weight = 96845.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.054670 restraints weight = 65560.892| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.9186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 35648 Z= 0.152 Angle : 0.846 15.656 48740 Z= 0.424 Chirality : 0.048 0.436 5582 Planarity : 0.005 0.098 5940 Dihedral : 21.046 176.486 5913 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.61 % Allowed : 11.89 % Favored : 87.51 % Rotamer: Outliers : 2.77 % Allowed : 26.75 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.12), residues: 4106 helix: -0.28 (0.15), residues: 1248 sheet: -2.22 (0.26), residues: 356 loop : -2.89 (0.11), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 905 HIS 0.009 0.001 HIS B 372 PHE 0.018 0.001 PHE X 152 TYR 0.020 0.001 TYR G 388 ARG 0.007 0.000 ARG X 129 Details of bonding type rmsd hydrogen bonds : bond 0.07759 ( 1040) hydrogen bonds : angle 5.65833 ( 2848) SS BOND : bond 0.00398 ( 4) SS BOND : angle 4.09011 ( 8) covalent geometry : bond 0.00338 (35642) covalent geometry : angle 0.84396 (48732) Misc. bond : bond 0.00024 ( 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 280 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 182 time to evaluate : 3.724 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 236 MET cc_start: 0.8785 (tpp) cc_final: 0.8399 (mmm) REVERT: A 351 MET cc_start: 0.8627 (ppp) cc_final: 0.8226 (ppp) REVERT: A 559 MET cc_start: 0.9080 (mpp) cc_final: 0.8580 (mpp) REVERT: A 634 GLU cc_start: 0.3187 (OUTLIER) cc_final: 0.2585 (tt0) REVERT: A 651 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8771 (pp) REVERT: A 675 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8981 (p) REVERT: A 694 GLU cc_start: 0.8593 (pm20) cc_final: 0.8208 (pm20) REVERT: A 1045 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7600 (mmm) REVERT: B 1 MET cc_start: 0.8557 (mtm) cc_final: 0.8317 (ttm) REVERT: B 57 MET cc_start: 0.9290 (mtm) cc_final: 0.9022 (mtm) REVERT: B 124 MET cc_start: 0.8466 (mtm) cc_final: 0.7773 (mtm) REVERT: B 125 MET cc_start: 0.8425 (ptp) cc_final: 0.7475 (ptp) REVERT: B 140 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6842 (mt) REVERT: B 204 SER cc_start: 0.9077 (t) cc_final: 0.8726 (p) REVERT: B 313 GLU cc_start: 0.8629 (pp20) cc_final: 0.7823 (mt-10) REVERT: B 363 LEU cc_start: 0.3357 (OUTLIER) cc_final: 0.2998 (tp) REVERT: B 538 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6556 (pm20) REVERT: B 800 GLU cc_start: 0.9200 (tt0) cc_final: 0.8994 (mp0) REVERT: B 1029 LEU cc_start: 0.4408 (OUTLIER) cc_final: 0.4099 (mt) REVERT: B 1035 GLU cc_start: 0.3843 (OUTLIER) cc_final: 0.3409 (pm20) REVERT: B 1071 MET cc_start: 0.2755 (OUTLIER) cc_final: 0.2075 (mpp) REVERT: B 1142 GLU cc_start: 0.8790 (tt0) cc_final: 0.8444 (tt0) REVERT: C 57 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7962 (mmp80) REVERT: C 171 MET cc_start: 0.7551 (tmm) cc_final: 0.7271 (ppp) REVERT: D 95 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6645 (mm-40) REVERT: D 228 SER cc_start: 0.4328 (OUTLIER) cc_final: 0.3764 (t) REVERT: E 18 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8584 (p) REVERT: E 92 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7108 (pt0) REVERT: F 65 MET cc_start: 0.9107 (ttm) cc_final: 0.8690 (mtm) REVERT: G 100 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8159 (mm-30) REVERT: G 340 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8734 (tpm170) REVERT: X 145 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8411 (pmm) REVERT: Y 58 TYR cc_start: 0.2514 (OUTLIER) cc_final: 0.2160 (m-80) REVERT: Y 120 MET cc_start: 0.5414 (tpp) cc_final: 0.5111 (tpp) REVERT: Y 135 MET cc_start: 0.8535 (ppp) cc_final: 0.8322 (ppp) outliers start: 98 outliers final: 68 residues processed: 270 average time/residue: 0.4332 time to fit residues: 200.7070 Evaluate side-chains 247 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 162 time to evaluate : 4.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 121 LEU 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 272 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 696 TYR 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 1045 MET 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 122 VAL Chi-restraints excluded: chain B residue 140 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 410 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 538 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 916 VAL Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1029 LEU 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 1107 TYR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1206 SER Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 95 GLN 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 18 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 593 VAL Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 341 TYR Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 64 ILE 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 Chi-restraints excluded: chain Y residue 134 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 298 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 385 optimal weight: 0.0020 chunk 136 optimal weight: 7.9990 chunk 375 optimal weight: 0.3980 chunk 114 optimal weight: 5.9990 chunk 291 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 chunk 379 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 120 optimal weight: 0.9980 overall best weight: 2.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS A 560 GLN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.074783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.051427 restraints weight = 190128.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.052884 restraints weight = 96087.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.053820 restraints weight = 64746.267| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.9237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35648 Z= 0.170 Angle : 0.824 15.153 48740 Z= 0.416 Chirality : 0.047 0.406 5582 Planarity : 0.005 0.126 5940 Dihedral : 20.953 177.050 5911 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.61 % Allowed : 12.40 % Favored : 86.99 % Rotamer: Outliers : 2.77 % Allowed : 26.94 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.12), residues: 4106 helix: -0.23 (0.15), residues: 1247 sheet: -2.30 (0.27), residues: 345 loop : -2.85 (0.11), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B1231 HIS 0.009 0.001 HIS B 372 PHE 0.019 0.001 PHE Y 75 TYR 0.015 0.001 TYR B 177 ARG 0.008 0.000 ARG E 329 Details of bonding type rmsd hydrogen bonds : bond 0.07605 ( 1040) hydrogen bonds : angle 5.60947 ( 2848) SS BOND : bond 0.00520 ( 4) SS BOND : angle 4.04037 ( 8) covalent geometry : bond 0.00386 (35642) covalent geometry : angle 0.82202 (48732) Misc. bond : bond 0.00018 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14823.73 seconds wall clock time: 256 minutes 7.40 seconds (15367.40 seconds total)