Starting phenix.real_space_refine on Fri Jun 20 13:58:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fuk_29459/06_2025/8fuk_29459.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fuk_29459/06_2025/8fuk_29459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fuk_29459/06_2025/8fuk_29459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fuk_29459/06_2025/8fuk_29459.map" model { file = "/net/cci-nas-00/data/ceres_data/8fuk_29459/06_2025/8fuk_29459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fuk_29459/06_2025/8fuk_29459.cif" } resolution = 3.36 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= 0.026 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 59 5.49 5 S 108 5.16 5 C 14806 2.51 5 N 4091 2.21 5 O 4544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23608 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1280 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p_pur': 20, 'rna3p_pyr': 14} Link IDs: {'rna2p': 26, 'rna3p': 33} Chain: "A" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2635 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 16, 'TRANS': 312} Chain breaks: 2 Chain: "B" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2696 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Chain: "C" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2630 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 311} Chain breaks: 2 Chain: "D" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2687 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 318} Chain breaks: 1 Chain: "E" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2662 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 315} Chain breaks: 2 Chain: "F" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2377 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 280} Chain breaks: 3 Chain: "G" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2653 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 17, 'TRANS': 321} Chain breaks: 4 Chain: "H" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1611 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "I" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1507 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain breaks: 2 Chain: "J" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 870 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain breaks: 3 Time building chain proxies: 15.24, per 1000 atoms: 0.65 Number of scatterers: 23608 At special positions: 0 Unit cell: (118.44, 168.26, 174.84, 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 108 16.00 P 59 15.00 O 4544 8.00 N 4091 7.00 C 14806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.76 Conformation dependent library (CDL) restraints added in 2.7 seconds 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5300 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 43 sheets defined 37.9% alpha, 18.4% beta 6 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 8.02 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.583A pdb=" N ASN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 146 removed outlier: 6.857A pdb=" N LYS A 144 " --> pdb=" O TRP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 260 through 268 removed outlier: 3.665A pdb=" N THR A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.714A pdb=" N GLU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 344 removed outlier: 3.528A pdb=" N LYS A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.826A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 Processing helix chain 'B' and resid 105 through 123 Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.922A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 136 " --> pdb=" O TYR B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 removed outlier: 6.627A pdb=" N LYS B 144 " --> pdb=" O TRP B 141 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 146 " --> pdb=" O TRP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 Processing helix chain 'B' and resid 186 through 199 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 291 through 294 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 312 through 323 removed outlier: 3.894A pdb=" N ASN B 323 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 344 Processing helix chain 'C' and resid 45 through 50 Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.655A pdb=" N GLN C 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 66 Processing helix chain 'C' and resid 105 through 123 removed outlier: 3.532A pdb=" N LYS C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 Processing helix chain 'C' and resid 139 through 147 removed outlier: 6.710A pdb=" N LYS C 144 " --> pdb=" O TRP C 141 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 146 " --> pdb=" O TRP C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 186 through 200 removed outlier: 3.783A pdb=" N GLU C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 291 through 294 Processing helix chain 'C' and resid 299 through 303 Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 328 through 344 Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 61 through 66 Processing helix chain 'D' and resid 105 through 123 removed outlier: 3.581A pdb=" N LYS D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.603A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 removed outlier: 6.576A pdb=" N LYS D 144 " --> pdb=" O TRP D 141 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR D 146 " --> pdb=" O TRP D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 186 through 199 removed outlier: 3.632A pdb=" N ILE D 194 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 312 through 321 Processing helix chain 'D' and resid 327 through 344 Processing helix chain 'E' and resid 45 through 51 removed outlier: 3.715A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 67 Processing helix chain 'E' and resid 105 through 123 removed outlier: 3.577A pdb=" N LYS E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 138 removed outlier: 3.611A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 146 removed outlier: 6.630A pdb=" N LYS E 144 " --> pdb=" O TRP E 141 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR E 146 " --> pdb=" O TRP E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 175 removed outlier: 3.677A pdb=" N TYR E 175 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'E' and resid 186 through 200 removed outlier: 3.874A pdb=" N ILE E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 194 " --> pdb=" O ILE E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 269 Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 312 through 322 Processing helix chain 'E' and resid 327 through 343 Processing helix chain 'F' and resid 105 through 123 removed outlier: 3.686A pdb=" N LYS F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 138 removed outlier: 3.825A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 147 removed outlier: 6.520A pdb=" N LYS F 144 " --> pdb=" O TRP F 141 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR F 146 " --> pdb=" O TRP F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 183 Processing helix chain 'F' and resid 186 through 200 removed outlier: 3.649A pdb=" N ILE F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 269 Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 305 through 311 Processing helix chain 'F' and resid 312 through 323 removed outlier: 3.812A pdb=" N ASN F 323 " --> pdb=" O VAL F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 344 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 218 through 230 removed outlier: 3.771A pdb=" N ARG G 228 " --> pdb=" O HIS G 224 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN G 230 " --> pdb=" O HIS G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 411 through 428 removed outlier: 3.753A pdb=" N ARG G 428 " --> pdb=" O ARG G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 499 Processing helix chain 'G' and resid 513 through 519 removed outlier: 4.337A pdb=" N LYS G 517 " --> pdb=" O ASP G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 530 removed outlier: 3.874A pdb=" N GLU G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 561 removed outlier: 3.835A pdb=" N GLU G 559 " --> pdb=" O ALA G 555 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP G 560 " --> pdb=" O ALA G 556 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 612 Processing helix chain 'H' and resid 16 through 35 Processing helix chain 'H' and resid 62 through 70 Processing helix chain 'H' and resid 72 through 80 removed outlier: 3.748A pdb=" N GLN H 80 " --> pdb=" O VAL H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 111 removed outlier: 3.800A pdb=" N LYS H 109 " --> pdb=" O GLN H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 Processing helix chain 'I' and resid 198 through 206 removed outlier: 3.968A pdb=" N ASN I 202 " --> pdb=" O CYS I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 230 removed outlier: 4.269A pdb=" N GLY I 229 " --> pdb=" O HIS I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 245 removed outlier: 4.408A pdb=" N GLN I 242 " --> pdb=" O PHE I 238 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE I 243 " --> pdb=" O SER I 239 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE I 244 " --> pdb=" O PHE I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 265 Processing helix chain 'I' and resid 274 through 279 Processing helix chain 'I' and resid 279 through 288 removed outlier: 4.282A pdb=" N ARG I 288 " --> pdb=" O PHE I 284 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 Processing helix chain 'I' and resid 317 through 320 removed outlier: 3.710A pdb=" N ASN I 320 " --> pdb=" O LEU I 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 317 through 320' Processing helix chain 'I' and resid 324 through 333 Processing helix chain 'I' and resid 335 through 345 Processing helix chain 'I' and resid 369 through 380 Processing helix chain 'I' and resid 386 through 390 Processing helix chain 'J' and resid 13 through 26 removed outlier: 3.947A pdb=" N GLY J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 45 Processing helix chain 'J' and resid 60 through 64 removed outlier: 3.735A pdb=" N ALA J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 81 removed outlier: 3.775A pdb=" N ARG J 71 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 139 removed outlier: 3.887A pdb=" N ALA J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER J 139 " --> pdb=" O ASN J 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 134 through 139' Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 15 removed outlier: 3.613A pdb=" N HIS A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 13 through 15 Processing sheet with id=AA4, first strand: chain 'A' and resid 35 through 42 removed outlier: 7.942A pdb=" N SER A 243 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLN A 72 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 251 Processing sheet with id=AA6, first strand: chain 'A' and resid 288 through 290 removed outlier: 3.631A pdb=" N HIS A 290 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 295 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 9 Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.516A pdb=" N SER B 88 " --> pdb=" O CYS B 19 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS B 84 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AB1, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AB2, first strand: chain 'B' and resid 289 through 290 Processing sheet with id=AB3, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AB4, first strand: chain 'C' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 23 current: chain 'C' and resid 151 through 159 Processing sheet with id=AB5, first strand: chain 'C' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 94 current: chain 'C' and resid 248 through 251 Processing sheet with id=AB6, first strand: chain 'C' and resid 35 through 42 removed outlier: 8.624A pdb=" N SER C 243 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N GLN C 72 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AB8, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.519A pdb=" N THR C 295 " --> pdb=" O HIS C 290 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 102 through 103 Processing sheet with id=AC1, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.510A pdb=" N SER D 88 " --> pdb=" O CYS D 19 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AC3, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AC4, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AC5, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AC6, first strand: chain 'D' and resid 289 through 290 Processing sheet with id=AC7, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AC8, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.551A pdb=" N SER E 92 " --> pdb=" O ASP E 14 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER E 88 " --> pdb=" O CYS E 19 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 23 current: chain 'E' and resid 152 through 159 Processing sheet with id=AC9, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.524A pdb=" N SER E 88 " --> pdb=" O CYS E 19 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 84 through 94 current: chain 'E' and resid 248 through 251 Processing sheet with id=AD1, first strand: chain 'E' and resid 35 through 42 Processing sheet with id=AD2, first strand: chain 'F' and resid 102 through 103 Processing sheet with id=AD3, first strand: chain 'F' and resid 29 through 31 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 31 removed outlier: 4.260A pdb=" N PHE F 20 " --> pdb=" O PRO F 257 " (cutoff:3.500A) removed outlier: 10.465A pdb=" N VAL F 22 " --> pdb=" O ARG F 255 " (cutoff:3.500A) removed outlier: 14.001A pdb=" N ARG F 255 " --> pdb=" O VAL F 22 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 72 through 75 removed outlier: 6.415A pdb=" N SER F 36 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE H 146 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR F 38 " --> pdb=" O ILE H 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 288 through 289 Processing sheet with id=AD7, first strand: chain 'G' and resid 201 through 203 removed outlier: 3.909A pdb=" N GLY G 569 " --> pdb=" O ILE G 594 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL G 568 " --> pdb=" O VAL G 625 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 236 through 240 Processing sheet with id=AD9, first strand: chain 'G' and resid 508 through 511 Processing sheet with id=AE1, first strand: chain 'G' and resid 508 through 511 removed outlier: 5.787A pdb=" N PHE G 387 " --> pdb=" O THR G 485 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR G 485 " --> pdb=" O PHE G 387 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL G 389 " --> pdb=" O LEU G 483 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU G 483 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU G 481 " --> pdb=" O PRO G 391 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL G 478 " --> pdb=" O HIS G 443 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER G 437 " --> pdb=" O ASN G 484 " (cutoff:3.500A) removed outlier: 15.508A pdb=" N PHE G 438 " --> pdb=" O LEU G 542 " (cutoff:3.500A) removed outlier: 10.628A pdb=" N LEU G 542 " --> pdb=" O PHE G 438 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE G 440 " --> pdb=" O LEU G 540 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 398 through 399 removed outlier: 4.037A pdb=" N ASP G 472 " --> pdb=" O ARG G 450 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG G 450 " --> pdb=" O ASP G 472 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 41 through 43 Processing sheet with id=AE4, first strand: chain 'H' and resid 41 through 43 removed outlier: 3.600A pdb=" N TYR H 5 " --> pdb=" O VAL H 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 167 through 171 Processing sheet with id=AE6, first strand: chain 'I' and resid 322 through 323 Processing sheet with id=AE7, first strand: chain 'J' and resid 95 through 96 921 hydrogen bonds defined for protein. 2445 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 8.65 Time building geometry restraints manager: 6.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7250 1.34 - 1.46: 4634 1.46 - 1.58: 12162 1.58 - 1.70: 119 1.70 - 1.82: 160 Bond restraints: 24325 Sorted by residual: bond pdb=" CB PRO J 87 " pdb=" CG PRO J 87 " ideal model delta sigma weight residual 1.492 1.651 -0.159 5.00e-02 4.00e+02 1.01e+01 bond pdb=" CG PRO J 86 " pdb=" CD PRO J 86 " ideal model delta sigma weight residual 1.503 1.549 -0.046 3.40e-02 8.65e+02 1.81e+00 bond pdb=" C4' U 1 30 " pdb=" O4' U 1 30 " ideal model delta sigma weight residual 1.451 1.433 0.018 1.50e-02 4.44e+03 1.52e+00 bond pdb=" C4' C 1 21 " pdb=" C3' C 1 21 " ideal model delta sigma weight residual 1.527 1.509 0.018 1.50e-02 4.44e+03 1.43e+00 bond pdb=" C4' A 1 12 " pdb=" O4' A 1 12 " ideal model delta sigma weight residual 1.451 1.433 0.018 1.50e-02 4.44e+03 1.43e+00 ... (remaining 24320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 32842 2.09 - 4.19: 396 4.19 - 6.28: 44 6.28 - 8.38: 11 8.38 - 10.47: 2 Bond angle restraints: 33295 Sorted by residual: angle pdb=" CA PRO J 87 " pdb=" N PRO J 87 " pdb=" CD PRO J 87 " ideal model delta sigma weight residual 112.00 101.53 10.47 1.40e+00 5.10e-01 5.60e+01 angle pdb=" N HIS J 31 " pdb=" CA HIS J 31 " pdb=" C HIS J 31 " ideal model delta sigma weight residual 113.29 105.80 7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" N MET I 228 " pdb=" CA MET I 228 " pdb=" CB MET I 228 " ideal model delta sigma weight residual 110.01 115.10 -5.09 1.45e+00 4.76e-01 1.23e+01 angle pdb=" CA LYS G 577 " pdb=" CB LYS G 577 " pdb=" CG LYS G 577 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N PRO J 87 " pdb=" CD PRO J 87 " pdb=" CG PRO J 87 " ideal model delta sigma weight residual 103.20 98.24 4.96 1.50e+00 4.44e-01 1.10e+01 ... (remaining 33290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.29: 13056 22.29 - 44.58: 1149 44.58 - 66.87: 230 66.87 - 89.16: 47 89.16 - 111.45: 4 Dihedral angle restraints: 14486 sinusoidal: 6336 harmonic: 8150 Sorted by residual: dihedral pdb=" O4' C 1 21 " pdb=" C1' C 1 21 " pdb=" N1 C 1 21 " pdb=" C2 C 1 21 " ideal model delta sinusoidal sigma weight residual 232.00 148.33 83.67 1 1.70e+01 3.46e-03 2.96e+01 dihedral pdb=" O4' U 1 33 " pdb=" C1' U 1 33 " pdb=" N1 U 1 33 " pdb=" C2 U 1 33 " ideal model delta sinusoidal sigma weight residual -128.00 -44.67 -83.33 1 1.70e+01 3.46e-03 2.94e+01 dihedral pdb=" O4' U 1 22 " pdb=" C1' U 1 22 " pdb=" N1 U 1 22 " pdb=" C2 U 1 22 " ideal model delta sinusoidal sigma weight residual -160.00 -94.98 -65.02 1 1.50e+01 4.44e-03 2.46e+01 ... (remaining 14483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2573 0.037 - 0.074: 827 0.074 - 0.111: 232 0.111 - 0.148: 66 0.148 - 0.184: 7 Chirality restraints: 3705 Sorted by residual: chirality pdb=" CB THR A 270 " pdb=" CA THR A 270 " pdb=" OG1 THR A 270 " pdb=" CG2 THR A 270 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA MET I 228 " pdb=" N MET I 228 " pdb=" C MET I 228 " pdb=" CB MET I 228 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" C1' A 1 12 " pdb=" O4' A 1 12 " pdb=" C2' A 1 12 " pdb=" N9 A 1 12 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 3702 not shown) Planarity restraints: 4033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 281 " 0.411 9.50e-02 1.11e+02 1.85e-01 2.67e+01 pdb=" NE ARG I 281 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG I 281 " 0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG I 281 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG I 281 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO J 86 " -0.061 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO J 87 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO J 87 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO J 87 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 274 " -0.258 9.50e-02 1.11e+02 1.17e-01 1.07e+01 pdb=" NE ARG I 274 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG I 274 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG I 274 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG I 274 " -0.000 2.00e-02 2.50e+03 ... (remaining 4030 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 286 2.63 - 3.20: 21234 3.20 - 3.77: 36377 3.77 - 4.33: 49444 4.33 - 4.90: 83092 Nonbonded interactions: 190433 Sorted by model distance: nonbonded pdb=" OG SER A 94 " pdb=" OE1 GLU A 96 " model vdw 2.068 3.040 nonbonded pdb=" O HIS F 299 " pdb=" OG1 THR F 302 " model vdw 2.217 3.040 nonbonded pdb=" OE1 GLU I 256 " pdb=" OH TYR I 306 " model vdw 2.217 3.040 nonbonded pdb=" OG SER A 95 " pdb=" O ALA A 197 " model vdw 2.227 3.040 nonbonded pdb=" OE2 GLU D 44 " pdb=" NZ LYS E 343 " model vdw 2.240 3.120 ... (remaining 190428 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 'A' and (resid 2 through 25 or resid 28 through 40 or resid 71 through 22 \ 8 or resid 243 through 272 or resid 283 through 317 or resid 327 through 348)) selection = (chain 'B' and (resid 2 through 25 or resid 28 through 40 or resid 71 through 22 \ 8 or resid 243 through 272 or resid 283 through 317 or resid 327 through 348)) selection = (chain 'C' and (resid 2 through 25 or resid 28 through 40 or resid 71 through 22 \ 8 or resid 243 through 272 or resid 283 through 348)) selection = (chain 'D' and (resid 2 through 25 or resid 28 through 40 or resid 71 through 22 \ 8 or resid 243 through 272 or resid 283 through 317 or resid 327 through 348)) selection = (chain 'E' and (resid 2 through 40 or resid 71 through 228 or resid 243 through \ 272 or resid 283 through 317 or resid 327 through 348)) selection = (chain 'F' and (resid 2 through 25 or resid 28 through 317 or resid 327 through \ 348)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 59.470 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.003 0.159 24325 Z= 0.131 Angle : 0.564 10.475 33295 Z= 0.304 Chirality : 0.041 0.184 3705 Planarity : 0.006 0.185 4033 Dihedral : 17.109 111.451 9186 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.24 % Allowed : 20.04 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.29 (0.16), residues: 2724 helix: 0.59 (0.18), residues: 883 sheet: 0.76 (0.24), residues: 497 loop : -0.20 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 539 HIS 0.014 0.001 HIS J 31 PHE 0.028 0.001 PHE A 306 TYR 0.020 0.001 TYR E 275 ARG 0.042 0.001 ARG I 281 Details of bonding type rmsd hydrogen bonds : bond 0.21344 ( 907) hydrogen bonds : angle 7.59582 ( 2473) covalent geometry : bond 0.00308 (24325) covalent geometry : angle 0.56357 (33295) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 234 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 132 GLN cc_start: 0.7603 (pm20) cc_final: 0.7053 (mm-40) REVERT: H 173 GLN cc_start: 0.7109 (tm-30) cc_final: 0.5909 (pm20) REVERT: I 388 SER cc_start: 0.7526 (t) cc_final: 0.7315 (p) outliers start: 6 outliers final: 2 residues processed: 236 average time/residue: 0.3978 time to fit residues: 149.7370 Evaluate side-chains 233 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 231 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain G residue 263 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN E 218 ASN F 179 GLN G 626 GLN ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.137732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.094629 restraints weight = 35992.674| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.06 r_work: 0.3095 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24325 Z= 0.205 Angle : 0.576 9.453 33295 Z= 0.305 Chirality : 0.042 0.205 3705 Planarity : 0.004 0.044 4033 Dihedral : 13.161 109.566 3904 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.79 % Allowed : 17.60 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.14 (0.16), residues: 2724 helix: 0.52 (0.17), residues: 908 sheet: 0.52 (0.24), residues: 515 loop : -0.29 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.008 0.001 HIS H 29 PHE 0.025 0.002 PHE A 306 TYR 0.018 0.002 TYR B 275 ARG 0.004 0.000 ARG F 283 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 907) hydrogen bonds : angle 5.31502 ( 2473) covalent geometry : bond 0.00488 (24325) covalent geometry : angle 0.57623 (33295) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 240 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9002 (pp) REVERT: A 220 MET cc_start: 0.8462 (mmt) cc_final: 0.8177 (mmt) REVERT: A 306 PHE cc_start: 0.7579 (t80) cc_final: 0.7295 (t80) REVERT: B 97 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8895 (pt) REVERT: G 577 LYS cc_start: 0.8066 (mmtp) cc_final: 0.7848 (mmtp) REVERT: H 18 GLU cc_start: 0.8929 (mp0) cc_final: 0.8667 (mp0) REVERT: H 94 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6658 (tm-30) REVERT: H 173 GLN cc_start: 0.7301 (tm-30) cc_final: 0.5503 (pm20) REVERT: H 190 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.6964 (pm20) REVERT: H 194 GLN cc_start: 0.7230 (tt0) cc_final: 0.6939 (tt0) REVERT: I 388 SER cc_start: 0.7708 (t) cc_final: 0.7506 (p) outliers start: 93 outliers final: 52 residues processed: 302 average time/residue: 0.3259 time to fit residues: 158.5586 Evaluate side-chains 275 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 482 ILE Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 626 GLN Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 276 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 HIS ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.096786 restraints weight = 35651.501| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.08 r_work: 0.3142 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24325 Z= 0.124 Angle : 0.507 9.458 33295 Z= 0.268 Chirality : 0.040 0.189 3705 Planarity : 0.004 0.040 4033 Dihedral : 13.014 109.009 3901 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.71 % Allowed : 18.49 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.20 (0.16), residues: 2724 helix: 0.66 (0.18), residues: 911 sheet: 0.46 (0.24), residues: 511 loop : -0.27 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.007 0.001 HIS H 29 PHE 0.011 0.001 PHE A 306 TYR 0.015 0.001 TYR E 275 ARG 0.003 0.000 ARG F 283 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 907) hydrogen bonds : angle 4.91584 ( 2473) covalent geometry : bond 0.00287 (24325) covalent geometry : angle 0.50725 (33295) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 236 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8831 (pp) REVERT: A 220 MET cc_start: 0.8478 (mmp) cc_final: 0.8223 (mmt) REVERT: B 97 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8787 (pt) REVERT: E 57 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8478 (tp) REVERT: E 324 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8234 (ptmm) REVERT: G 577 LYS cc_start: 0.8205 (mmtp) cc_final: 0.7964 (mmtp) REVERT: H 94 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6642 (tm-30) REVERT: H 154 GLU cc_start: 0.7540 (tp30) cc_final: 0.7110 (tp30) REVERT: H 173 GLN cc_start: 0.7195 (tm-30) cc_final: 0.5469 (pm20) REVERT: J 15 GLU cc_start: 0.8526 (mp0) cc_final: 0.8295 (mp0) REVERT: J 88 GLU cc_start: 0.8016 (tp30) cc_final: 0.7663 (tp30) outliers start: 91 outliers final: 54 residues processed: 301 average time/residue: 0.3317 time to fit residues: 159.6595 Evaluate side-chains 275 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 218 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 525 LEU Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 267 optimal weight: 8.9990 chunk 129 optimal weight: 0.5980 chunk 151 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 273 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 258 optimal weight: 0.3980 chunk 194 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 104 ASN ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 105 GLN ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.139899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.095927 restraints weight = 36229.435| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.32 r_work: 0.3113 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24325 Z= 0.113 Angle : 0.487 9.518 33295 Z= 0.256 Chirality : 0.039 0.170 3705 Planarity : 0.004 0.042 4033 Dihedral : 12.901 108.641 3901 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.79 % Allowed : 19.43 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.28 (0.16), residues: 2724 helix: 0.77 (0.18), residues: 907 sheet: 0.44 (0.23), residues: 514 loop : -0.24 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 152 HIS 0.006 0.001 HIS H 29 PHE 0.010 0.001 PHE F 306 TYR 0.016 0.001 TYR E 275 ARG 0.003 0.000 ARG F 283 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 907) hydrogen bonds : angle 4.70344 ( 2473) covalent geometry : bond 0.00260 (24325) covalent geometry : angle 0.48654 (33295) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 241 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8752 (pp) REVERT: A 220 MET cc_start: 0.8556 (mmp) cc_final: 0.8333 (mmt) REVERT: B 97 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8683 (pt) REVERT: B 348 GLN cc_start: 0.8295 (pp30) cc_final: 0.8043 (pp30) REVERT: C 183 ASN cc_start: 0.8117 (m-40) cc_final: 0.7833 (m-40) REVERT: D 55 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8590 (tp40) REVERT: E 57 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8434 (tp) REVERT: E 324 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8161 (ptmm) REVERT: G 577 LYS cc_start: 0.8164 (mmtp) cc_final: 0.7941 (mmtp) REVERT: H 94 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6681 (tm-30) REVERT: H 190 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7099 (pm20) outliers start: 93 outliers final: 61 residues processed: 308 average time/residue: 0.3533 time to fit residues: 174.3282 Evaluate side-chains 278 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 212 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 482 ILE Chi-restraints excluded: chain G residue 525 LEU Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 389 PHE Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 24 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 205 optimal weight: 20.0000 chunk 232 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN C 67 GLN C 135 ASN ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 ASN G 520 ASN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN I 265 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.134515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.091605 restraints weight = 36411.985| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.33 r_work: 0.3027 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 24325 Z= 0.249 Angle : 0.596 9.530 33295 Z= 0.315 Chirality : 0.043 0.171 3705 Planarity : 0.004 0.044 4033 Dihedral : 13.031 113.485 3901 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.48 % Allowed : 19.47 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.10 (0.16), residues: 2724 helix: 0.47 (0.17), residues: 897 sheet: 0.26 (0.23), residues: 509 loop : -0.49 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 152 HIS 0.006 0.001 HIS B 84 PHE 0.016 0.002 PHE B 89 TYR 0.020 0.002 TYR B 275 ARG 0.006 0.000 ARG H 168 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 907) hydrogen bonds : angle 4.97923 ( 2473) covalent geometry : bond 0.00597 (24325) covalent geometry : angle 0.59571 (33295) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 224 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8868 (pp) REVERT: B 97 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8836 (pt) REVERT: B 348 GLN cc_start: 0.8268 (pp30) cc_final: 0.7909 (pp30) REVERT: E 324 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8141 (ptmm) REVERT: F 156 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7720 (pp) REVERT: G 577 LYS cc_start: 0.8115 (mmtp) cc_final: 0.7902 (mmtp) REVERT: H 94 GLU cc_start: 0.7517 (mm-30) cc_final: 0.6773 (tm-30) REVERT: J 15 GLU cc_start: 0.8417 (mp0) cc_final: 0.8163 (mp0) REVERT: J 39 ARG cc_start: 0.7844 (mmm160) cc_final: 0.7186 (mtp-110) outliers start: 110 outliers final: 76 residues processed: 303 average time/residue: 0.3382 time to fit residues: 165.6040 Evaluate side-chains 295 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 216 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 153 ASN Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 482 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 389 PHE Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 131 optimal weight: 0.8980 chunk 219 optimal weight: 10.0000 chunk 241 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 201 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 chunk 265 optimal weight: 9.9990 chunk 180 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN H 105 GLN I 265 HIS I 296 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.135954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.091988 restraints weight = 36207.047| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.30 r_work: 0.3056 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24325 Z= 0.182 Angle : 0.544 9.579 33295 Z= 0.286 Chirality : 0.041 0.174 3705 Planarity : 0.004 0.046 4033 Dihedral : 12.959 110.707 3901 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.60 % Allowed : 19.67 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.09 (0.16), residues: 2724 helix: 0.52 (0.17), residues: 902 sheet: 0.22 (0.23), residues: 511 loop : -0.50 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.006 0.001 HIS B 84 PHE 0.012 0.001 PHE B 89 TYR 0.015 0.001 TYR B 275 ARG 0.003 0.000 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 907) hydrogen bonds : angle 4.83279 ( 2473) covalent geometry : bond 0.00432 (24325) covalent geometry : angle 0.54439 (33295) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 217 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8852 (pp) REVERT: A 75 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7962 (t80) REVERT: A 346 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7343 (mpp) REVERT: B 97 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8803 (pt) REVERT: B 348 GLN cc_start: 0.8281 (pp30) cc_final: 0.7867 (pp30) REVERT: E 180 ASP cc_start: 0.8513 (t0) cc_final: 0.8134 (t0) REVERT: E 324 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8078 (ptmm) REVERT: F 156 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7684 (pp) REVERT: G 577 LYS cc_start: 0.8144 (mmtp) cc_final: 0.7928 (mmtp) REVERT: H 94 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6671 (tm-30) REVERT: I 333 ASN cc_start: 0.8765 (t0) cc_final: 0.8504 (t0) REVERT: J 39 ARG cc_start: 0.7988 (mmm160) cc_final: 0.7312 (mtp-110) REVERT: J 137 TYR cc_start: 0.7234 (m-80) cc_final: 0.6822 (m-80) outliers start: 113 outliers final: 85 residues processed: 300 average time/residue: 0.3323 time to fit residues: 161.2669 Evaluate side-chains 301 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 211 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 153 ASN Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 389 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 108 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 149 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 153 ASN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN I 265 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.136295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.092362 restraints weight = 36282.516| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.31 r_work: 0.3059 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24325 Z= 0.171 Angle : 0.540 9.618 33295 Z= 0.283 Chirality : 0.041 0.183 3705 Planarity : 0.004 0.045 4033 Dihedral : 12.940 110.737 3901 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.97 % Allowed : 19.67 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.09 (0.16), residues: 2724 helix: 0.52 (0.17), residues: 909 sheet: 0.23 (0.24), residues: 510 loop : -0.50 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 247 HIS 0.006 0.001 HIS B 84 PHE 0.020 0.001 PHE H 31 TYR 0.015 0.001 TYR E 275 ARG 0.003 0.000 ARG H 175 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 907) hydrogen bonds : angle 4.79565 ( 2473) covalent geometry : bond 0.00407 (24325) covalent geometry : angle 0.53957 (33295) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 226 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8847 (pp) REVERT: A 75 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8027 (t80) REVERT: B 97 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8798 (pt) REVERT: B 348 GLN cc_start: 0.8301 (pp30) cc_final: 0.7856 (pp30) REVERT: C 275 TYR cc_start: 0.7780 (p90) cc_final: 0.7388 (p90) REVERT: E 57 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8452 (tp) REVERT: E 180 ASP cc_start: 0.8514 (t0) cc_final: 0.8125 (t0) REVERT: E 324 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8078 (ptmm) REVERT: F 156 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7677 (pp) REVERT: H 94 GLU cc_start: 0.7421 (mm-30) cc_final: 0.6594 (tm-30) REVERT: I 333 ASN cc_start: 0.8765 (t0) cc_final: 0.8516 (t0) REVERT: J 15 GLU cc_start: 0.8437 (mp0) cc_final: 0.8189 (mp0) REVERT: J 39 ARG cc_start: 0.8002 (mmm160) cc_final: 0.7310 (mtp-110) REVERT: J 137 TYR cc_start: 0.7278 (m-80) cc_final: 0.6955 (m-80) outliers start: 122 outliers final: 97 residues processed: 314 average time/residue: 0.3376 time to fit residues: 171.1331 Evaluate side-chains 322 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 220 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 153 ASN Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 482 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 389 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 135 optimal weight: 0.6980 chunk 101 optimal weight: 0.0870 chunk 96 optimal weight: 0.6980 chunk 212 optimal weight: 8.9990 chunk 184 optimal weight: 0.0270 chunk 44 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 268 optimal weight: 0.7980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN B 42 GLN E 153 ASN E 290 HIS I 265 HIS J 31 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096905 restraints weight = 36042.369| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.33 r_work: 0.3118 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24325 Z= 0.097 Angle : 0.493 9.560 33295 Z= 0.258 Chirality : 0.039 0.189 3705 Planarity : 0.004 0.049 4033 Dihedral : 12.831 109.837 3901 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.34 % Allowed : 21.43 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.18 (0.16), residues: 2724 helix: 0.80 (0.18), residues: 908 sheet: 0.33 (0.24), residues: 508 loop : -0.36 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 247 HIS 0.005 0.001 HIS H 29 PHE 0.012 0.001 PHE F 306 TYR 0.018 0.001 TYR E 275 ARG 0.004 0.000 ARG H 103 Details of bonding type rmsd hydrogen bonds : bond 0.02998 ( 907) hydrogen bonds : angle 4.54246 ( 2473) covalent geometry : bond 0.00216 (24325) covalent geometry : angle 0.49323 (33295) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 248 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8738 (pp) REVERT: A 80 TYR cc_start: 0.8117 (t80) cc_final: 0.7816 (t80) REVERT: A 96 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: B 97 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8663 (pt) REVERT: B 348 GLN cc_start: 0.8135 (pp30) cc_final: 0.7763 (pp30) REVERT: C 183 ASN cc_start: 0.8100 (m-40) cc_final: 0.7818 (m-40) REVERT: C 275 TYR cc_start: 0.7589 (p90) cc_final: 0.7280 (p90) REVERT: E 57 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8425 (tp) REVERT: E 180 ASP cc_start: 0.8420 (t0) cc_final: 0.8027 (t0) REVERT: E 324 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8063 (ptmm) REVERT: H 94 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6589 (tm-30) REVERT: H 102 ARG cc_start: 0.5206 (mtt180) cc_final: 0.4524 (mtt-85) REVERT: I 333 ASN cc_start: 0.8766 (t0) cc_final: 0.8541 (t0) REVERT: I 386 ASN cc_start: 0.8052 (t0) cc_final: 0.7804 (t0) REVERT: J 39 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7337 (mtp-110) REVERT: J 88 GLU cc_start: 0.7626 (tp30) cc_final: 0.7374 (tp30) REVERT: J 137 TYR cc_start: 0.7204 (m-80) cc_final: 0.6913 (m-80) outliers start: 82 outliers final: 61 residues processed: 310 average time/residue: 0.3463 time to fit residues: 170.6364 Evaluate side-chains 290 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 225 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 153 ASN Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 67 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 184 optimal weight: 0.0060 chunk 258 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS J 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.096660 restraints weight = 35864.128| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.31 r_work: 0.3114 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24325 Z= 0.106 Angle : 0.507 10.065 33295 Z= 0.263 Chirality : 0.039 0.172 3705 Planarity : 0.004 0.055 4033 Dihedral : 12.775 108.693 3901 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.22 % Allowed : 21.47 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.23 (0.16), residues: 2724 helix: 0.78 (0.17), residues: 921 sheet: 0.38 (0.24), residues: 512 loop : -0.31 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 539 HIS 0.008 0.001 HIS J 31 PHE 0.011 0.001 PHE F 306 TYR 0.014 0.001 TYR E 275 ARG 0.003 0.000 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 907) hydrogen bonds : angle 4.52431 ( 2473) covalent geometry : bond 0.00243 (24325) covalent geometry : angle 0.50732 (33295) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 229 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8707 (pp) REVERT: A 96 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: B 97 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8644 (pt) REVERT: B 348 GLN cc_start: 0.7987 (pp30) cc_final: 0.7776 (pp30) REVERT: C 183 ASN cc_start: 0.8023 (m-40) cc_final: 0.7765 (m-40) REVERT: C 275 TYR cc_start: 0.7511 (p90) cc_final: 0.7280 (p90) REVERT: E 57 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8393 (tp) REVERT: E 180 ASP cc_start: 0.8432 (t0) cc_final: 0.8022 (t0) REVERT: E 324 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8036 (ptmm) REVERT: H 94 GLU cc_start: 0.7441 (mm-30) cc_final: 0.6618 (tm-30) REVERT: H 102 ARG cc_start: 0.5207 (mtt180) cc_final: 0.4473 (mtt-85) REVERT: H 154 GLU cc_start: 0.7383 (tp30) cc_final: 0.6763 (tp30) REVERT: I 333 ASN cc_start: 0.8799 (t0) cc_final: 0.8581 (t0) REVERT: J 15 GLU cc_start: 0.8407 (mp0) cc_final: 0.8181 (mp0) REVERT: J 39 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7278 (mtp-110) REVERT: J 137 TYR cc_start: 0.7223 (m-80) cc_final: 0.6902 (m-80) outliers start: 79 outliers final: 65 residues processed: 284 average time/residue: 0.3440 time to fit residues: 155.6464 Evaluate side-chains 299 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 230 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 153 ASN Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 256 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 223 optimal weight: 10.0000 chunk 236 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN E 153 ASN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN I 265 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.139272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095252 restraints weight = 36195.967| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.32 r_work: 0.3094 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24325 Z= 0.128 Angle : 0.521 10.192 33295 Z= 0.270 Chirality : 0.040 0.171 3705 Planarity : 0.004 0.057 4033 Dihedral : 12.782 108.275 3901 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.10 % Allowed : 21.87 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.20 (0.16), residues: 2724 helix: 0.76 (0.17), residues: 922 sheet: 0.38 (0.24), residues: 510 loop : -0.33 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 247 HIS 0.005 0.001 HIS H 29 PHE 0.020 0.001 PHE J 17 TYR 0.018 0.001 TYR E 275 ARG 0.003 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 907) hydrogen bonds : angle 4.55978 ( 2473) covalent geometry : bond 0.00299 (24325) covalent geometry : angle 0.52118 (33295) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 232 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8812 (pp) REVERT: A 96 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: B 348 GLN cc_start: 0.8072 (pp30) cc_final: 0.7856 (pp30) REVERT: C 183 ASN cc_start: 0.8125 (m-40) cc_final: 0.7840 (m-40) REVERT: C 275 TYR cc_start: 0.7610 (p90) cc_final: 0.7396 (p90) REVERT: E 57 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8445 (tp) REVERT: E 180 ASP cc_start: 0.8513 (t0) cc_final: 0.8117 (t0) REVERT: E 324 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8097 (ptmm) REVERT: H 94 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6599 (tm-30) REVERT: H 102 ARG cc_start: 0.5215 (mtt180) cc_final: 0.4432 (mtt-85) REVERT: H 154 GLU cc_start: 0.7476 (tp30) cc_final: 0.6916 (tp30) REVERT: I 333 ASN cc_start: 0.8782 (t0) cc_final: 0.8559 (t0) REVERT: J 15 GLU cc_start: 0.8420 (mp0) cc_final: 0.8175 (mp0) REVERT: J 39 ARG cc_start: 0.8003 (mmm160) cc_final: 0.7320 (mtp-110) REVERT: J 137 TYR cc_start: 0.7230 (m-80) cc_final: 0.6911 (m-80) outliers start: 76 outliers final: 66 residues processed: 289 average time/residue: 0.3465 time to fit residues: 159.9300 Evaluate side-chains 290 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 221 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 153 ASN Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 255 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 274 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 153 ASN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.137508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095482 restraints weight = 35996.935| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.38 r_work: 0.3082 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24325 Z= 0.166 Angle : 0.548 9.915 33295 Z= 0.286 Chirality : 0.041 0.169 3705 Planarity : 0.004 0.056 4033 Dihedral : 12.842 109.469 3901 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.05 % Allowed : 21.87 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.12 (0.16), residues: 2724 helix: 0.67 (0.17), residues: 913 sheet: 0.33 (0.24), residues: 510 loop : -0.36 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 152 HIS 0.006 0.001 HIS B 84 PHE 0.020 0.001 PHE J 17 TYR 0.015 0.001 TYR B 275 ARG 0.003 0.000 ARG H 168 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 907) hydrogen bonds : angle 4.66152 ( 2473) covalent geometry : bond 0.00397 (24325) covalent geometry : angle 0.54806 (33295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14836.35 seconds wall clock time: 257 minutes 32.75 seconds (15452.75 seconds total)