Starting phenix.real_space_refine on Sat Jul 4 00:00:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nb1_49206/07_2026/9nb1_49206.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nb1_49206/07_2026/9nb1_49206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nb1_49206/07_2026/9nb1_49206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nb1_49206/07_2026/9nb1_49206.map" model { file = "/net/cci-nas-00/data/ceres_data/9nb1_49206/07_2026/9nb1_49206.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nb1_49206/07_2026/9nb1_49206.cif" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 58 5.49 5 S 99 5.16 5 C 10290 2.51 5 N 2895 2.21 5 O 3221 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16565 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 652 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "C" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 903 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "E" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 670 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 579 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "G" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2425 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 11, 'TRANS': 294} Chain breaks: 1 Chain: "K" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "Y" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 599 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 12, 'rna3p_pyr': 7} Link IDs: {'rna2p': 9, 'rna3p': 18} Chain: "Z" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 630 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 15} Link IDs: {'rna2p': 6, 'rna3p': 23} Chain: "B" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 612 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 792 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "H" Number of atoms: 3951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3951 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 475} Chain breaks: 1 Chain: "I" Number of atoms: 4070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4070 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 23, 'TRANS': 488} Chain breaks: 2 Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.79, per 1000 atoms: 0.17 Number of scatterers: 16565 At special positions: 0 Unit cell: (112.885, 124.49, 155.085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 99 16.00 P 58 15.00 O 3221 8.00 N 2895 7.00 C 10290 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: 0.97 Conformation dependent library (CDL) restraints added in 460.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 701 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 73 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 158 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 71 " pdb=" ZN H 702 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 76 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 418 " 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3616 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 17 sheets defined 37.3% alpha, 18.2% beta 16 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.554A pdb=" N LYS A 78 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.759A pdb=" N LYS A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 16 removed outlier: 4.433A pdb=" N ILE C 12 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 24 removed outlier: 4.241A pdb=" N LEU C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 89 through 107 removed outlier: 5.550A pdb=" N GLU C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN C 106 " --> pdb=" O HIS C 102 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 Processing helix chain 'F' and resid 6 through 13 Processing helix chain 'G' and resid 63 through 67 removed outlier: 3.858A pdb=" N SER G 66 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE G 67 " --> pdb=" O GLY G 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 63 through 67' Processing helix chain 'J' and resid 31 through 45 removed outlier: 3.988A pdb=" N VAL J 37 " --> pdb=" O SER J 33 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU J 45 " --> pdb=" O ASN J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 64 removed outlier: 4.547A pdb=" N VAL J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN J 64 " --> pdb=" O GLU J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 68 No H-bonds generated for 'chain 'J' and resid 66 through 68' Processing helix chain 'J' and resid 69 through 79 removed outlier: 3.544A pdb=" N PHE J 73 " --> pdb=" O LEU J 69 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASP J 75 " --> pdb=" O ASP J 71 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLU J 76 " --> pdb=" O ASN J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 83 removed outlier: 3.716A pdb=" N ASP J 83 " --> pdb=" O PHE J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 80 through 83' Processing helix chain 'J' and resid 85 through 103 removed outlier: 3.935A pdb=" N ARG J 89 " --> pdb=" O SER J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 111 Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 123 through 147 removed outlier: 4.008A pdb=" N GLN J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS J 138 " --> pdb=" O THR J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 removed outlier: 3.580A pdb=" N ASP J 159 " --> pdb=" O GLU J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 176 through 194 removed outlier: 3.898A pdb=" N GLY J 189 " --> pdb=" O LYS J 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR J 193 " --> pdb=" O GLY J 189 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 216 removed outlier: 3.594A pdb=" N ARG J 215 " --> pdb=" O SER J 212 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE J 216 " --> pdb=" O LEU J 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 212 through 216' Processing helix chain 'J' and resid 224 through 243 removed outlier: 3.709A pdb=" N MET J 243 " --> pdb=" O LEU J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 267 Processing helix chain 'J' and resid 270 through 284 removed outlier: 4.289A pdb=" N GLN J 276 " --> pdb=" O SER J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 309 removed outlier: 3.591A pdb=" N LEU J 309 " --> pdb=" O LEU J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 316 removed outlier: 6.015A pdb=" N ALA J 313 " --> pdb=" O LYS J 310 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU J 315 " --> pdb=" O PRO J 312 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU J 316 " --> pdb=" O ALA J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 329 removed outlier: 4.400A pdb=" N THR J 323 " --> pdb=" O ALA J 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 331 through 338 removed outlier: 3.990A pdb=" N ASN J 338 " --> pdb=" O GLU J 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 716 through 722 removed outlier: 4.103A pdb=" N ARG K 721 " --> pdb=" O ILE K 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 13 removed outlier: 3.681A pdb=" N ILE B 13 " --> pdb=" O LEU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 77 removed outlier: 3.912A pdb=" N LEU B 77 " --> pdb=" O GLY B 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'D' and resid 143 through 148 removed outlier: 3.551A pdb=" N ARG D 147 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 166 Processing helix chain 'H' and resid 48 through 52 removed outlier: 3.605A pdb=" N ASP H 51 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA H 52 " --> pdb=" O GLY H 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 48 through 52' Processing helix chain 'H' and resid 55 through 59 removed outlier: 3.543A pdb=" N LEU H 58 " --> pdb=" O TYR H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.574A pdb=" N GLU H 63 " --> pdb=" O ASP H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 78 Processing helix chain 'H' and resid 79 through 86 Processing helix chain 'H' and resid 97 through 107 removed outlier: 4.030A pdb=" N TRP H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 116 removed outlier: 3.974A pdb=" N ILE H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 130 removed outlier: 3.946A pdb=" N GLU H 130 " --> pdb=" O THR H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 135 removed outlier: 3.726A pdb=" N ILE H 135 " --> pdb=" O MET H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 232 Processing helix chain 'H' and resid 245 through 260 Processing helix chain 'H' and resid 274 through 285 removed outlier: 4.604A pdb=" N ALA H 280 " --> pdb=" O LYS H 276 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL H 281 " --> pdb=" O LYS H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 297 removed outlier: 3.775A pdb=" N GLN H 296 " --> pdb=" O LYS H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 317 removed outlier: 3.650A pdb=" N PHE H 317 " --> pdb=" O MET H 314 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 344 Processing helix chain 'H' and resid 362 through 367 Processing helix chain 'H' and resid 368 through 370 No H-bonds generated for 'chain 'H' and resid 368 through 370' Processing helix chain 'H' and resid 398 through 410 Processing helix chain 'H' and resid 420 through 435 removed outlier: 3.588A pdb=" N TYR H 435 " --> pdb=" O LEU H 431 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 472 Processing helix chain 'I' and resid 42 through 50 removed outlier: 4.026A pdb=" N ASP I 46 " --> pdb=" O MET I 42 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER I 47 " --> pdb=" O ASP I 43 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS I 50 " --> pdb=" O ASP I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 69 Processing helix chain 'I' and resid 69 through 77 removed outlier: 4.692A pdb=" N TYR I 73 " --> pdb=" O GLY I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 107 removed outlier: 4.074A pdb=" N MET I 96 " --> pdb=" O LYS I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 123 Processing helix chain 'I' and resid 211 through 229 Processing helix chain 'I' and resid 242 through 257 Processing helix chain 'I' and resid 261 through 265 removed outlier: 3.605A pdb=" N TYR I 264 " --> pdb=" O LEU I 261 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER I 265 " --> pdb=" O GLY I 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 261 through 265' Processing helix chain 'I' and resid 272 through 281 Processing helix chain 'I' and resid 283 through 287 Processing helix chain 'I' and resid 288 through 298 Processing helix chain 'I' and resid 313 through 319 removed outlier: 3.820A pdb=" N ARG I 319 " --> pdb=" O SER I 315 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 345 removed outlier: 4.177A pdb=" N ARG I 339 " --> pdb=" O CYS I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 363 through 370 Processing helix chain 'I' and resid 548 through 556 removed outlier: 3.939A pdb=" N ILE I 553 " --> pdb=" O ILE I 549 " (cutoff:3.500A) Processing helix chain 'I' and resid 567 through 582 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.646A pdb=" N ALA A 56 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN A 60 " --> pdb=" O ALA G 72 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET G 69 " --> pdb=" O LYS G 20 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS G 20 " --> pdb=" O MET G 69 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL G 41 " --> pdb=" O ARG G 32 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL G 60 " --> pdb=" O ILE G 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.646A pdb=" N ALA A 56 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE A 46 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG A 29 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL A 48 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 27 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N ILE A 17 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A 73 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR A 19 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU A 71 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU A 21 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B 69 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS B 64 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE B 48 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL B 66 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ASP B 46 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY B 68 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE B 41 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS B 45 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE B 28 " --> pdb=" O CYS B 45 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU B 47 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 26 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR B 15 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 20 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER B 79 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG C 53 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D 347 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 197 " --> pdb=" O VAL D 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 72 through 75 removed outlier: 3.919A pdb=" N LYS E 72 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA E 61 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU E 56 " --> pdb=" O PHE E 50 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE E 50 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU E 58 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE E 48 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASP E 60 " --> pdb=" O CYS E 46 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N CYS E 46 " --> pdb=" O ASP E 60 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU E 44 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N MET E 41 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU E 35 " --> pdb=" O MET E 41 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE E 43 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU E 86 " --> pdb=" O TRP E 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 77 through 79 removed outlier: 3.664A pdb=" N ILE F 72 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LYS F 22 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE F 72 " --> pdb=" O MET F 20 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET F 20 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY F 31 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N MET F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS F 30 " --> pdb=" O GLU F 48 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR F 32 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN F 46 " --> pdb=" O TYR F 32 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN F 43 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL F 62 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA F 45 " --> pdb=" O GLY F 60 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY F 60 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR F 47 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N HIS F 58 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU F 49 " --> pdb=" O SER F 56 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU F 61 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N HIS D 172 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N VAL D 356 " --> pdb=" O ASN D 170 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN D 170 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY D 181 " --> pdb=" O ILE D 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 26 through 27 removed outlier: 4.204A pdb=" N HIS G 26 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN G 53 " --> pdb=" O ALA G 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 203 through 206 Processing sheet with id=AA7, first strand: chain 'H' and resid 137 through 138 removed outlier: 6.432A pdb=" N ILE H 138 " --> pdb=" O THR H 93 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N MET H 95 " --> pdb=" O ILE H 138 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU H 67 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N THR H 96 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LYS H 36 " --> pdb=" O LEU H 66 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N LEU H 68 " --> pdb=" O LYS H 36 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET H 38 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE H 29 " --> pdb=" O ARG H 15 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 144 through 146 removed outlier: 3.614A pdb=" N PHE H 151 " --> pdb=" O LYS H 144 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR H 176 " --> pdb=" O PHE H 165 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY H 419 " --> pdb=" O SER H 205 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 308 through 310 removed outlier: 6.130A pdb=" N ILE H 268 " --> pdb=" O SER H 309 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY H 236 " --> pdb=" O VAL H 325 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA H 327 " --> pdb=" O GLY H 236 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE H 238 " --> pdb=" O ALA H 327 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU H 237 " --> pdb=" O ILE H 353 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 373 through 375 removed outlier: 3.896A pdb=" N LEU H 382 " --> pdb=" O ILE H 374 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 464 through 466 removed outlier: 5.498A pdb=" N LYS H 465 " --> pdb=" O ILE H 494 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU I 701 " --> pdb=" O VAL I 634 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP I 636 " --> pdb=" O THR I 699 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ARG I 609 " --> pdb=" O LEU I 700 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 127 through 129 removed outlier: 6.201A pdb=" N ILE I 84 " --> pdb=" O GLN I 127 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU I 129 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA I 86 " --> pdb=" O LEU I 129 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL I 58 " --> pdb=" O TYR I 85 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N THR I 87 " --> pdb=" O VAL I 58 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU I 59 " --> pdb=" O ARG I 29 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU I 31 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU I 7 " --> pdb=" O VAL I 597 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 135 through 136 removed outlier: 3.796A pdb=" N VAL I 135 " --> pdb=" O ILE I 146 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 149 through 150 Processing sheet with id=AB6, first strand: chain 'I' and resid 170 through 172 removed outlier: 7.360A pdb=" N VAL I 171 " --> pdb=" O ILE I 199 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ASP I 201 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU I 198 " --> pdb=" O ILE I 562 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL I 564 " --> pdb=" O LEU I 198 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N THR I 200 " --> pdb=" O VAL I 564 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'I' and resid 310 through 311 removed outlier: 5.593A pdb=" N LEU I 268 " --> pdb=" O CYS I 311 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU I 327 " --> pdb=" O ALA I 267 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL I 233 " --> pdb=" O VAL I 326 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU I 234 " --> pdb=" O ILE I 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 375 through 384 removed outlier: 3.570A pdb=" N ILE I 376 " --> pdb=" O ILE I 529 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.22 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: 5146 1.34 - 1.46: 3277 1.46 - 1.58: 8279 1.58 - 1.70: 115 1.70 - 1.82: 165 Bond restraints: 16982 Sorted by residual: bond pdb=" N ASP G 35 " pdb=" CA ASP G 35 " ideal model delta sigma weight residual 1.456 1.430 0.026 1.04e-02 9.25e+03 6.14e+00 bond pdb=" CG GLU J 188 " pdb=" CD GLU J 188 " ideal model delta sigma weight residual 1.516 1.455 0.061 2.50e-02 1.60e+03 5.90e+00 bond pdb=" CA LYS I 164 " pdb=" C LYS I 164 " ideal model delta sigma weight residual 1.523 1.552 -0.030 1.24e-02 6.50e+03 5.72e+00 bond pdb=" CA ARG I 299 " pdb=" CB ARG I 299 " ideal model delta sigma weight residual 1.524 1.553 -0.028 1.30e-02 5.92e+03 4.77e+00 bond pdb=" CA LEU J 171 " pdb=" C LEU J 171 " ideal model delta sigma weight residual 1.518 1.589 -0.071 4.01e-02 6.22e+02 3.13e+00 ... (remaining 16977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 22499 2.30 - 4.61: 552 4.61 - 6.91: 118 6.91 - 9.21: 32 9.21 - 11.52: 7 Bond angle restraints: 23208 Sorted by residual: angle pdb=" N ILE E 48 " pdb=" CA ILE E 48 " pdb=" C ILE E 48 " ideal model delta sigma weight residual 112.96 107.67 5.29 1.00e+00 1.00e+00 2.80e+01 angle pdb=" N GLY H 335 " pdb=" CA GLY H 335 " pdb=" C GLY H 335 " ideal model delta sigma weight residual 112.37 121.67 -9.30 1.84e+00 2.95e-01 2.55e+01 angle pdb=" N GLU H 255 " pdb=" CA GLU H 255 " pdb=" CB GLU H 255 " ideal model delta sigma weight residual 110.28 117.40 -7.12 1.55e+00 4.16e-01 2.11e+01 angle pdb=" C1' C Y 44 " pdb=" N1 C Y 44 " pdb=" C2 C Y 44 " ideal model delta sigma weight residual 118.80 123.65 -4.85 1.10e+00 8.26e-01 1.95e+01 angle pdb=" N ASP G 35 " pdb=" CA ASP G 35 " pdb=" CB ASP G 35 " ideal model delta sigma weight residual 111.10 106.49 4.61 1.05e+00 9.07e-01 1.93e+01 ... (remaining 23203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.32: 9737 26.32 - 52.65: 527 52.65 - 78.97: 107 78.97 - 105.29: 15 105.29 - 131.62: 1 Dihedral angle restraints: 10387 sinusoidal: 4813 harmonic: 5574 Sorted by residual: dihedral pdb=" CA ARG H 488 " pdb=" C ARG H 488 " pdb=" N ASN H 489 " pdb=" CA ASN H 489 " ideal model delta harmonic sigma weight residual 180.00 152.24 27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA TYR I 264 " pdb=" C TYR I 264 " pdb=" N SER I 265 " pdb=" CA SER I 265 " ideal model delta harmonic sigma weight residual 180.00 154.66 25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA MET H 95 " pdb=" C MET H 95 " pdb=" N THR H 96 " pdb=" CA THR H 96 " ideal model delta harmonic sigma weight residual -180.00 -155.60 -24.40 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 10384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2044 0.054 - 0.107: 507 0.107 - 0.161: 128 0.161 - 0.214: 12 0.214 - 0.268: 5 Chirality restraints: 2696 Sorted by residual: chirality pdb=" C3' A Y 49 " pdb=" C4' A Y 49 " pdb=" O3' A Y 49 " pdb=" C2' A Y 49 " both_signs ideal model delta sigma weight residual False -2.48 -2.21 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE F 51 " pdb=" CA ILE F 51 " pdb=" CG1 ILE F 51 " pdb=" CG2 ILE F 51 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LYS I 164 " pdb=" N LYS I 164 " pdb=" C LYS I 164 " pdb=" CB LYS I 164 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2693 not shown) Planarity restraints: 2754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 158 " 0.030 2.00e-02 2.50e+03 2.70e-02 1.82e+01 pdb=" CG TRP J 158 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP J 158 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP J 158 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP J 158 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 158 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 158 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 158 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 158 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP J 158 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU I 703 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO I 704 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO I 704 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 704 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 34 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C PHE G 34 " 0.049 2.00e-02 2.50e+03 pdb=" O PHE G 34 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP G 35 " -0.016 2.00e-02 2.50e+03 ... (remaining 2751 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 703 2.73 - 3.27: 16332 3.27 - 3.81: 26826 3.81 - 4.36: 31504 4.36 - 4.90: 52727 Nonbonded interactions: 128092 Sorted by model distance: nonbonded pdb=" OD2 ASP H 75 " pdb="ZN ZN H 702 " model vdw 2.186 2.230 nonbonded pdb=" OD1 ASP G 35 " pdb=" CD PRO G 36 " model vdw 2.420 3.440 nonbonded pdb=" O ASN E 83 " pdb=" ND2 ASN E 83 " model vdw 2.454 3.120 nonbonded pdb=" O LEU H 251 " pdb=" OE1 GLU H 255 " model vdw 2.515 3.040 nonbonded pdb=" OG SER I 3 " pdb=" OE1 GLU I 168 " model vdw 2.538 3.040 ... (remaining 128087 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.350 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.440 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 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 : 0.004 0.071 16987 Z= 0.188 Angle : 0.911 11.516 23208 Z= 0.480 Chirality : 0.051 0.268 2696 Planarity : 0.006 0.080 2754 Dihedral : 15.994 131.618 6771 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.93 % Favored : 93.91 % Rotamer: Outliers : 0.23 % Allowed : 0.35 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.18), residues: 1888 helix: -1.08 (0.19), residues: 606 sheet: -0.99 (0.31), residues: 297 loop : -1.51 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 488 TYR 0.030 0.002 TYR J 278 PHE 0.029 0.002 PHE G 34 TRP 0.073 0.003 TRP J 158 HIS 0.009 0.001 HIS D 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (16982) covalent geometry : angle 0.91084 / 0.48 (23208) hydrogen bonds : bond 0.17958 / 11.56 ( 605) hydrogen bonds : angle 7.56987 / 5.34 ( 1664) metal coordination : bond 0.00537 / 0.28 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 325 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 VAL cc_start: 0.8893 (m) cc_final: 0.8653 (m) REVERT: C 70 ASP cc_start: 0.8295 (p0) cc_final: 0.8012 (p0) REVERT: C 87 ASP cc_start: 0.7448 (m-30) cc_final: 0.6694 (p0) REVERT: F 19 VAL cc_start: 0.9008 (m) cc_final: 0.8724 (p) REVERT: G 32 ARG cc_start: 0.8689 (tpp-160) cc_final: 0.8452 (mmt90) REVERT: J 105 GLU cc_start: 0.8091 (tp30) cc_final: 0.6854 (pt0) REVERT: J 271 MET cc_start: 0.8245 (ppp) cc_final: 0.7289 (mmt) REVERT: J 300 ASN cc_start: 0.8112 (m110) cc_final: 0.7601 (p0) REVERT: K 716 ASP cc_start: 0.7542 (m-30) cc_final: 0.7225 (m-30) REVERT: B 11 GLN cc_start: 0.8361 (pm20) cc_final: 0.8045 (pm20) REVERT: B 41 ILE cc_start: 0.8095 (tp) cc_final: 0.7334 (mt) REVERT: H 150 LYS cc_start: 0.7662 (mttm) cc_final: 0.6958 (pttt) REVERT: H 289 MET cc_start: 0.6752 (mmp) cc_final: 0.6193 (tpp) REVERT: H 376 THR cc_start: 0.7806 (m) cc_final: 0.7283 (p) REVERT: H 386 MET cc_start: 0.7454 (ttt) cc_final: 0.7044 (ttt) REVERT: I 167 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: I 374 GLU cc_start: 0.6524 (mm-30) cc_final: 0.5584 (mm-30) REVERT: I 378 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7650 (mm-30) outliers start: 4 outliers final: 2 residues processed: 328 average time/residue: 0.0973 time to fit residues: 51.2487 Evaluate side-chains 259 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 256 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 164 LYS Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain I residue 168 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 40 HIS C 102 HIS E 83 ASN F 43 GLN F 68 ASN G 26 HIS J 42 GLN J 81 GLN ** J 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 252 ASN J 266 GLN J 311 HIS ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 371 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.129454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.104356 restraints weight = 39937.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.106997 restraints weight = 24180.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.108850 restraints weight = 17187.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.110087 restraints weight = 13581.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.111024 restraints weight = 11578.301| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16987 Z= 0.179 Angle : 0.694 8.944 23208 Z= 0.361 Chirality : 0.046 0.214 2696 Planarity : 0.005 0.070 2754 Dihedral : 14.500 134.803 2951 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.72 % Favored : 94.23 % Rotamer: Outliers : 2.00 % Allowed : 9.98 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.18), residues: 1888 helix: -0.55 (0.20), residues: 606 sheet: -0.77 (0.30), residues: 313 loop : -1.52 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 488 TYR 0.047 0.002 TYR J 278 PHE 0.022 0.002 PHE H 469 TRP 0.040 0.002 TRP J 158 HIS 0.006 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (16982) covalent geometry : angle 0.69363 / 0.36 (23208) hydrogen bonds : bond 0.05049 / 3.35 ( 605) hydrogen bonds : angle 5.94876 / 4.15 ( 1664) metal coordination : bond 0.00543 / 0.32 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 272 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7589 (tp30) REVERT: A 38 ASN cc_start: 0.7135 (t0) cc_final: 0.6670 (t0) REVERT: C 47 ASP cc_start: 0.8146 (p0) cc_final: 0.7864 (p0) REVERT: C 70 ASP cc_start: 0.8325 (p0) cc_final: 0.7908 (p0) REVERT: C 102 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.7503 (t-90) REVERT: F 43 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.7059 (pp30) REVERT: G 8 GLU cc_start: 0.7001 (pt0) cc_final: 0.6748 (pt0) REVERT: G 32 ARG cc_start: 0.8704 (tpp-160) cc_final: 0.8418 (mmt90) REVERT: J 105 GLU cc_start: 0.8171 (tp30) cc_final: 0.6912 (pt0) REVERT: J 138 LYS cc_start: 0.7142 (mttp) cc_final: 0.6895 (mtmm) REVERT: J 164 MET cc_start: 0.6636 (ttm) cc_final: 0.6164 (ttm) REVERT: J 243 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.6388 (pmm) REVERT: J 271 MET cc_start: 0.8346 (ppp) cc_final: 0.7401 (mmt) REVERT: K 716 ASP cc_start: 0.7893 (m-30) cc_final: 0.7484 (m-30) REVERT: H 84 LEU cc_start: 0.8706 (mm) cc_final: 0.8480 (mt) REVERT: H 122 LEU cc_start: 0.8283 (mt) cc_final: 0.7986 (mp) REVERT: H 150 LYS cc_start: 0.7854 (mttm) cc_final: 0.7145 (pttt) REVERT: H 255 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: H 289 MET cc_start: 0.7047 (mmp) cc_final: 0.6501 (tpp) REVERT: H 386 MET cc_start: 0.7691 (ttt) cc_final: 0.7331 (ttt) REVERT: I 167 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: I 276 VAL cc_start: 0.7874 (t) cc_final: 0.7654 (t) REVERT: I 374 GLU cc_start: 0.6263 (mm-30) cc_final: 0.5173 (mm-30) REVERT: I 378 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7680 (mm-30) REVERT: I 384 ARG cc_start: 0.7376 (ttp80) cc_final: 0.7156 (ttp80) outliers start: 34 outliers final: 24 residues processed: 289 average time/residue: 0.1021 time to fit residues: 46.7764 Evaluate side-chains 276 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 247 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 225 TYR Chi-restraints excluded: chain J residue 243 MET Chi-restraints excluded: chain J residue 245 HIS Chi-restraints excluded: chain J residue 266 GLN Chi-restraints excluded: chain K residue 715 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 255 GLU Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 309 SER Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain I residue 164 LYS Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 581 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 182 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 76 optimal weight: 0.0570 chunk 185 optimal weight: 5.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 102 HIS ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 252 ASN J 266 GLN ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.131500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.106360 restraints weight = 39986.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.108960 restraints weight = 24683.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.110731 restraints weight = 17800.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.111727 restraints weight = 14237.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.112764 restraints weight = 12325.176| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16987 Z= 0.147 Angle : 0.668 11.125 23208 Z= 0.342 Chirality : 0.045 0.389 2696 Planarity : 0.004 0.066 2754 Dihedral : 14.371 133.611 2948 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.60 % Rotamer: Outliers : 2.29 % Allowed : 13.44 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.18), residues: 1888 helix: -0.39 (0.20), residues: 606 sheet: -0.84 (0.29), residues: 328 loop : -1.46 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 265 TYR 0.017 0.002 TYR I 207 PHE 0.025 0.002 PHE D 339 TRP 0.027 0.001 TRP J 158 HIS 0.011 0.001 HIS C 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (16982) covalent geometry : angle 0.66764 / 0.34 (23208) hydrogen bonds : bond 0.04557 / 3.04 ( 605) hydrogen bonds : angle 5.63981 / 3.90 ( 1664) metal coordination : bond 0.00289 / 0.17 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASN cc_start: 0.7144 (t0) cc_final: 0.6763 (t0) REVERT: C 70 ASP cc_start: 0.8173 (p0) cc_final: 0.7846 (p0) REVERT: C 78 ASN cc_start: 0.7011 (t0) cc_final: 0.6563 (t0) REVERT: F 20 MET cc_start: 0.7686 (tpp) cc_final: 0.7475 (tpt) REVERT: G 8 GLU cc_start: 0.7137 (pt0) cc_final: 0.6755 (pt0) REVERT: G 11 LYS cc_start: 0.8854 (pttt) cc_final: 0.8649 (pttt) REVERT: G 32 ARG cc_start: 0.8614 (tpp-160) cc_final: 0.8342 (mmt90) REVERT: J 105 GLU cc_start: 0.8042 (tp30) cc_final: 0.6907 (pt0) REVERT: J 138 LYS cc_start: 0.7064 (mttp) cc_final: 0.6705 (mtmm) REVERT: J 243 MET cc_start: 0.6670 (ppp) cc_final: 0.6317 (pmm) REVERT: J 271 MET cc_start: 0.8247 (ppp) cc_final: 0.7388 (mmt) REVERT: K 716 ASP cc_start: 0.7457 (m-30) cc_final: 0.7175 (m-30) REVERT: H 150 LYS cc_start: 0.7889 (mttm) cc_final: 0.7218 (pttt) REVERT: H 289 MET cc_start: 0.7024 (mmp) cc_final: 0.6501 (tpp) REVERT: H 386 MET cc_start: 0.7594 (ttt) cc_final: 0.7220 (ttt) REVERT: I 276 VAL cc_start: 0.8098 (t) cc_final: 0.7863 (t) REVERT: I 374 GLU cc_start: 0.6281 (mm-30) cc_final: 0.5154 (mm-30) REVERT: I 378 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7343 (mm-30) REVERT: I 384 ARG cc_start: 0.7440 (ttp80) cc_final: 0.6776 (ptm-80) outliers start: 39 outliers final: 30 residues processed: 282 average time/residue: 0.1049 time to fit residues: 46.1583 Evaluate side-chains 275 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 225 TYR Chi-restraints excluded: chain J residue 266 GLN Chi-restraints excluded: chain K residue 715 ASN Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 424 MET Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 581 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 133 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 102 HIS ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN J 266 GLN D 337 GLN ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.129943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.105437 restraints weight = 39825.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.108037 restraints weight = 26596.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.109701 restraints weight = 17867.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.110304 restraints weight = 14112.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.110757 restraints weight = 13412.231| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16987 Z= 0.149 Angle : 0.643 12.177 23208 Z= 0.329 Chirality : 0.045 0.377 2696 Planarity : 0.004 0.063 2754 Dihedral : 14.241 133.303 2941 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.77 % Favored : 94.17 % Rotamer: Outliers : 2.64 % Allowed : 15.20 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.19), residues: 1888 helix: -0.31 (0.20), residues: 618 sheet: -0.83 (0.29), residues: 336 loop : -1.51 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 265 TYR 0.046 0.002 TYR J 278 PHE 0.027 0.002 PHE I 114 TRP 0.026 0.001 TRP J 158 HIS 0.008 0.001 HIS C 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (16982) covalent geometry : angle 0.64277 / 0.33 (23208) hydrogen bonds : bond 0.04313 / 2.88 ( 605) hydrogen bonds : angle 5.41998 / 3.73 ( 1664) metal coordination : bond 0.00323 / 0.19 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7655 (mm-30) REVERT: A 38 ASN cc_start: 0.7296 (t0) cc_final: 0.7001 (t0) REVERT: C 47 ASP cc_start: 0.8245 (p0) cc_final: 0.7905 (p0) REVERT: C 70 ASP cc_start: 0.8196 (p0) cc_final: 0.7629 (p0) REVERT: C 71 ASP cc_start: 0.7548 (p0) cc_final: 0.7226 (p0) REVERT: C 78 ASN cc_start: 0.7257 (t0) cc_final: 0.6687 (t0) REVERT: E 51 ASP cc_start: 0.7643 (t70) cc_final: 0.7162 (t0) REVERT: G 8 GLU cc_start: 0.7244 (pt0) cc_final: 0.6810 (pt0) REVERT: G 11 LYS cc_start: 0.8919 (pttt) cc_final: 0.8688 (pttt) REVERT: G 32 ARG cc_start: 0.8629 (tpp-160) cc_final: 0.8269 (mmt90) REVERT: J 105 GLU cc_start: 0.8006 (tp30) cc_final: 0.6905 (pt0) REVERT: J 138 LYS cc_start: 0.7099 (mttp) cc_final: 0.6667 (mtmm) REVERT: J 231 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7554 (tp30) REVERT: J 243 MET cc_start: 0.6701 (ppp) cc_final: 0.6402 (pmm) REVERT: J 271 MET cc_start: 0.8252 (ppp) cc_final: 0.7426 (mmt) REVERT: K 716 ASP cc_start: 0.7501 (m-30) cc_final: 0.7183 (m-30) REVERT: H 289 MET cc_start: 0.7084 (mmp) cc_final: 0.6565 (tpp) REVERT: H 386 MET cc_start: 0.7721 (ttt) cc_final: 0.7314 (ttt) REVERT: I 212 ARG cc_start: 0.7969 (mmm160) cc_final: 0.7697 (tpt-90) REVERT: I 276 VAL cc_start: 0.7980 (t) cc_final: 0.7743 (t) REVERT: I 374 GLU cc_start: 0.6359 (mm-30) cc_final: 0.5111 (mm-30) REVERT: I 378 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7445 (mm-30) REVERT: I 384 ARG cc_start: 0.7565 (ttp80) cc_final: 0.6966 (ptm-80) outliers start: 45 outliers final: 36 residues processed: 279 average time/residue: 0.1023 time to fit residues: 44.9321 Evaluate side-chains 279 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 225 TYR Chi-restraints excluded: chain K residue 715 ASN Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 309 SER Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 424 MET Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 581 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 121 optimal weight: 6.9990 chunk 159 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.128683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.104539 restraints weight = 39764.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.107933 restraints weight = 25776.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.109071 restraints weight = 16430.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.110029 restraints weight = 13119.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.110319 restraints weight = 11932.318| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16987 Z= 0.114 Angle : 0.613 13.021 23208 Z= 0.311 Chirality : 0.044 0.405 2696 Planarity : 0.004 0.057 2754 Dihedral : 14.152 132.023 2941 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.14 % Favored : 94.81 % Rotamer: Outliers : 2.41 % Allowed : 16.31 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.19), residues: 1888 helix: -0.17 (0.20), residues: 618 sheet: -0.62 (0.29), residues: 345 loop : -1.48 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 488 TYR 0.019 0.001 TYR J 278 PHE 0.029 0.001 PHE I 114 TRP 0.023 0.001 TRP J 158 HIS 0.008 0.001 HIS C 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (16982) covalent geometry : angle 0.61336 / 0.31 (23208) hydrogen bonds : bond 0.03850 / 2.58 ( 605) hydrogen bonds : angle 5.20695 / 3.56 ( 1664) metal coordination : bond 0.00141 / 0.09 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7577 (tp30) REVERT: A 38 ASN cc_start: 0.7372 (t0) cc_final: 0.7110 (t0) REVERT: C 70 ASP cc_start: 0.8229 (p0) cc_final: 0.7650 (p0) REVERT: C 71 ASP cc_start: 0.7655 (p0) cc_final: 0.7373 (p0) REVERT: C 78 ASN cc_start: 0.7214 (t0) cc_final: 0.6672 (t0) REVERT: C 87 ASP cc_start: 0.7350 (m-30) cc_final: 0.6783 (p0) REVERT: E 51 ASP cc_start: 0.7811 (t70) cc_final: 0.7365 (t70) REVERT: G 8 GLU cc_start: 0.7284 (pt0) cc_final: 0.6775 (pt0) REVERT: G 11 LYS cc_start: 0.8939 (pttt) cc_final: 0.8665 (pttt) REVERT: G 32 ARG cc_start: 0.8707 (tpp-160) cc_final: 0.8444 (mmt90) REVERT: J 105 GLU cc_start: 0.8116 (tp30) cc_final: 0.6947 (pt0) REVERT: J 138 LYS cc_start: 0.6992 (mttp) cc_final: 0.6526 (mtmm) REVERT: J 231 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7620 (tp30) REVERT: J 243 MET cc_start: 0.6753 (ppp) cc_final: 0.6525 (pmm) REVERT: J 271 MET cc_start: 0.8164 (ppp) cc_final: 0.7506 (mmt) REVERT: K 716 ASP cc_start: 0.7511 (m-30) cc_final: 0.7146 (m-30) REVERT: B 17 MET cc_start: 0.7763 (tpp) cc_final: 0.7530 (tpp) REVERT: B 47 GLU cc_start: 0.7022 (tt0) cc_final: 0.6779 (tt0) REVERT: H 289 MET cc_start: 0.6957 (mmp) cc_final: 0.6468 (tpp) REVERT: H 386 MET cc_start: 0.7650 (ttt) cc_final: 0.7188 (ttt) REVERT: I 212 ARG cc_start: 0.7961 (mmm160) cc_final: 0.7669 (tpt-90) REVERT: I 276 VAL cc_start: 0.7995 (t) cc_final: 0.7751 (t) REVERT: I 374 GLU cc_start: 0.6580 (mm-30) cc_final: 0.5336 (mm-30) REVERT: I 378 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7425 (mm-30) REVERT: I 384 ARG cc_start: 0.7583 (ttp80) cc_final: 0.6988 (ptm-80) outliers start: 41 outliers final: 26 residues processed: 279 average time/residue: 0.1022 time to fit residues: 44.6754 Evaluate side-chains 263 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 225 TYR Chi-restraints excluded: chain K residue 715 ASN Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 168 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 78 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 160 optimal weight: 0.0370 chunk 116 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 60 optimal weight: 0.0470 chunk 162 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.126544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.102419 restraints weight = 40338.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.105229 restraints weight = 25714.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.106602 restraints weight = 17109.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.107568 restraints weight = 13913.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.107878 restraints weight = 12976.052| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16987 Z= 0.144 Angle : 0.625 10.304 23208 Z= 0.320 Chirality : 0.044 0.217 2696 Planarity : 0.004 0.057 2754 Dihedral : 14.159 132.568 2941 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 2.99 % Allowed : 17.14 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.19), residues: 1888 helix: -0.16 (0.20), residues: 618 sheet: -0.73 (0.29), residues: 335 loop : -1.47 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 49 TYR 0.046 0.002 TYR J 278 PHE 0.027 0.002 PHE I 114 TRP 0.022 0.002 TRP J 158 HIS 0.006 0.001 HIS I 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (16982) covalent geometry : angle 0.62450 / 0.32 (23208) hydrogen bonds : bond 0.04043 / 2.71 ( 605) hydrogen bonds : angle 5.15972 / 3.53 ( 1664) metal coordination : bond 0.00235 / 0.15 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 251 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASN cc_start: 0.7432 (t0) cc_final: 0.7172 (t0) REVERT: C 70 ASP cc_start: 0.8240 (p0) cc_final: 0.7698 (p0) REVERT: C 71 ASP cc_start: 0.7745 (p0) cc_final: 0.7477 (p0) REVERT: C 78 ASN cc_start: 0.7160 (t0) cc_final: 0.6543 (t0) REVERT: E 51 ASP cc_start: 0.7909 (t70) cc_final: 0.7493 (t0) REVERT: G 8 GLU cc_start: 0.7206 (pt0) cc_final: 0.6823 (pt0) REVERT: G 11 LYS cc_start: 0.8928 (pttt) cc_final: 0.8696 (pttt) REVERT: J 105 GLU cc_start: 0.8086 (tp30) cc_final: 0.6934 (pt0) REVERT: J 138 LYS cc_start: 0.7189 (mttp) cc_final: 0.6780 (mtmm) REVERT: J 231 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7831 (mm-30) REVERT: J 271 MET cc_start: 0.8241 (ppp) cc_final: 0.7707 (mmt) REVERT: K 716 ASP cc_start: 0.7541 (m-30) cc_final: 0.7140 (m-30) REVERT: B 17 MET cc_start: 0.7963 (tpp) cc_final: 0.7711 (tpp) REVERT: H 289 MET cc_start: 0.7113 (mmp) cc_final: 0.6620 (tpp) REVERT: H 386 MET cc_start: 0.7769 (ttt) cc_final: 0.7342 (ttt) REVERT: I 212 ARG cc_start: 0.8065 (mmm160) cc_final: 0.7747 (tpt-90) REVERT: I 276 VAL cc_start: 0.7999 (t) cc_final: 0.7733 (t) REVERT: I 374 GLU cc_start: 0.6365 (mm-30) cc_final: 0.5441 (mm-30) REVERT: I 378 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7403 (mm-30) REVERT: I 384 ARG cc_start: 0.7633 (ttp80) cc_final: 0.7014 (ptm-80) outliers start: 51 outliers final: 42 residues processed: 286 average time/residue: 0.1003 time to fit residues: 45.1798 Evaluate side-chains 278 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 225 TYR Chi-restraints excluded: chain K residue 715 ASN Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 309 SER Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 164 LYS Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 381 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 15 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 18 optimal weight: 0.0770 chunk 177 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 41 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.124276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.099738 restraints weight = 40460.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.103231 restraints weight = 25370.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.104303 restraints weight = 16429.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.104712 restraints weight = 13153.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.105074 restraints weight = 12590.406| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 2.291 16987 Z= 0.613 Angle : 0.667 10.862 23208 Z= 0.344 Chirality : 0.045 0.216 2696 Planarity : 0.004 0.054 2754 Dihedral : 14.260 132.560 2941 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.73 % Favored : 93.22 % Rotamer: Outliers : 2.76 % Allowed : 18.08 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.19), residues: 1888 helix: -0.22 (0.20), residues: 618 sheet: -0.96 (0.28), residues: 363 loop : -1.46 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 488 TYR 0.024 0.002 TYR J 278 PHE 0.025 0.002 PHE I 114 TRP 0.021 0.002 TRP J 158 HIS 0.005 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (16982) covalent geometry : angle 0.66692 / 0.34 (23208) hydrogen bonds : bond 0.04347 / 2.91 ( 605) hydrogen bonds : angle 5.25492 / 3.60 ( 1664) metal coordination : bond 1.02477 / 48.80 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 248 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7714 (mm-30) REVERT: C 70 ASP cc_start: 0.8274 (p0) cc_final: 0.7690 (p0) REVERT: C 71 ASP cc_start: 0.7731 (p0) cc_final: 0.7505 (p0) REVERT: C 78 ASN cc_start: 0.7243 (t0) cc_final: 0.6598 (t0) REVERT: E 51 ASP cc_start: 0.7889 (t70) cc_final: 0.7462 (t0) REVERT: E 78 MET cc_start: 0.8432 (tmm) cc_final: 0.8084 (tmm) REVERT: F 55 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6547 (pp) REVERT: G 8 GLU cc_start: 0.7312 (pt0) cc_final: 0.6928 (pt0) REVERT: G 11 LYS cc_start: 0.8961 (pttt) cc_final: 0.8716 (pttt) REVERT: J 105 GLU cc_start: 0.8137 (tp30) cc_final: 0.6947 (pt0) REVERT: J 138 LYS cc_start: 0.7233 (mttp) cc_final: 0.6714 (mtmm) REVERT: J 231 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7993 (mm-30) REVERT: J 271 MET cc_start: 0.8008 (ppp) cc_final: 0.7729 (mmt) REVERT: K 716 ASP cc_start: 0.7580 (m-30) cc_final: 0.7092 (m-30) REVERT: B 17 MET cc_start: 0.8112 (tpp) cc_final: 0.7642 (tpp) REVERT: H 386 MET cc_start: 0.7930 (ttt) cc_final: 0.7472 (ttt) REVERT: I 168 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: I 212 ARG cc_start: 0.8258 (mmm160) cc_final: 0.8023 (tpt-90) REVERT: I 276 VAL cc_start: 0.8044 (t) cc_final: 0.7813 (t) REVERT: I 378 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7475 (mm-30) REVERT: I 384 ARG cc_start: 0.7638 (ttp80) cc_final: 0.7001 (ptm-80) outliers start: 47 outliers final: 40 residues processed: 280 average time/residue: 0.0986 time to fit residues: 43.6954 Evaluate side-chains 282 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 240 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 225 TYR Chi-restraints excluded: chain K residue 715 ASN Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 309 SER Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 164 LYS Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 381 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 104 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 143 optimal weight: 0.0770 chunk 93 optimal weight: 0.4980 chunk 28 optimal weight: 0.0670 chunk 111 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 97 optimal weight: 0.0270 chunk 26 optimal weight: 2.9990 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 41 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.128066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.104240 restraints weight = 39728.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.107303 restraints weight = 25324.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.108625 restraints weight = 16663.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.109344 restraints weight = 13012.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.109729 restraints weight = 12252.021| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 16987 Z= 0.114 Angle : 0.641 14.752 23208 Z= 0.322 Chirality : 0.044 0.352 2696 Planarity : 0.004 0.056 2754 Dihedral : 14.113 130.180 2941 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.60 % Rotamer: Outliers : 1.82 % Allowed : 19.01 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.19), residues: 1888 helix: -0.08 (0.20), residues: 619 sheet: -0.59 (0.29), residues: 357 loop : -1.40 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 488 TYR 0.046 0.001 TYR J 278 PHE 0.022 0.001 PHE I 114 TRP 0.023 0.002 TRP J 158 HIS 0.014 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (16982) covalent geometry : angle 0.64129 / 0.32 (23208) hydrogen bonds : bond 0.03613 / 2.44 ( 605) hydrogen bonds : angle 5.00477 / 3.41 ( 1664) metal coordination : bond 0.03165 / 1.57 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 70 ASP cc_start: 0.8260 (p0) cc_final: 0.7816 (p0) REVERT: C 71 ASP cc_start: 0.7696 (p0) cc_final: 0.7495 (p0) REVERT: C 78 ASN cc_start: 0.7028 (t0) cc_final: 0.6581 (t0) REVERT: E 51 ASP cc_start: 0.7842 (t70) cc_final: 0.7480 (t0) REVERT: F 55 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6469 (pp) REVERT: G 8 GLU cc_start: 0.7171 (pt0) cc_final: 0.6676 (pt0) REVERT: G 11 LYS cc_start: 0.8901 (pttt) cc_final: 0.8621 (pttt) REVERT: J 105 GLU cc_start: 0.8047 (tp30) cc_final: 0.6914 (pt0) REVERT: J 110 LEU cc_start: 0.8871 (mt) cc_final: 0.8379 (tt) REVERT: J 138 LYS cc_start: 0.7084 (mttp) cc_final: 0.6679 (mtmm) REVERT: J 231 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7912 (mm-30) REVERT: K 716 ASP cc_start: 0.7427 (m-30) cc_final: 0.7007 (m-30) REVERT: B 17 MET cc_start: 0.8093 (tpp) cc_final: 0.7549 (tpp) REVERT: H 289 MET cc_start: 0.7024 (mmp) cc_final: 0.6543 (tpp) REVERT: H 386 MET cc_start: 0.7680 (ttt) cc_final: 0.7295 (ttt) REVERT: I 212 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7744 (tpt-90) REVERT: I 276 VAL cc_start: 0.8083 (t) cc_final: 0.7834 (t) REVERT: I 374 GLU cc_start: 0.6412 (mm-30) cc_final: 0.5148 (mm-30) REVERT: I 378 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7467 (mm-30) REVERT: I 384 ARG cc_start: 0.7643 (ttp80) cc_final: 0.7358 (ptm-80) outliers start: 31 outliers final: 24 residues processed: 278 average time/residue: 0.0924 time to fit residues: 40.9254 Evaluate side-chains 270 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain J residue 57 GLN Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 225 TYR Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 508 MET Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 381 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 48 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 chunk 173 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.126945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.103071 restraints weight = 40144.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.106309 restraints weight = 25856.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.107557 restraints weight = 16829.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.108406 restraints weight = 13053.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.108732 restraints weight = 12240.850| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16987 Z= 0.125 Angle : 0.640 13.269 23208 Z= 0.324 Chirality : 0.044 0.335 2696 Planarity : 0.004 0.054 2754 Dihedral : 14.081 131.037 2941 Min Nonbonded Distance : 1.534 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.51 % Favored : 94.39 % Rotamer: Outliers : 1.70 % Allowed : 19.84 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.19), residues: 1888 helix: -0.04 (0.20), residues: 619 sheet: -0.65 (0.29), residues: 355 loop : -1.38 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 488 TYR 0.020 0.001 TYR J 278 PHE 0.023 0.001 PHE I 114 TRP 0.021 0.002 TRP J 158 HIS 0.017 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (16982) covalent geometry : angle 0.64044 / 0.32 (23208) hydrogen bonds : bond 0.03713 / 2.51 ( 605) hydrogen bonds : angle 5.03062 / 3.42 ( 1664) metal coordination : bond 0.02791 / 1.36 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 252 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7462 (tp30) REVERT: C 70 ASP cc_start: 0.8221 (p0) cc_final: 0.7769 (p0) REVERT: C 71 ASP cc_start: 0.7667 (p0) cc_final: 0.7456 (p0) REVERT: C 78 ASN cc_start: 0.6961 (t0) cc_final: 0.6439 (t0) REVERT: E 51 ASP cc_start: 0.7833 (t70) cc_final: 0.7396 (t0) REVERT: F 20 MET cc_start: 0.7570 (mmm) cc_final: 0.7156 (tpt) REVERT: F 55 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6529 (pp) REVERT: G 8 GLU cc_start: 0.7174 (pt0) cc_final: 0.6678 (pt0) REVERT: G 11 LYS cc_start: 0.8893 (pttt) cc_final: 0.8641 (pttt) REVERT: J 105 GLU cc_start: 0.8064 (tp30) cc_final: 0.6921 (pt0) REVERT: J 110 LEU cc_start: 0.8887 (mt) cc_final: 0.8391 (tt) REVERT: J 138 LYS cc_start: 0.7170 (mttp) cc_final: 0.6728 (mtmm) REVERT: J 231 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7940 (mm-30) REVERT: K 716 ASP cc_start: 0.7414 (m-30) cc_final: 0.6994 (m-30) REVERT: B 17 MET cc_start: 0.8100 (tpp) cc_final: 0.7575 (tpp) REVERT: H 289 MET cc_start: 0.7056 (mmp) cc_final: 0.6584 (tpp) REVERT: H 386 MET cc_start: 0.7760 (ttt) cc_final: 0.7338 (ttt) REVERT: H 427 LEU cc_start: 0.5928 (tp) cc_final: 0.5317 (tp) REVERT: I 118 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7628 (t70) REVERT: I 212 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7930 (tpt-90) REVERT: I 276 VAL cc_start: 0.8061 (t) cc_final: 0.7795 (t) REVERT: I 374 GLU cc_start: 0.6438 (mm-30) cc_final: 0.5148 (mm-30) REVERT: I 378 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7518 (mm-30) REVERT: I 384 ARG cc_start: 0.7624 (ttp80) cc_final: 0.7006 (ptm-80) outliers start: 29 outliers final: 24 residues processed: 269 average time/residue: 0.1049 time to fit residues: 44.4785 Evaluate side-chains 271 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 225 TYR Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 590 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 183 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 64 optimal weight: 0.0030 chunk 18 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 41 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.126269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.102549 restraints weight = 39930.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.105628 restraints weight = 25942.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.106853 restraints weight = 17113.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.107708 restraints weight = 13336.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.108034 restraints weight = 12387.496| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16987 Z= 0.134 Angle : 0.662 15.324 23208 Z= 0.333 Chirality : 0.045 0.393 2696 Planarity : 0.004 0.054 2754 Dihedral : 14.080 131.068 2941 Min Nonbonded Distance : 1.575 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.04 % Favored : 93.91 % Rotamer: Outliers : 1.76 % Allowed : 20.31 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.19), residues: 1888 helix: -0.04 (0.21), residues: 617 sheet: -0.66 (0.29), residues: 347 loop : -1.38 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG H 488 TYR 0.044 0.002 TYR J 278 PHE 0.023 0.002 PHE I 114 TRP 0.021 0.002 TRP I 254 HIS 0.016 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (16982) covalent geometry : angle 0.66207 / 0.33 (23208) hydrogen bonds : bond 0.03761 / 2.54 ( 605) hydrogen bonds : angle 5.02991 / 3.42 ( 1664) metal coordination : bond 0.02271 / 1.11 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 70 ASP cc_start: 0.8221 (p0) cc_final: 0.7783 (p0) REVERT: C 78 ASN cc_start: 0.6989 (t0) cc_final: 0.6497 (t0) REVERT: C 106 ASN cc_start: 0.6463 (OUTLIER) cc_final: 0.5938 (p0) REVERT: E 51 ASP cc_start: 0.7930 (t70) cc_final: 0.7474 (t0) REVERT: F 20 MET cc_start: 0.7610 (mmm) cc_final: 0.7222 (tpt) REVERT: F 55 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6553 (pp) REVERT: G 8 GLU cc_start: 0.7192 (pt0) cc_final: 0.6676 (pt0) REVERT: G 11 LYS cc_start: 0.8896 (pttt) cc_final: 0.8652 (pttt) REVERT: G 28 GLN cc_start: 0.7284 (pm20) cc_final: 0.6500 (pm20) REVERT: J 105 GLU cc_start: 0.8050 (tp30) cc_final: 0.6920 (pt0) REVERT: J 110 LEU cc_start: 0.8915 (mt) cc_final: 0.8423 (tt) REVERT: J 138 LYS cc_start: 0.7142 (mttp) cc_final: 0.6644 (mtmm) REVERT: J 231 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8008 (mm-30) REVERT: K 716 ASP cc_start: 0.7385 (m-30) cc_final: 0.6978 (m-30) REVERT: H 289 MET cc_start: 0.7091 (mmp) cc_final: 0.6630 (tpp) REVERT: H 386 MET cc_start: 0.7807 (ttt) cc_final: 0.7443 (ttt) REVERT: H 427 LEU cc_start: 0.5977 (tp) cc_final: 0.5359 (tp) REVERT: I 118 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7691 (t70) REVERT: I 276 VAL cc_start: 0.8059 (t) cc_final: 0.7804 (t) REVERT: I 374 GLU cc_start: 0.6305 (mm-30) cc_final: 0.4983 (mm-30) REVERT: I 378 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7507 (mm-30) REVERT: I 384 ARG cc_start: 0.7575 (ttp80) cc_final: 0.6942 (ptm-80) outliers start: 30 outliers final: 25 residues processed: 265 average time/residue: 0.1025 time to fit residues: 43.2008 Evaluate side-chains 269 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain J residue 57 GLN Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 225 TYR Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 590 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 76 optimal weight: 0.1980 chunk 123 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 134 optimal weight: 0.9990 chunk 34 optimal weight: 0.0010 chunk 60 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.0470 chunk 183 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 41 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.128398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.104763 restraints weight = 39769.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.107902 restraints weight = 25359.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.109187 restraints weight = 16584.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.110230 restraints weight = 12826.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.110612 restraints weight = 11785.174| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16987 Z= 0.113 Angle : 0.643 14.840 23208 Z= 0.323 Chirality : 0.044 0.394 2696 Planarity : 0.004 0.056 2754 Dihedral : 13.986 129.838 2941 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.08 % Favored : 94.86 % Rotamer: Outliers : 1.58 % Allowed : 20.54 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.19), residues: 1888 helix: 0.06 (0.21), residues: 616 sheet: -0.61 (0.28), residues: 358 loop : -1.28 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 488 TYR 0.030 0.001 TYR J 278 PHE 0.022 0.001 PHE I 114 TRP 0.020 0.002 TRP I 345 HIS 0.014 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (16982) covalent geometry : angle 0.64315 / 0.32 (23208) hydrogen bonds : bond 0.03411 / 2.31 ( 605) hydrogen bonds : angle 4.95376 / 3.36 ( 1664) metal coordination : bond 0.01864 / 0.91 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2234.31 seconds wall clock time: 39 minutes 32.68 seconds (2372.68 seconds total)