Starting phenix.real_space_refine on Fri Mar 6 06:45:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vbw_21146/03_2026/6vbw_21146_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vbw_21146/03_2026/6vbw_21146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vbw_21146/03_2026/6vbw_21146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vbw_21146/03_2026/6vbw_21146.map" model { file = "/net/cci-nas-00/data/ceres_data/6vbw_21146/03_2026/6vbw_21146_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vbw_21146/03_2026/6vbw_21146_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 4 6.06 5 P 106 5.49 5 S 151 5.16 5 C 18147 2.51 5 N 5035 2.21 5 O 5644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29087 Number of models: 1 Model: "" Number of chains: 15 Chain: "M" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 807 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "K" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1275 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 16, 'rna3p_pur': 20, 'rna3p_pyr': 15} Link IDs: {'rna2p': 25, 'rna3p': 35} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3538 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 8 Chain: "B" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2704 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "C" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2713 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 17, 'TRANS': 321} Chain breaks: 1 Chain: "D" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2729 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 17, 'TRANS': 323} Chain breaks: 1 Chain: "F" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2729 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 17, 'TRANS': 323} Chain breaks: 1 Chain: "E" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2720 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain breaks: 1 Chain: "G" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2490 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 15, 'TRANS': 291} Chain breaks: 2 Chain: "H" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1113 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 4 Chain: "I" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3050 Classifications: {'peptide': 374} Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 355} Chain breaks: 3 Chain: "J" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3075 Classifications: {'peptide': 378} Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 359} Chain breaks: 2 Chain: "I" 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} Chain: "J" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23981 SG CYS I 128 72.997 57.935 19.198 1.00 80.43 S ATOM 24002 SG CYS I 131 68.813 57.124 20.895 1.00 80.78 S ATOM 24256 SG CYS I 161 79.685 69.141 13.876 1.00 82.72 S ATOM 24405 SG CYS I 181 78.026 71.966 11.567 1.00 82.94 S ATOM 27052 SG CYS J 131 47.969 21.496 60.377 1.00 92.95 S Time building chain proxies: 6.30, per 1000 atoms: 0.22 Number of scatterers: 29087 At special positions: 0 Unit cell: (122.36, 201.096, 186.2, 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 4 29.99 S 151 16.00 P 106 15.00 O 5644 8.00 N 5035 7.00 C 18147 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: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 401 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 131 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 128 " pdb="ZN ZN I 401 " - pdb=" ND1 HIS I 153 " pdb=" ZN I 402 " pdb="ZN ZN I 402 " - pdb=" SG CYS I 161 " pdb="ZN ZN I 402 " - pdb=" SG CYS I 181 " pdb=" ZN J 401 " pdb="ZN ZN J 401 " - pdb=" SG CYS J 131 " 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6370 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 51 sheets defined 33.0% alpha, 13.9% beta 16 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 3.728A pdb=" N PHE A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 68 through 81 removed outlier: 3.750A pdb=" N ILE A 76 " --> pdb=" O TRP A 72 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 79 " --> pdb=" O CYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.611A pdb=" N TYR A 129 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 130 " --> pdb=" O SER A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 130' Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.700A pdb=" N LYS A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.602A pdb=" N HIS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 411 through 427 removed outlier: 3.579A pdb=" N PHE A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 499 removed outlier: 3.966A pdb=" N LEU A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A 498 " --> pdb=" O ASP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 519 removed outlier: 4.368A pdb=" N LYS A 517 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 519 " --> pdb=" O PHE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.622A pdb=" N GLU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.842A pdb=" N ALA A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 105 through 123 removed outlier: 3.697A pdb=" N THR B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 removed outlier: 3.534A pdb=" N ALA B 129 " --> pdb=" O TRP B 125 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 136 " --> pdb=" O TYR B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 removed outlier: 3.577A pdb=" N LEU B 142 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LYS B 144 " --> pdb=" O TRP B 141 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 146 " --> pdb=" O TRP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.807A pdb=" N PHE B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 removed outlier: 3.816A pdb=" N THR B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 removed outlier: 3.892A pdb=" N GLY B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 removed outlier: 3.643A pdb=" N GLN B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 319 removed outlier: 3.760A pdb=" N GLU B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 344 Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.730A pdb=" N ALA C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 123 removed outlier: 3.546A pdb=" N GLN C 114 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 4.184A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.777A pdb=" N PHE C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 200 Processing helix chain 'C' and resid 260 through 269 removed outlier: 3.558A pdb=" N ALA C 267 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.506A pdb=" N ILE C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 314 through 321 removed outlier: 3.615A pdb=" N GLU C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 344 removed outlier: 4.286A pdb=" N MET C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'D' and resid 105 through 123 removed outlier: 4.145A pdb=" N VAL D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 4.103A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE D 136 " --> pdb=" O TYR D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 175 Processing helix chain 'D' and resid 177 through 183 removed outlier: 3.607A pdb=" N PHE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 197 removed outlier: 3.679A pdb=" N ILE D 194 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 removed outlier: 3.757A pdb=" N ALA D 267 " --> pdb=" O LYS D 263 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 314 through 322 removed outlier: 3.744A pdb=" N GLU D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 342 removed outlier: 3.654A pdb=" N PHE D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 123 removed outlier: 3.508A pdb=" N LYS F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN F 114 " --> pdb=" O GLN F 110 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR F 121 " --> pdb=" O GLU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 135 removed outlier: 3.501A pdb=" N ALA F 129 " --> pdb=" O TRP F 125 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 183 Processing helix chain 'F' and resid 184 through 186 No H-bonds generated for 'chain 'F' and resid 184 through 186' Processing helix chain 'F' and resid 187 through 198 removed outlier: 3.754A pdb=" N GLU F 192 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 269 removed outlier: 3.821A pdb=" N ALA F 267 " --> pdb=" O LYS F 263 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 269 " --> pdb=" O GLY F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 311 removed outlier: 3.518A pdb=" N GLN F 311 " --> pdb=" O PHE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 321 removed outlier: 4.248A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL F 319 " --> pdb=" O HIS F 315 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU F 320 " --> pdb=" O TYR F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 340 removed outlier: 4.245A pdb=" N ASP F 333 " --> pdb=" O GLU F 329 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET F 334 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN F 340 " --> pdb=" O PHE F 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 99 removed outlier: 3.576A pdb=" N ARG E 98 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN E 99 " --> pdb=" O GLU E 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 95 through 99' Processing helix chain 'E' and resid 105 through 113 removed outlier: 3.639A pdb=" N GLN E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 123 removed outlier: 3.911A pdb=" N THR E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 138 removed outlier: 4.003A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE E 136 " --> pdb=" O TYR E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 175 Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 187 through 200 removed outlier: 3.803A pdb=" N MET E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE E 194 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 269 removed outlier: 3.822A pdb=" N ALA E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA E 269 " --> pdb=" O GLY E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 311 Processing helix chain 'E' and resid 312 through 321 removed outlier: 3.547A pdb=" N ILE E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 330 Processing helix chain 'E' and resid 331 through 344 removed outlier: 3.516A pdb=" N ASN E 340 " --> pdb=" O PHE E 336 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E 341 " --> pdb=" O LEU E 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 123 removed outlier: 3.646A pdb=" N GLN G 114 " --> pdb=" O GLN G 110 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 138 removed outlier: 3.746A pdb=" N ASN G 135 " --> pdb=" O ARG G 131 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE G 136 " --> pdb=" O TYR G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 175 Processing helix chain 'G' and resid 177 through 183 removed outlier: 3.946A pdb=" N PHE G 181 " --> pdb=" O SER G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 200 removed outlier: 4.205A pdb=" N MET G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE G 194 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR G 196 " --> pdb=" O GLU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 269 removed outlier: 3.945A pdb=" N ALA G 267 " --> pdb=" O LYS G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 311 Processing helix chain 'G' and resid 314 through 321 removed outlier: 3.806A pdb=" N GLU G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL G 319 " --> pdb=" O HIS G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 340 removed outlier: 3.640A pdb=" N ASP G 333 " --> pdb=" O GLU G 329 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET G 334 " --> pdb=" O THR G 330 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN G 340 " --> pdb=" O PHE G 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 35 removed outlier: 3.928A pdb=" N LYS H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS H 24 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG H 26 " --> pdb=" O ALA H 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN H 32 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR H 33 " --> pdb=" O HIS H 29 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN H 34 " --> pdb=" O GLY H 30 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR H 35 " --> pdb=" O PHE H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 80 removed outlier: 4.264A pdb=" N GLN H 76 " --> pdb=" O HIS H 72 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 123 Processing helix chain 'I' and resid 13 through 25 removed outlier: 3.721A pdb=" N ILE I 19 " --> pdb=" O GLU I 15 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA I 22 " --> pdb=" O PHE I 18 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 3.877A pdb=" N PHE I 33 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 60 removed outlier: 3.654A pdb=" N ILE I 59 " --> pdb=" O ILE I 56 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASN I 60 " --> pdb=" O THR I 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 56 through 60' Processing helix chain 'I' and resid 67 through 82 removed outlier: 4.029A pdb=" N LYS I 77 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU I 78 " --> pdb=" O SER I 74 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA I 79 " --> pdb=" O PHE I 75 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLN I 80 " --> pdb=" O LEU I 76 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 120 No H-bonds generated for 'chain 'I' and resid 118 through 120' Processing helix chain 'I' and resid 139 through 144 Processing helix chain 'I' and resid 197 through 206 removed outlier: 3.712A pdb=" N GLY I 206 " --> pdb=" O ASN I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 232 removed outlier: 3.755A pdb=" N TRP I 226 " --> pdb=" O GLY I 222 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET I 228 " --> pdb=" O VAL I 224 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY I 229 " --> pdb=" O HIS I 225 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE I 230 " --> pdb=" O TRP I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 245 removed outlier: 3.559A pdb=" N VAL I 241 " --> pdb=" O HIS I 237 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE I 244 " --> pdb=" O PHE I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 264 removed outlier: 3.842A pdb=" N ILE I 254 " --> pdb=" O SER I 250 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE I 255 " --> pdb=" O PHE I 251 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP I 257 " --> pdb=" O SER I 253 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU I 260 " --> pdb=" O GLU I 256 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU I 264 " --> pdb=" O GLU I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 279 Processing helix chain 'I' and resid 279 through 285 Processing helix chain 'I' and resid 297 through 309 removed outlier: 3.849A pdb=" N GLY I 301 " --> pdb=" O ASN I 297 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN I 309 " --> pdb=" O CYS I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 320 Processing helix chain 'I' and resid 325 through 333 removed outlier: 3.529A pdb=" N THR I 329 " --> pdb=" O ALA I 325 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET I 331 " --> pdb=" O GLU I 327 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 345 removed outlier: 3.638A pdb=" N ILE I 339 " --> pdb=" O SER I 335 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU I 344 " --> pdb=" O ALA I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 380 removed outlier: 4.495A pdb=" N CYS I 374 " --> pdb=" O GLY I 370 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU I 375 " --> pdb=" O ASP I 371 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA I 378 " --> pdb=" O CYS I 374 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE I 380 " --> pdb=" O TRP I 376 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 25 removed outlier: 3.667A pdb=" N PHE J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE J 19 " --> pdb=" O GLU J 15 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG J 20 " --> pdb=" O SER J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 44 removed outlier: 3.565A pdb=" N ASP J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE J 44 " --> pdb=" O PHE J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 52 removed outlier: 3.519A pdb=" N PHE J 52 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 removed outlier: 3.768A pdb=" N ILE J 59 " --> pdb=" O ILE J 56 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN J 60 " --> pdb=" O THR J 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 60' Processing helix chain 'J' and resid 67 through 82 removed outlier: 3.642A pdb=" N THR J 72 " --> pdb=" O SER J 68 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA J 73 " --> pdb=" O SER J 69 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA J 79 " --> pdb=" O PHE J 75 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN J 80 " --> pdb=" O LEU J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 93 removed outlier: 3.665A pdb=" N ALA J 93 " --> pdb=" O LEU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 135 Processing helix chain 'J' and resid 139 through 144 removed outlier: 3.648A pdb=" N TRP J 142 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS J 143 " --> pdb=" O TYR J 140 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE J 144 " --> pdb=" O LEU J 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 139 through 144' Processing helix chain 'J' and resid 197 through 204 Processing helix chain 'J' and resid 216 through 232 removed outlier: 3.811A pdb=" N TRP J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU J 223 " --> pdb=" O TYR J 219 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL J 224 " --> pdb=" O ARG J 220 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS J 225 " --> pdb=" O TRP J 221 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP J 226 " --> pdb=" O GLY J 222 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY J 229 " --> pdb=" O HIS J 225 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS J 231 " --> pdb=" O TRP J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 244 removed outlier: 3.696A pdb=" N PHE J 244 " --> pdb=" O PHE J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 265 removed outlier: 3.573A pdb=" N GLU J 256 " --> pdb=" O HIS J 252 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP J 257 " --> pdb=" O SER J 253 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU J 264 " --> pdb=" O GLU J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 280 Processing helix chain 'J' and resid 282 through 286 removed outlier: 3.913A pdb=" N SER J 286 " --> pdb=" O PHE J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 309 removed outlier: 4.060A pdb=" N CYS J 305 " --> pdb=" O GLY J 301 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU J 307 " --> pdb=" O LEU J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 320 Processing helix chain 'J' and resid 325 through 333 removed outlier: 3.755A pdb=" N THR J 329 " --> pdb=" O ALA J 325 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL J 330 " --> pdb=" O LEU J 326 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET J 331 " --> pdb=" O GLU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 345 removed outlier: 3.548A pdb=" N ILE J 339 " --> pdb=" O SER J 335 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU J 344 " --> pdb=" O ALA J 340 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN J 345 " --> pdb=" O SER J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 369 through 380 removed outlier: 3.589A pdb=" N LEU J 377 " --> pdb=" O PHE J 373 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA J 378 " --> pdb=" O CYS J 374 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.718A pdb=" N ALA A 217 " --> pdb=" O ASN A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 201 through 204 removed outlier: 4.316A pdb=" N LYS A 587 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 569 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLY A 596 " --> pdb=" O CYS A 567 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N CYS A 567 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 598 " --> pdb=" O ALA A 565 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 16.150A pdb=" N SER A 566 " --> pdb=" O PRO A 627 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 568 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA6, first strand: chain 'A' and resid 503 through 504 removed outlier: 5.854A pdb=" N PHE A 479 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 447 through 450 removed outlier: 4.391A pdb=" N ASP A 472 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.728A pdb=" N TYR B 9 " --> pdb=" O GLY B 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AB1, first strand: chain 'B' and resid 35 through 41 removed outlier: 3.536A pdb=" N VAL B 73 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 88 through 89 removed outlier: 3.844A pdb=" N CYS B 151 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP B 152 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP B 170 " --> pdb=" O TRP B 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AB4, first strand: chain 'B' and resid 270 through 272 Processing sheet with id=AB5, first strand: chain 'B' and resid 289 through 290 removed outlier: 3.740A pdb=" N THR B 295 " --> pdb=" O HIS B 290 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 102 through 103 removed outlier: 3.963A pdb=" N GLY C 345 " --> pdb=" O TYR C 9 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.511A pdb=" N CYS C 19 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 88 " --> pdb=" O CYS C 19 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS C 84 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP C 152 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 170 " --> pdb=" O TRP C 152 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 29 through 31 removed outlier: 4.201A pdb=" N PHE C 20 " --> pdb=" O PRO C 257 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N VAL C 22 " --> pdb=" O ARG C 255 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N ARG C 255 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 35 through 41 Processing sheet with id=AC1, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.692A pdb=" N THR C 295 " --> pdb=" O HIS C 290 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 102 through 103 removed outlier: 3.759A pdb=" N GLY D 345 " --> pdb=" O TYR D 9 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.616A pdb=" N CYS D 87 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 29 through 31 removed outlier: 4.093A pdb=" N PHE D 20 " --> pdb=" O PRO D 257 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N VAL D 22 " --> pdb=" O ARG D 255 " (cutoff:3.500A) removed outlier: 14.201A pdb=" N ARG D 255 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 35 through 41 Processing sheet with id=AC6, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AC7, first strand: chain 'D' and resid 289 through 290 removed outlier: 3.693A pdb=" N THR D 295 " --> pdb=" O HIS D 290 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 102 through 103 removed outlier: 3.659A pdb=" N GLY F 345 " --> pdb=" O TYR F 9 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 29 through 31 removed outlier: 3.606A pdb=" N CYS F 19 " --> pdb=" O SER F 88 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER F 88 " --> pdb=" O CYS F 19 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS F 87 " --> pdb=" O ALA F 211 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N CYS F 151 " --> pdb=" O HIS F 214 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP F 152 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP F 170 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL F 166 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 29 through 31 removed outlier: 4.075A pdb=" N PHE F 20 " --> pdb=" O PRO F 257 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N VAL F 22 " --> pdb=" O ARG F 255 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N ARG F 255 " --> pdb=" O VAL F 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 35 through 41 removed outlier: 3.515A pdb=" N VAL F 73 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN F 69 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 270 through 272 Processing sheet with id=AD4, first strand: chain 'F' and resid 289 through 290 removed outlier: 3.843A pdb=" N THR F 295 " --> pdb=" O HIS F 290 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AD6, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.516A pdb=" N HIS E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 24 current: chain 'E' and resid 151 through 156 Processing sheet with id=AD7, first strand: chain 'E' and resid 28 through 31 removed outlier: 3.566A pdb=" N ARG E 28 " --> pdb=" O TRP E 24 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 84 through 93 current: chain 'E' and resid 248 through 250 Processing sheet with id=AD8, first strand: chain 'E' and resid 35 through 41 removed outlier: 3.772A pdb=" N ASN E 35 " --> pdb=" O PHE E 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 270 through 272 Processing sheet with id=AE1, first strand: chain 'E' and resid 289 through 290 removed outlier: 3.508A pdb=" N THR E 295 " --> pdb=" O HIS E 290 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 102 through 103 removed outlier: 3.707A pdb=" N GLY G 345 " --> pdb=" O TYR G 9 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 18 through 24 current: chain 'G' and resid 152 through 156 Processing sheet with id=AE4, first strand: chain 'G' and resid 28 through 31 removed outlier: 3.813A pdb=" N ARG G 28 " --> pdb=" O TRP G 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 84 through 93 current: chain 'G' and resid 248 through 250 Processing sheet with id=AE5, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AE6, first strand: chain 'G' and resid 270 through 272 Processing sheet with id=AE7, first strand: chain 'G' and resid 289 through 290 Processing sheet with id=AE8, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.511A pdb=" N SER H 57 " --> pdb=" O SER H 43 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 102 through 103 removed outlier: 3.789A pdb=" N ARG H 102 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG H 168 " --> pdb=" O ARG H 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'H' and resid 153 through 155 Processing sheet with id=AF2, first strand: chain 'I' and resid 95 through 97 removed outlier: 4.147A pdb=" N ALA I 107 " --> pdb=" O THR I 97 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 149 through 150 removed outlier: 3.861A pdb=" N VAL I 155 " --> pdb=" O CYS I 150 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 322 through 323 removed outlier: 3.516A pdb=" N PHE I 367 " --> pdb=" O MET I 323 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 95 through 100 removed outlier: 4.113A pdb=" N THR J 97 " --> pdb=" O ALA J 107 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ALA J 107 " --> pdb=" O THR J 97 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 322 through 323 765 hydrogen bonds defined for protein. 2100 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5920 1.33 - 1.45: 8095 1.45 - 1.57: 15592 1.57 - 1.69: 209 1.69 - 1.82: 219 Bond restraints: 30035 Sorted by residual: bond pdb=" N ILE C 258 " pdb=" CA ILE C 258 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.13e+01 bond pdb=" N ILE D 258 " pdb=" CA ILE D 258 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.03e+01 bond pdb=" N ILE A 211 " pdb=" CA ILE A 211 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.92e+00 bond pdb=" N ILE F 258 " pdb=" CA ILE F 258 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.08e-02 8.57e+03 9.64e+00 bond pdb=" N SER A 521 " pdb=" CA SER A 521 " ideal model delta sigma weight residual 1.453 1.491 -0.037 1.22e-02 6.72e+03 9.41e+00 ... (remaining 30030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 39795 2.86 - 5.71: 1238 5.71 - 8.57: 145 8.57 - 11.43: 32 11.43 - 14.28: 2 Bond angle restraints: 41212 Sorted by residual: angle pdb=" CA GLY B 345 " pdb=" C GLY B 345 " pdb=" O GLY B 345 " ideal model delta sigma weight residual 122.23 118.21 4.02 6.90e-01 2.10e+00 3.39e+01 angle pdb=" O3' DA L 76 " pdb=" C3' DA L 76 " pdb=" C2' DA L 76 " ideal model delta sigma weight residual 111.50 119.94 -8.44 1.50e+00 4.44e-01 3.17e+01 angle pdb=" C LEU F 40 " pdb=" N GLY F 41 " pdb=" CA GLY F 41 " ideal model delta sigma weight residual 122.43 117.84 4.59 8.90e-01 1.26e+00 2.66e+01 angle pdb=" C4' U K 21 " pdb=" C3' U K 21 " pdb=" O3' U K 21 " ideal model delta sigma weight residual 109.40 101.95 7.45 1.50e+00 4.44e-01 2.46e+01 angle pdb=" C ALA E 45 " pdb=" N ALA E 46 " pdb=" CA ALA E 46 " ideal model delta sigma weight residual 121.54 130.98 -9.44 1.91e+00 2.74e-01 2.45e+01 ... (remaining 41207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 17262 34.55 - 69.11: 517 69.11 - 103.66: 49 103.66 - 138.21: 2 138.21 - 172.76: 2 Dihedral angle restraints: 17832 sinusoidal: 8037 harmonic: 9795 Sorted by residual: dihedral pdb=" O4' U K 42 " pdb=" C1' U K 42 " pdb=" N1 U K 42 " pdb=" C2 U K 42 " ideal model delta sinusoidal sigma weight residual 200.00 76.45 123.55 1 1.50e+01 4.44e-03 6.62e+01 dihedral pdb=" O4' U K 20 " pdb=" C1' U K 20 " pdb=" N1 U K 20 " pdb=" C2 U K 20 " ideal model delta sinusoidal sigma weight residual -128.00 44.76 -172.76 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C K 38 " pdb=" C1' C K 38 " pdb=" N1 C K 38 " pdb=" C2 C K 38 " ideal model delta sinusoidal sigma weight residual 232.00 66.31 165.69 1 1.70e+01 3.46e-03 6.54e+01 ... (remaining 17829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3653 0.081 - 0.163: 761 0.163 - 0.244: 122 0.244 - 0.325: 31 0.325 - 0.406: 2 Chirality restraints: 4569 Sorted by residual: chirality pdb=" C3' DA L 76 " pdb=" C4' DA L 76 " pdb=" O3' DA L 76 " pdb=" C2' DA L 76 " both_signs ideal model delta sigma weight residual False -2.66 -2.25 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CA ARG A 584 " pdb=" N ARG A 584 " pdb=" C ARG A 584 " pdb=" CB ARG A 584 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CG LEU C 215 " pdb=" CB LEU C 215 " pdb=" CD1 LEU C 215 " pdb=" CD2 LEU C 215 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 4566 not shown) Planarity restraints: 4876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 9 " -0.026 2.00e-02 2.50e+03 2.45e-02 1.20e+01 pdb=" CG TYR E 9 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR E 9 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR E 9 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR E 9 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR E 9 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 9 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 9 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 9 " 0.025 2.00e-02 2.50e+03 2.42e-02 1.17e+01 pdb=" CG TYR G 9 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR G 9 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR G 9 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR G 9 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR G 9 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR G 9 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR G 9 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 9 " 0.023 2.00e-02 2.50e+03 2.39e-02 1.14e+01 pdb=" CG TYR F 9 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR F 9 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR F 9 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR F 9 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR F 9 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR F 9 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR F 9 " 0.004 2.00e-02 2.50e+03 ... (remaining 4873 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 404 2.63 - 3.19: 23840 3.19 - 3.76: 44254 3.76 - 4.33: 62797 4.33 - 4.90: 103041 Nonbonded interactions: 234336 Sorted by model distance: nonbonded pdb=" O2' U K 21 " pdb=" O4' U K 22 " model vdw 2.057 3.040 nonbonded pdb=" O2' G K 18 " pdb=" O4' C K 19 " model vdw 2.088 3.040 nonbonded pdb=" O2 C K 46 " pdb=" N2 G K 60 " model vdw 2.129 3.120 nonbonded pdb=" O ASP A 183 " pdb=" OD1 ASP A 183 " model vdw 2.137 3.040 nonbonded pdb=" O SER G 95 " pdb=" OG SER G 95 " model vdw 2.138 3.040 ... (remaining 234331 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 39 or resid 71 through 229 or resid 243 through \ 349)) selection = (chain 'C' and (resid 1 through 39 or resid 71 through 229 or resid 243 through \ 349)) selection = (chain 'D' and (resid 1 through 39 or resid 71 through 229 or resid 243 through \ 349)) selection = (chain 'E' and (resid 1 through 39 or resid 71 through 229 or resid 243 through \ 349)) selection = (chain 'F' and (resid 1 through 39 or resid 71 through 229 or resid 243 through \ 349)) selection = (chain 'G' and (resid 1 through 229 or resid 243 through 349)) } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 1 through 265 or resid 270 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 31.240 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.012 0.683 30041 Z= 0.539 Angle : 1.187 14.283 41212 Z= 0.693 Chirality : 0.072 0.406 4569 Planarity : 0.008 0.072 4876 Dihedral : 15.582 172.765 11462 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.52 % Favored : 91.39 % Rotamer: Outliers : 1.96 % Allowed : 4.66 % Favored : 93.38 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.97 % 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: -4.69 (0.11), residues: 3275 helix: -4.22 (0.08), residues: 1021 sheet: -2.19 (0.22), residues: 491 loop : -2.69 (0.12), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG J 346 TYR 0.059 0.004 TYR G 9 PHE 0.035 0.004 PHE C 207 TRP 0.036 0.004 TRP E 274 HIS 0.022 0.003 HIS F 335 Details of bonding type rmsd covalent geometry : bond 0.01115 (30035) covalent geometry : angle 1.18730 (41212) hydrogen bonds : bond 0.32757 ( 789) hydrogen bonds : angle 11.04785 ( 2178) metal coordination : bond 0.34345 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 632 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.6920 (mt) cc_final: 0.6596 (pp) REVERT: A 560 ASP cc_start: 0.7143 (m-30) cc_final: 0.6846 (t0) REVERT: A 562 GLN cc_start: 0.7171 (mm110) cc_final: 0.6894 (mp10) REVERT: B 250 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8087 (t) REVERT: C 39 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8530 (pp) REVERT: C 204 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7736 (tm) REVERT: D 201 THR cc_start: 0.8935 (t) cc_final: 0.8574 (m) REVERT: D 220 MET cc_start: 0.7589 (mmm) cc_final: 0.7159 (mmt) REVERT: F 35 ASN cc_start: 0.8103 (m-40) cc_final: 0.7896 (m-40) REVERT: F 287 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7701 (p90) REVERT: G 201 THR cc_start: 0.8456 (t) cc_final: 0.8112 (p) REVERT: H 102 ARG cc_start: 0.4394 (OUTLIER) cc_final: 0.3625 (tpt170) REVERT: H 156 SER cc_start: 0.5500 (p) cc_final: 0.4779 (t) REVERT: I 11 ASP cc_start: 0.6316 (p0) cc_final: 0.6018 (p0) REVERT: I 62 TYR cc_start: 0.8182 (p90) cc_final: 0.7935 (p90) outliers start: 58 outliers final: 21 residues processed: 676 average time/residue: 0.2008 time to fit residues: 206.2206 Evaluate side-chains 434 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 408 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 287 PHE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 172 ARG Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 227 PHE Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain J residue 309 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 226 HIS A 227 GLN A 420 HIS A 486 ASN A 493 GLN A 562 GLN A 581 ASN B 6 ASN B 77 HIS B 299 HIS C 77 HIS C 153 ASN C 299 HIS C 349 HIS D 72 GLN D 77 HIS D 145 ASN D 174 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS F 77 HIS F 110 GLN F 145 ASN F 214 HIS ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 349 HIS E 77 HIS E 299 HIS E 349 HIS ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN G 299 HIS G 349 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN H 71 GLN H 105 GLN I 46 HIS I 66 ASN I 151 HIS I 153 HIS I 194 HIS I 214 ASN ** I 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 237 HIS J 309 ASN J 324 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.189956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.147356 restraints weight = 37836.476| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 4.26 r_work: 0.3209 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.933 30041 Z= 0.398 Angle : 0.630 9.708 41212 Z= 0.336 Chirality : 0.042 0.213 4569 Planarity : 0.006 0.058 4876 Dihedral : 17.447 178.494 5109 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.04 % Allowed : 9.25 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -3.47 (0.13), residues: 3275 helix: -2.72 (0.12), residues: 1057 sheet: -1.72 (0.22), residues: 511 loop : -2.17 (0.13), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 37 TYR 0.021 0.002 TYR A 210 PHE 0.016 0.002 PHE I 2 TRP 0.022 0.002 TRP I 203 HIS 0.011 0.001 HIS I 237 Details of bonding type rmsd covalent geometry : bond 0.00303 (30035) covalent geometry : angle 0.62984 (41212) hydrogen bonds : bond 0.04680 ( 789) hydrogen bonds : angle 6.03711 ( 2178) metal coordination : bond 0.78937 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 447 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4229 (tpp) cc_final: 0.3685 (tpp) REVERT: A 181 LEU cc_start: 0.7035 (mt) cc_final: 0.6526 (pp) REVERT: A 190 ASN cc_start: 0.8192 (t0) cc_final: 0.7904 (t0) REVERT: A 560 ASP cc_start: 0.7375 (m-30) cc_final: 0.6693 (t0) REVERT: A 568 VAL cc_start: 0.8749 (t) cc_final: 0.8544 (m) REVERT: A 575 GLU cc_start: 0.6591 (mm-30) cc_final: 0.6305 (pm20) REVERT: A 583 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.6952 (tp) REVERT: B 27 ASP cc_start: 0.8029 (m-30) cc_final: 0.7827 (m-30) REVERT: B 110 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7258 (mm-40) REVERT: B 126 THR cc_start: 0.8456 (m) cc_final: 0.8108 (p) REVERT: C 146 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8811 (p) REVERT: C 287 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.5810 (p90) REVERT: D 146 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8419 (p) REVERT: D 176 THR cc_start: 0.9079 (m) cc_final: 0.8808 (p) REVERT: D 287 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7405 (p90) REVERT: F 210 ARG cc_start: 0.8274 (ttm110) cc_final: 0.7737 (ttm110) REVERT: F 337 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8841 (tp) REVERT: E 192 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: E 287 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.6980 (p90) REVERT: G 172 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8159 (ttp80) REVERT: G 183 ASN cc_start: 0.8360 (m-40) cc_final: 0.8119 (t0) REVERT: H 101 PHE cc_start: 0.5773 (m-80) cc_final: 0.5436 (m-10) REVERT: H 102 ARG cc_start: 0.4873 (OUTLIER) cc_final: 0.3513 (tpt170) REVERT: H 134 ASP cc_start: 0.5450 (t70) cc_final: 0.4806 (t70) REVERT: H 169 MET cc_start: 0.4919 (tmt) cc_final: 0.2699 (mmm) REVERT: I 11 ASP cc_start: 0.6039 (p0) cc_final: 0.5503 (p0) REVERT: I 62 TYR cc_start: 0.8252 (p90) cc_final: 0.7350 (p90) REVERT: I 119 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.6002 (tp) REVERT: I 140 TYR cc_start: 0.6732 (p90) cc_final: 0.6421 (p90) REVERT: I 260 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6530 (mm-30) REVERT: I 365 TYR cc_start: 0.6230 (m-80) cc_final: 0.5853 (m-80) REVERT: J 258 GLU cc_start: 0.7750 (tp30) cc_final: 0.7333 (tp30) REVERT: J 342 MET cc_start: 0.3421 (mtm) cc_final: 0.3200 (ptp) REVERT: J 368 HIS cc_start: 0.8238 (m-70) cc_final: 0.8020 (m-70) REVERT: J 380 PHE cc_start: 0.7468 (m-80) cc_final: 0.6974 (m-80) outliers start: 90 outliers final: 33 residues processed: 523 average time/residue: 0.1919 time to fit residues: 154.5959 Evaluate side-chains 390 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 346 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 287 PHE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 172 ARG Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 255 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 319 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 270 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 334 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN B 69 ASN B 311 GLN C 42 GLN C 311 GLN ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 HIS D 110 GLN D 299 HIS F 110 GLN F 145 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN G 214 HIS ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 237 HIS I 324 ASN I 345 GLN J 296 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.185775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.141956 restraints weight = 37702.277| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.56 r_work: 0.3046 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 30041 Z= 0.187 Angle : 0.632 8.623 41212 Z= 0.332 Chirality : 0.043 0.212 4569 Planarity : 0.005 0.052 4876 Dihedral : 17.081 174.501 5088 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.34 % Allowed : 11.48 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -2.85 (0.13), residues: 3275 helix: -1.89 (0.14), residues: 1060 sheet: -1.52 (0.22), residues: 521 loop : -1.97 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 220 TYR 0.023 0.002 TYR D 275 PHE 0.022 0.002 PHE E 287 TRP 0.020 0.002 TRP C 161 HIS 0.013 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00445 (30035) covalent geometry : angle 0.63169 (41212) hydrogen bonds : bond 0.04696 ( 789) hydrogen bonds : angle 5.51909 ( 2178) metal coordination : bond 0.01428 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 367 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4273 (tpp) cc_final: 0.3734 (tpp) REVERT: A 181 LEU cc_start: 0.7009 (mt) cc_final: 0.6494 (pp) REVERT: A 186 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6522 (tt) REVERT: A 190 ASN cc_start: 0.8299 (t0) cc_final: 0.8007 (t0) REVERT: A 535 GLU cc_start: 0.6407 (mt-10) cc_final: 0.5845 (pm20) REVERT: A 560 ASP cc_start: 0.7518 (m-30) cc_final: 0.6625 (t0) REVERT: A 568 VAL cc_start: 0.8807 (t) cc_final: 0.8592 (m) REVERT: A 622 TYR cc_start: 0.7724 (p90) cc_final: 0.7489 (p90) REVERT: B 27 ASP cc_start: 0.8138 (m-30) cc_final: 0.7920 (m-30) REVERT: B 28 ARG cc_start: 0.8649 (ttp80) cc_final: 0.8431 (ttp-170) REVERT: C 39 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8632 (pp) REVERT: C 287 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.6020 (p90) REVERT: D 146 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8411 (p) REVERT: D 176 THR cc_start: 0.9195 (m) cc_final: 0.8970 (p) REVERT: D 287 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7598 (p90) REVERT: F 107 LYS cc_start: 0.9037 (mmmt) cc_final: 0.8694 (tttm) REVERT: F 170 ASP cc_start: 0.8287 (t0) cc_final: 0.8031 (t0) REVERT: F 337 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8986 (tp) REVERT: E 192 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: E 287 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7271 (p90) REVERT: G 172 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8320 (ttp80) REVERT: G 183 ASN cc_start: 0.8388 (m-40) cc_final: 0.8132 (t0) REVERT: H 101 PHE cc_start: 0.5782 (m-80) cc_final: 0.5375 (m-10) REVERT: H 102 ARG cc_start: 0.4106 (OUTLIER) cc_final: 0.3094 (tpt170) REVERT: H 156 SER cc_start: 0.4983 (p) cc_final: 0.4456 (t) REVERT: H 169 MET cc_start: 0.4182 (tmt) cc_final: 0.3140 (mmm) REVERT: I 11 ASP cc_start: 0.6132 (p0) cc_final: 0.5495 (p0) REVERT: I 62 TYR cc_start: 0.8421 (p90) cc_final: 0.7534 (p90) REVERT: I 119 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5774 (tt) REVERT: I 140 TYR cc_start: 0.6615 (p90) cc_final: 0.6242 (p90) REVERT: I 151 HIS cc_start: 0.6334 (p90) cc_final: 0.5492 (p90) REVERT: I 260 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6514 (mm-30) REVERT: I 365 TYR cc_start: 0.6341 (m-80) cc_final: 0.6032 (m-80) REVERT: J 244 PHE cc_start: 0.7337 (m-80) cc_final: 0.6673 (m-80) REVERT: J 258 GLU cc_start: 0.7831 (tp30) cc_final: 0.6813 (mm-30) REVERT: J 304 LEU cc_start: 0.6590 (mt) cc_final: 0.6264 (mt) REVERT: J 309 ASN cc_start: 0.7634 (m-40) cc_final: 0.6907 (m110) REVERT: J 342 MET cc_start: 0.3443 (mtm) cc_final: 0.3111 (ptp) REVERT: J 368 HIS cc_start: 0.8420 (m-70) cc_final: 0.8127 (m-70) REVERT: J 380 PHE cc_start: 0.7841 (m-80) cc_final: 0.7400 (m-80) outliers start: 99 outliers final: 59 residues processed: 451 average time/residue: 0.1909 time to fit residues: 134.0084 Evaluate side-chains 404 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 334 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 287 PHE Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 349 HIS Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 172 ARG Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 323 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain J residue 255 ILE Chi-restraints excluded: chain J residue 388 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 101 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 113 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 228 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 257 optimal weight: 0.0980 chunk 95 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 311 GLN F 110 GLN F 179 GLN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 HIS I 345 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.188699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.146805 restraints weight = 37637.404| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.36 r_work: 0.3123 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30041 Z= 0.117 Angle : 0.545 8.618 41212 Z= 0.286 Chirality : 0.040 0.200 4569 Planarity : 0.005 0.052 4876 Dihedral : 16.801 174.275 5082 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.80 % Allowed : 13.40 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -2.35 (0.14), residues: 3275 helix: -1.29 (0.15), residues: 1065 sheet: -1.31 (0.22), residues: 536 loop : -1.78 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 210 TYR 0.020 0.001 TYR D 275 PHE 0.015 0.001 PHE I 2 TRP 0.015 0.001 TRP I 203 HIS 0.006 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00267 (30035) covalent geometry : angle 0.54471 (41212) hydrogen bonds : bond 0.03751 ( 789) hydrogen bonds : angle 5.11123 ( 2178) metal coordination : bond 0.00894 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 366 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.7620 (mt0) cc_final: 0.7011 (mm-40) REVERT: A 177 MET cc_start: 0.4460 (tpp) cc_final: 0.3976 (tpp) REVERT: A 181 LEU cc_start: 0.6950 (mt) cc_final: 0.6489 (pp) REVERT: A 190 ASN cc_start: 0.8264 (t0) cc_final: 0.8018 (t0) REVERT: A 560 ASP cc_start: 0.7590 (m-30) cc_final: 0.6777 (t0) REVERT: A 619 TYR cc_start: 0.6878 (m-80) cc_final: 0.6324 (m-80) REVERT: B 27 ASP cc_start: 0.8112 (m-30) cc_final: 0.7894 (m-30) REVERT: B 28 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8446 (ttp-170) REVERT: B 43 MET cc_start: 0.9140 (tpp) cc_final: 0.8780 (mmt) REVERT: C 287 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.5943 (p90) REVERT: D 146 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8388 (p) REVERT: D 210 ARG cc_start: 0.8366 (ttm110) cc_final: 0.8079 (ttp-170) REVERT: D 287 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7457 (p90) REVERT: F 107 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8641 (tttm) REVERT: F 210 ARG cc_start: 0.8452 (ttm110) cc_final: 0.7855 (ttm110) REVERT: F 337 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9019 (tp) REVERT: E 287 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7038 (p90) REVERT: E 291 ARG cc_start: 0.7653 (tpp80) cc_final: 0.7331 (ttm-80) REVERT: G 172 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8237 (ttp80) REVERT: G 183 ASN cc_start: 0.8359 (m-40) cc_final: 0.8130 (t0) REVERT: H 102 ARG cc_start: 0.4208 (OUTLIER) cc_final: 0.3095 (tpt170) REVERT: H 150 HIS cc_start: 0.7179 (t-90) cc_final: 0.6470 (m170) REVERT: H 156 SER cc_start: 0.5015 (p) cc_final: 0.4463 (t) REVERT: H 169 MET cc_start: 0.4064 (tmt) cc_final: 0.3265 (mmm) REVERT: I 11 ASP cc_start: 0.6439 (p0) cc_final: 0.6212 (p0) REVERT: I 29 ASP cc_start: 0.5591 (t70) cc_final: 0.4858 (p0) REVERT: I 62 TYR cc_start: 0.8438 (p90) cc_final: 0.7754 (p90) REVERT: I 119 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5526 (tp) REVERT: I 260 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6475 (mm-30) REVERT: I 323 MET cc_start: 0.2437 (ppp) cc_final: 0.2072 (pmm) REVERT: J 256 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7551 (pt0) REVERT: J 258 GLU cc_start: 0.7762 (tp30) cc_final: 0.7350 (tp30) REVERT: J 304 LEU cc_start: 0.6751 (mt) cc_final: 0.6470 (mt) REVERT: J 309 ASN cc_start: 0.7710 (m-40) cc_final: 0.6983 (m110) REVERT: J 368 HIS cc_start: 0.8463 (m-70) cc_final: 0.8201 (m-70) REVERT: J 380 PHE cc_start: 0.8049 (m-80) cc_final: 0.7531 (m-80) outliers start: 83 outliers final: 52 residues processed: 431 average time/residue: 0.1849 time to fit residues: 124.8776 Evaluate side-chains 395 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 335 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 287 PHE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 349 HIS Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 172 ARG Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain I residue 31 HIS Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 255 ILE Chi-restraints excluded: chain J residue 388 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 6 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 126 optimal weight: 0.1980 chunk 35 optimal weight: 0.0770 chunk 186 optimal weight: 7.9990 chunk 269 optimal weight: 9.9990 chunk 176 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 311 GLN D 42 GLN D 72 GLN F 110 GLN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** 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 = 0.4095 r_free = 0.4095 target = 0.185534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141159 restraints weight = 37584.091| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 4.66 r_work: 0.3092 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30041 Z= 0.173 Angle : 0.590 9.730 41212 Z= 0.307 Chirality : 0.042 0.202 4569 Planarity : 0.005 0.052 4876 Dihedral : 16.738 174.270 5078 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.54 % Allowed : 13.23 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -2.17 (0.14), residues: 3275 helix: -1.03 (0.15), residues: 1059 sheet: -1.36 (0.22), residues: 558 loop : -1.70 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 291 TYR 0.020 0.002 TYR D 275 PHE 0.019 0.002 PHE D 287 TRP 0.015 0.001 TRP C 161 HIS 0.014 0.001 HIS I 31 Details of bonding type rmsd covalent geometry : bond 0.00412 (30035) covalent geometry : angle 0.59021 (41212) hydrogen bonds : bond 0.04066 ( 789) hydrogen bonds : angle 5.10947 ( 2178) metal coordination : bond 0.00454 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 345 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.7729 (mt0) cc_final: 0.6860 (mm-40) REVERT: A 123 TYR cc_start: 0.8170 (t80) cc_final: 0.7612 (t80) REVERT: A 177 MET cc_start: 0.4381 (tpp) cc_final: 0.4007 (tpp) REVERT: A 181 LEU cc_start: 0.6972 (mt) cc_final: 0.6483 (pp) REVERT: A 190 ASN cc_start: 0.8363 (t0) cc_final: 0.8067 (t0) REVERT: A 535 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6663 (mt-10) REVERT: A 545 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.6517 (mp10) REVERT: A 560 ASP cc_start: 0.7529 (m-30) cc_final: 0.6597 (t0) REVERT: A 619 TYR cc_start: 0.7049 (m-80) cc_final: 0.6477 (m-80) REVERT: B 27 ASP cc_start: 0.8145 (m-30) cc_final: 0.7910 (m-30) REVERT: B 28 ARG cc_start: 0.8671 (ttp80) cc_final: 0.8425 (ttp-170) REVERT: B 43 MET cc_start: 0.9227 (tpp) cc_final: 0.8873 (mmt) REVERT: C 39 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8658 (pp) REVERT: C 287 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.5883 (p90) REVERT: D 6 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8540 (t0) REVERT: D 146 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8388 (p) REVERT: D 210 ARG cc_start: 0.8441 (ttm110) cc_final: 0.8149 (ttp-170) REVERT: D 287 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7493 (p90) REVERT: D 295 THR cc_start: 0.8624 (p) cc_final: 0.8408 (t) REVERT: F 107 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8764 (pttp) REVERT: F 170 ASP cc_start: 0.8207 (t0) cc_final: 0.7951 (t0) REVERT: F 337 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9022 (tp) REVERT: E 287 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7131 (p90) REVERT: G 172 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8293 (ttp80) REVERT: G 183 ASN cc_start: 0.8387 (m-40) cc_final: 0.8160 (t0) REVERT: H 83 PHE cc_start: 0.4700 (OUTLIER) cc_final: 0.2909 (m-80) REVERT: H 102 ARG cc_start: 0.4224 (OUTLIER) cc_final: 0.3106 (tpt-90) REVERT: H 156 SER cc_start: 0.4749 (p) cc_final: 0.4306 (t) REVERT: I 11 ASP cc_start: 0.6165 (p0) cc_final: 0.5937 (p0) REVERT: I 29 ASP cc_start: 0.5535 (t70) cc_final: 0.4891 (p0) REVERT: I 62 TYR cc_start: 0.8280 (p90) cc_final: 0.7400 (p90) REVERT: I 119 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5728 (tt) REVERT: I 260 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6585 (mm-30) REVERT: I 323 MET cc_start: 0.2100 (ppp) cc_final: 0.1844 (pmm) REVERT: I 365 TYR cc_start: 0.5983 (m-80) cc_final: 0.5716 (m-80) REVERT: J 244 PHE cc_start: 0.6927 (m-80) cc_final: 0.6619 (m-80) REVERT: J 256 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7730 (pt0) REVERT: J 258 GLU cc_start: 0.7586 (tp30) cc_final: 0.7322 (tp30) REVERT: J 304 LEU cc_start: 0.6393 (mt) cc_final: 0.6164 (mt) REVERT: J 309 ASN cc_start: 0.7457 (m-40) cc_final: 0.6774 (m110) REVERT: J 368 HIS cc_start: 0.8161 (m-70) cc_final: 0.7912 (m-70) REVERT: J 380 PHE cc_start: 0.7419 (m-80) cc_final: 0.6935 (m-80) outliers start: 105 outliers final: 69 residues processed: 432 average time/residue: 0.1873 time to fit residues: 127.3091 Evaluate side-chains 406 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 325 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 545 GLN Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain D residue 6 ASN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 287 PHE Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 349 HIS Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 172 ARG Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 323 ASN Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 255 ILE Chi-restraints excluded: chain J residue 388 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 4 optimal weight: 7.9990 chunk 277 optimal weight: 0.0270 chunk 152 optimal weight: 0.7980 chunk 225 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 280 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 317 optimal weight: 20.0000 chunk 301 optimal weight: 30.0000 chunk 103 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 overall best weight: 2.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 493 GLN C 311 GLN D 84 HIS ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS I 345 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.183366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.140957 restraints weight = 37507.954| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.42 r_work: 0.2999 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 30041 Z= 0.226 Angle : 0.638 8.902 41212 Z= 0.332 Chirality : 0.044 0.207 4569 Planarity : 0.005 0.054 4876 Dihedral : 16.841 174.911 5078 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.78 % Allowed : 13.74 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -2.12 (0.14), residues: 3275 helix: -0.93 (0.15), residues: 1057 sheet: -1.39 (0.22), residues: 562 loop : -1.69 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 210 TYR 0.022 0.002 TYR D 275 PHE 0.024 0.002 PHE E 287 TRP 0.016 0.002 TRP B 152 HIS 0.007 0.001 HIS E 335 Details of bonding type rmsd covalent geometry : bond 0.00544 (30035) covalent geometry : angle 0.63777 (41212) hydrogen bonds : bond 0.04385 ( 789) hydrogen bonds : angle 5.19683 ( 2178) metal coordination : bond 0.00431 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 326 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.6125 (tt) cc_final: 0.5903 (tt) REVERT: A 123 TYR cc_start: 0.8262 (t80) cc_final: 0.7732 (t80) REVERT: A 177 MET cc_start: 0.4776 (tpp) cc_final: 0.4464 (tpp) REVERT: A 181 LEU cc_start: 0.7019 (mt) cc_final: 0.6459 (pp) REVERT: A 190 ASN cc_start: 0.8252 (t0) cc_final: 0.7987 (t0) REVERT: A 545 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6638 (mp10) REVERT: A 560 ASP cc_start: 0.7641 (m-30) cc_final: 0.6663 (t0) REVERT: A 583 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8077 (tp) REVERT: B 28 ARG cc_start: 0.8658 (ttp80) cc_final: 0.8416 (ttp-170) REVERT: C 39 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8697 (pp) REVERT: C 220 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7519 (mpp) REVERT: C 287 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.6032 (p90) REVERT: D 6 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8555 (t0) REVERT: D 146 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8430 (p) REVERT: D 287 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7673 (p90) REVERT: D 295 THR cc_start: 0.8663 (p) cc_final: 0.8434 (t) REVERT: F 170 ASP cc_start: 0.8349 (t0) cc_final: 0.8140 (t0) REVERT: F 337 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9049 (tp) REVERT: E 287 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7346 (p90) REVERT: G 183 ASN cc_start: 0.8372 (m-40) cc_final: 0.8144 (t0) REVERT: H 83 PHE cc_start: 0.4780 (OUTLIER) cc_final: 0.2881 (m-80) REVERT: H 102 ARG cc_start: 0.3820 (OUTLIER) cc_final: 0.2717 (tpt170) REVERT: I 11 ASP cc_start: 0.6451 (p0) cc_final: 0.6228 (p0) REVERT: I 62 TYR cc_start: 0.8506 (p90) cc_final: 0.7702 (p90) REVERT: I 260 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6547 (mm-30) REVERT: I 323 MET cc_start: 0.2974 (ppp) cc_final: 0.2651 (pmm) REVERT: J 228 MET cc_start: 0.7558 (ppp) cc_final: 0.7231 (ppp) REVERT: J 244 PHE cc_start: 0.7153 (m-80) cc_final: 0.6897 (m-80) REVERT: J 256 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7568 (pt0) REVERT: J 304 LEU cc_start: 0.6874 (mt) cc_final: 0.6618 (mt) REVERT: J 309 ASN cc_start: 0.7824 (m-40) cc_final: 0.7040 (m110) REVERT: J 368 HIS cc_start: 0.8514 (m-70) cc_final: 0.8195 (m-70) REVERT: J 380 PHE cc_start: 0.8068 (m-80) cc_final: 0.7711 (m-80) outliers start: 112 outliers final: 73 residues processed: 415 average time/residue: 0.1868 time to fit residues: 121.4454 Evaluate side-chains 401 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 316 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 545 GLN Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain D residue 6 ASN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 287 PHE Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 349 HIS Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 323 ASN Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 255 ILE Chi-restraints excluded: chain J residue 388 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 217 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 216 optimal weight: 0.0670 chunk 157 optimal weight: 0.5980 chunk 175 optimal weight: 0.1980 chunk 301 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 110 optimal weight: 0.0670 chunk 103 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS I 153 HIS I 214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.188566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.145054 restraints weight = 37854.344| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.43 r_work: 0.3124 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30041 Z= 0.101 Angle : 0.527 9.065 41212 Z= 0.274 Chirality : 0.039 0.183 4569 Planarity : 0.004 0.055 4876 Dihedral : 16.626 173.757 5074 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.73 % Allowed : 14.89 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.75 (0.14), residues: 3275 helix: -0.49 (0.16), residues: 1074 sheet: -1.21 (0.23), residues: 532 loop : -1.57 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 291 TYR 0.019 0.001 TYR D 275 PHE 0.011 0.001 PHE D 227 TRP 0.015 0.001 TRP E 159 HIS 0.006 0.001 HIS I 296 Details of bonding type rmsd covalent geometry : bond 0.00226 (30035) covalent geometry : angle 0.52652 (41212) hydrogen bonds : bond 0.03271 ( 789) hydrogen bonds : angle 4.80915 ( 2178) metal coordination : bond 0.01447 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 363 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.7574 (mt0) cc_final: 0.6922 (mm-40) REVERT: A 177 MET cc_start: 0.4234 (tpp) cc_final: 0.3912 (tpp) REVERT: A 181 LEU cc_start: 0.7045 (mt) cc_final: 0.6526 (pp) REVERT: A 190 ASN cc_start: 0.8360 (t0) cc_final: 0.8118 (t0) REVERT: A 560 ASP cc_start: 0.7626 (m-30) cc_final: 0.6675 (t0) REVERT: A 583 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7924 (tp) REVERT: A 619 TYR cc_start: 0.7232 (m-80) cc_final: 0.6909 (m-80) REVERT: B 27 ASP cc_start: 0.8116 (m-30) cc_final: 0.7884 (m-30) REVERT: B 28 ARG cc_start: 0.8686 (ttp80) cc_final: 0.8405 (ttp-170) REVERT: B 43 MET cc_start: 0.9078 (tpp) cc_final: 0.8794 (mmt) REVERT: C 39 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8519 (pp) REVERT: C 287 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.5965 (p90) REVERT: D 146 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8361 (p) REVERT: D 287 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7347 (p90) REVERT: F 170 ASP cc_start: 0.8181 (t0) cc_final: 0.7807 (t0) REVERT: F 210 ARG cc_start: 0.8445 (ttm110) cc_final: 0.7881 (ttm110) REVERT: F 337 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8974 (tp) REVERT: E 287 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.6957 (p90) REVERT: E 291 ARG cc_start: 0.7768 (tpp80) cc_final: 0.7492 (ttm-80) REVERT: G 172 ARG cc_start: 0.8330 (ttp80) cc_final: 0.7940 (ttp80) REVERT: G 183 ASN cc_start: 0.8275 (m-40) cc_final: 0.8075 (t0) REVERT: H 23 LYS cc_start: 0.6795 (mttt) cc_final: 0.6409 (tptp) REVERT: H 83 PHE cc_start: 0.4779 (OUTLIER) cc_final: 0.3147 (m-80) REVERT: H 102 ARG cc_start: 0.3907 (OUTLIER) cc_final: 0.2918 (tpt-90) REVERT: I 29 ASP cc_start: 0.5924 (t0) cc_final: 0.5013 (p0) REVERT: I 62 TYR cc_start: 0.8377 (p90) cc_final: 0.7677 (p90) REVERT: I 260 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6596 (mm-30) REVERT: I 323 MET cc_start: 0.2691 (ppp) cc_final: 0.2470 (pmm) REVERT: J 228 MET cc_start: 0.7563 (ppp) cc_final: 0.7335 (ppp) REVERT: J 256 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7633 (pt0) REVERT: J 264 GLU cc_start: 0.5939 (tp30) cc_final: 0.5697 (tp30) REVERT: J 304 LEU cc_start: 0.6884 (mt) cc_final: 0.6617 (mt) REVERT: J 309 ASN cc_start: 0.7697 (m-40) cc_final: 0.6954 (m110) REVERT: J 368 HIS cc_start: 0.8514 (m-70) cc_final: 0.8238 (m-70) REVERT: J 380 PHE cc_start: 0.7893 (m-80) cc_final: 0.7473 (m-80) outliers start: 81 outliers final: 56 residues processed: 428 average time/residue: 0.1928 time to fit residues: 128.0302 Evaluate side-chains 402 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 337 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 287 PHE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 349 HIS Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 323 ASN Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 255 ILE Chi-restraints excluded: chain J residue 298 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 147 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 277 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 327 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 311 GLN D 110 GLN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS ** I 194 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 = 0.4096 r_free = 0.4096 target = 0.185451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142536 restraints weight = 37710.655| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.41 r_work: 0.3060 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30041 Z= 0.153 Angle : 0.570 8.656 41212 Z= 0.295 Chirality : 0.041 0.186 4569 Planarity : 0.005 0.075 4876 Dihedral : 16.583 173.868 5074 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.80 % Allowed : 15.02 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.68 (0.14), residues: 3275 helix: -0.38 (0.16), residues: 1068 sheet: -1.17 (0.22), residues: 559 loop : -1.55 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 210 TYR 0.020 0.001 TYR D 275 PHE 0.020 0.001 PHE E 287 TRP 0.014 0.001 TRP B 152 HIS 0.011 0.001 HIS I 194 Details of bonding type rmsd covalent geometry : bond 0.00364 (30035) covalent geometry : angle 0.56979 (41212) hydrogen bonds : bond 0.03669 ( 789) hydrogen bonds : angle 4.89320 ( 2178) metal coordination : bond 0.00159 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 329 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.7658 (mt0) cc_final: 0.6868 (mm-40) REVERT: A 177 MET cc_start: 0.4398 (tpp) cc_final: 0.4040 (tpp) REVERT: A 181 LEU cc_start: 0.7118 (mt) cc_final: 0.6509 (pp) REVERT: A 190 ASN cc_start: 0.8360 (t0) cc_final: 0.8112 (t0) REVERT: A 560 ASP cc_start: 0.7619 (m-30) cc_final: 0.6652 (t0) REVERT: A 583 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8036 (tp) REVERT: A 619 TYR cc_start: 0.7265 (m-80) cc_final: 0.6689 (m-80) REVERT: B 27 ASP cc_start: 0.8071 (m-30) cc_final: 0.7830 (m-30) REVERT: B 28 ARG cc_start: 0.8722 (ttp80) cc_final: 0.8472 (ttp-170) REVERT: B 43 MET cc_start: 0.9187 (tpp) cc_final: 0.8877 (mmt) REVERT: B 98 ARG cc_start: 0.7981 (mmt90) cc_final: 0.7745 (mmt90) REVERT: C 39 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8613 (pp) REVERT: C 287 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.5873 (p90) REVERT: D 86 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7825 (mm-30) REVERT: D 146 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8384 (p) REVERT: D 287 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7421 (p90) REVERT: D 348 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8461 (pt0) REVERT: F 146 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8432 (m) REVERT: F 170 ASP cc_start: 0.8291 (t0) cc_final: 0.7967 (t0) REVERT: F 210 ARG cc_start: 0.8510 (ttm110) cc_final: 0.7873 (ttm110) REVERT: F 337 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8967 (tp) REVERT: E 287 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7168 (p90) REVERT: E 291 ARG cc_start: 0.7822 (tpp80) cc_final: 0.7561 (ttm-80) REVERT: G 172 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8040 (ttp80) REVERT: G 183 ASN cc_start: 0.8315 (m-40) cc_final: 0.8113 (t0) REVERT: H 83 PHE cc_start: 0.4875 (OUTLIER) cc_final: 0.3220 (m-80) REVERT: H 102 ARG cc_start: 0.3810 (OUTLIER) cc_final: 0.2754 (tpt-90) REVERT: H 150 HIS cc_start: 0.7505 (t70) cc_final: 0.6964 (m-70) REVERT: I 11 ASP cc_start: 0.6387 (p0) cc_final: 0.6166 (p0) REVERT: I 29 ASP cc_start: 0.5979 (t0) cc_final: 0.5003 (p0) REVERT: I 62 TYR cc_start: 0.8394 (p90) cc_final: 0.7625 (p90) REVERT: I 194 HIS cc_start: 0.3589 (t70) cc_final: 0.3242 (t-90) REVERT: I 260 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6555 (mm-30) REVERT: I 323 MET cc_start: 0.2875 (ppp) cc_final: 0.2652 (pmm) REVERT: J 228 MET cc_start: 0.7587 (ppp) cc_final: 0.7373 (ppp) REVERT: J 256 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7677 (pt0) REVERT: J 304 LEU cc_start: 0.6918 (mt) cc_final: 0.6658 (mt) REVERT: J 309 ASN cc_start: 0.7740 (m-40) cc_final: 0.7476 (m-40) REVERT: J 368 HIS cc_start: 0.8529 (m-70) cc_final: 0.8176 (m-70) REVERT: J 380 PHE cc_start: 0.7918 (m-80) cc_final: 0.7477 (m-80) outliers start: 83 outliers final: 67 residues processed: 393 average time/residue: 0.1866 time to fit residues: 114.9771 Evaluate side-chains 397 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 318 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 348 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 287 PHE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 349 HIS Chi-restraints excluded: chain E residue 43 MET Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 255 ILE Chi-restraints excluded: chain J residue 388 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 250 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 256 optimal weight: 0.9990 chunk 307 optimal weight: 50.0000 chunk 272 optimal weight: 5.9990 chunk 287 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 0.0070 chunk 88 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN C 311 GLN D 110 GLN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.187643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.143543 restraints weight = 37925.875| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 4.48 r_work: 0.3168 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30041 Z= 0.113 Angle : 0.538 10.195 41212 Z= 0.280 Chirality : 0.040 0.179 4569 Planarity : 0.004 0.065 4876 Dihedral : 16.520 173.199 5074 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.90 % Allowed : 15.19 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.47 (0.14), residues: 3275 helix: -0.15 (0.16), residues: 1066 sheet: -1.06 (0.23), residues: 531 loop : -1.47 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 210 TYR 0.019 0.001 TYR D 275 PHE 0.014 0.001 PHE E 287 TRP 0.013 0.001 TRP B 152 HIS 0.011 0.001 HIS I 194 Details of bonding type rmsd covalent geometry : bond 0.00263 (30035) covalent geometry : angle 0.53820 (41212) hydrogen bonds : bond 0.03313 ( 789) hydrogen bonds : angle 4.77487 ( 2178) metal coordination : bond 0.00149 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 334 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.7525 (mt0) cc_final: 0.7127 (mm-40) REVERT: A 177 MET cc_start: 0.4219 (tpp) cc_final: 0.3860 (tpp) REVERT: A 181 LEU cc_start: 0.6950 (mt) cc_final: 0.6368 (pp) REVERT: A 190 ASN cc_start: 0.8395 (t0) cc_final: 0.8115 (t0) REVERT: A 545 GLN cc_start: 0.6549 (mm-40) cc_final: 0.6304 (mp10) REVERT: A 560 ASP cc_start: 0.7524 (m-30) cc_final: 0.6580 (t0) REVERT: A 583 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.8013 (tp) REVERT: A 619 TYR cc_start: 0.6934 (m-80) cc_final: 0.6510 (m-80) REVERT: B 27 ASP cc_start: 0.8022 (m-30) cc_final: 0.7788 (m-30) REVERT: B 28 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8404 (ttp-170) REVERT: B 43 MET cc_start: 0.9081 (tpp) cc_final: 0.8807 (mmt) REVERT: C 39 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8560 (pp) REVERT: C 287 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.5811 (p90) REVERT: D 86 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: D 146 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8356 (p) REVERT: D 287 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7351 (p90) REVERT: F 210 ARG cc_start: 0.8398 (ttm110) cc_final: 0.7814 (ttm110) REVERT: E 96 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7618 (mm-30) REVERT: E 287 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7024 (p90) REVERT: E 291 ARG cc_start: 0.7727 (tpp80) cc_final: 0.7452 (ttm-80) REVERT: G 172 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8019 (ttp80) REVERT: G 183 ASN cc_start: 0.8236 (m-40) cc_final: 0.8034 (t0) REVERT: G 220 MET cc_start: 0.7695 (ttm) cc_final: 0.7484 (ttt) REVERT: H 23 LYS cc_start: 0.6682 (mttt) cc_final: 0.6280 (tptp) REVERT: H 83 PHE cc_start: 0.4682 (OUTLIER) cc_final: 0.3319 (m-80) REVERT: H 102 ARG cc_start: 0.4174 (OUTLIER) cc_final: 0.3032 (tpt170) REVERT: H 150 HIS cc_start: 0.7215 (t70) cc_final: 0.6746 (m-70) REVERT: I 29 ASP cc_start: 0.5694 (t0) cc_final: 0.4689 (p0) REVERT: I 62 TYR cc_start: 0.8186 (p90) cc_final: 0.7310 (p90) REVERT: I 96 ARG cc_start: 0.7095 (mtm-85) cc_final: 0.6694 (ttp-110) REVERT: I 194 HIS cc_start: 0.3948 (t70) cc_final: 0.3659 (t70) REVERT: I 260 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6611 (mm-30) REVERT: J 228 MET cc_start: 0.7537 (ppp) cc_final: 0.7315 (ppp) REVERT: J 251 PHE cc_start: 0.7658 (t80) cc_final: 0.7396 (t80) REVERT: J 304 LEU cc_start: 0.6587 (mt) cc_final: 0.6369 (mt) REVERT: J 368 HIS cc_start: 0.8144 (m-70) cc_final: 0.7912 (m-70) REVERT: J 380 PHE cc_start: 0.7281 (m-80) cc_final: 0.6839 (m-80) outliers start: 86 outliers final: 66 residues processed: 403 average time/residue: 0.1867 time to fit residues: 117.4135 Evaluate side-chains 398 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 322 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 287 PHE Chi-restraints excluded: chain F residue 349 HIS Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 323 ASN Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain J residue 250 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 51 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 260 optimal weight: 9.9990 chunk 156 optimal weight: 0.7980 chunk 283 optimal weight: 0.0070 chunk 187 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 chunk 338 optimal weight: 1.9990 chunk 179 optimal weight: 0.0980 chunk 257 optimal weight: 3.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 311 GLN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.187886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144504 restraints weight = 37607.505| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 4.03 r_work: 0.3173 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30041 Z= 0.114 Angle : 0.537 9.911 41212 Z= 0.279 Chirality : 0.040 0.170 4569 Planarity : 0.004 0.064 4876 Dihedral : 16.437 172.558 5074 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.80 % Allowed : 15.46 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.36 (0.15), residues: 3275 helix: 0.01 (0.16), residues: 1066 sheet: -1.07 (0.23), residues: 552 loop : -1.43 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 210 TYR 0.019 0.001 TYR D 275 PHE 0.015 0.001 PHE E 287 TRP 0.013 0.001 TRP B 152 HIS 0.007 0.001 HIS I 194 Details of bonding type rmsd covalent geometry : bond 0.00266 (30035) covalent geometry : angle 0.53738 (41212) hydrogen bonds : bond 0.03268 ( 789) hydrogen bonds : angle 4.71604 ( 2178) metal coordination : bond 0.00095 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 331 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.7430 (mt0) cc_final: 0.6632 (mm-40) REVERT: A 177 MET cc_start: 0.4320 (tpp) cc_final: 0.3988 (tpp) REVERT: A 181 LEU cc_start: 0.7020 (mt) cc_final: 0.6397 (pp) REVERT: A 190 ASN cc_start: 0.8403 (t0) cc_final: 0.8118 (t0) REVERT: A 545 GLN cc_start: 0.6538 (mm-40) cc_final: 0.6217 (mp10) REVERT: A 560 ASP cc_start: 0.7544 (m-30) cc_final: 0.6626 (t0) REVERT: B 27 ASP cc_start: 0.8044 (m-30) cc_final: 0.7830 (m-30) REVERT: B 28 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8409 (ttp-170) REVERT: B 43 MET cc_start: 0.9117 (tpp) cc_final: 0.8861 (mmt) REVERT: C 39 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8548 (pp) REVERT: C 287 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.5796 (p90) REVERT: D 86 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7657 (mm-30) REVERT: D 146 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8349 (p) REVERT: D 287 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7325 (p90) REVERT: F 146 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8375 (m) REVERT: F 210 ARG cc_start: 0.8377 (ttm110) cc_final: 0.7787 (ttm110) REVERT: E 96 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: E 287 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.6937 (p90) REVERT: E 291 ARG cc_start: 0.7689 (tpp80) cc_final: 0.7420 (ttm-80) REVERT: G 172 ARG cc_start: 0.8386 (ttp80) cc_final: 0.7955 (ttp80) REVERT: G 183 ASN cc_start: 0.8267 (m-40) cc_final: 0.8062 (t0) REVERT: H 23 LYS cc_start: 0.6676 (mttt) cc_final: 0.6282 (tptp) REVERT: H 83 PHE cc_start: 0.4483 (OUTLIER) cc_final: 0.3223 (m-80) REVERT: H 102 ARG cc_start: 0.4061 (OUTLIER) cc_final: 0.2982 (tpt170) REVERT: H 150 HIS cc_start: 0.7222 (t70) cc_final: 0.7007 (m-70) REVERT: I 29 ASP cc_start: 0.5762 (t0) cc_final: 0.4757 (p0) REVERT: I 62 TYR cc_start: 0.8212 (p90) cc_final: 0.7323 (p90) REVERT: I 96 ARG cc_start: 0.7146 (mtm-85) cc_final: 0.6668 (ttp-110) REVERT: I 194 HIS cc_start: 0.4042 (t70) cc_final: 0.3792 (t70) REVERT: I 260 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6646 (mm-30) REVERT: J 228 MET cc_start: 0.7545 (ppp) cc_final: 0.7324 (ppp) REVERT: J 251 PHE cc_start: 0.7680 (t80) cc_final: 0.7444 (t80) REVERT: J 304 LEU cc_start: 0.6647 (mt) cc_final: 0.6428 (mt) REVERT: J 309 ASN cc_start: 0.7360 (m-40) cc_final: 0.6875 (m110) REVERT: J 380 PHE cc_start: 0.7239 (m-80) cc_final: 0.6827 (m-80) outliers start: 83 outliers final: 65 residues processed: 398 average time/residue: 0.1863 time to fit residues: 115.5294 Evaluate side-chains 393 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 318 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 287 PHE Chi-restraints excluded: chain F residue 349 HIS Chi-restraints excluded: chain E residue 43 MET Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 388 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 263 optimal weight: 0.0370 chunk 92 optimal weight: 0.0770 chunk 22 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 293 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 252 optimal weight: 1.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN C 311 GLN D 110 GLN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.188187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.144394 restraints weight = 37961.338| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 4.19 r_work: 0.3172 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30041 Z= 0.113 Angle : 0.535 9.403 41212 Z= 0.278 Chirality : 0.040 0.167 4569 Planarity : 0.004 0.065 4876 Dihedral : 16.398 172.600 5072 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.63 % Allowed : 15.73 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.27 (0.15), residues: 3275 helix: 0.12 (0.16), residues: 1064 sheet: -0.99 (0.23), residues: 545 loop : -1.40 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 210 TYR 0.018 0.001 TYR I 147 PHE 0.014 0.001 PHE E 287 TRP 0.013 0.001 TRP B 152 HIS 0.007 0.001 HIS I 194 Details of bonding type rmsd covalent geometry : bond 0.00265 (30035) covalent geometry : angle 0.53518 (41212) hydrogen bonds : bond 0.03219 ( 789) hydrogen bonds : angle 4.70223 ( 2178) metal coordination : bond 0.00114 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7509.11 seconds wall clock time: 129 minutes 11.89 seconds (7751.89 seconds total)