Starting phenix.real_space_refine on Mon Sep 14 07:21:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vbw_21146/09_2026/6vbw_21146_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vbw_21146/09_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_21146/09_2026/6vbw_21146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vbw_21146/09_2026/6vbw_21146.map" model { file = "/net/cci-nas-00/data/ceres_data/6vbw_21146/09_2026/6vbw_21146_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vbw_21146/09_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 5.93, per 1000 atoms: 0.20 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: 2.05 Conformation dependent library (CDL) restraints added in 742.3 milliseconds 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: 3.46 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: 5.16 Time building geometry restraints manager: 2.74 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=" N7 A K 29 " pdb=" C5 A K 29 " ideal model delta sigma weight residual 1.388 1.364 0.024 6.00e-03 2.78e+04 1.53e+01 bond pdb=" C4 C K 28 " pdb=" C5 C K 28 " ideal model delta sigma weight residual 1.425 1.395 0.030 8.00e-03 1.56e+04 1.42e+01 bond pdb=" N9 G K 24 " pdb=" C4 G K 24 " ideal model delta sigma weight residual 1.375 1.345 0.030 8.00e-03 1.56e+04 1.41e+01 bond pdb=" C2 U K 31 " pdb=" N3 U K 31 " ideal model delta sigma weight residual 1.373 1.347 0.026 7.00e-03 2.04e+04 1.33e+01 bond pdb=" N7 DA L 63 " pdb=" C5 DA L 63 " ideal model delta sigma weight residual 1.388 1.367 0.021 6.00e-03 2.78e+04 1.25e+01 ... (remaining 30030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 39763 2.86 - 5.71: 1269 5.71 - 8.57: 145 8.57 - 11.43: 33 11.43 - 14.28: 2 Bond angle restraints: 41212 Sorted by residual: angle pdb=" O5' C K 28 " pdb=" C5' C K 28 " pdb=" C4' C K 28 " ideal model delta sigma weight residual 109.40 114.64 -5.24 8.00e-01 1.56e+00 4.29e+01 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=" O5' U K 2 " pdb=" C5' U K 2 " pdb=" C4' U K 2 " ideal model delta sigma weight residual 109.40 113.55 -4.15 8.00e-01 1.56e+00 2.69e+01 angle pdb=" O4' DA L 88 " pdb=" C4' DA L 88 " pdb=" C3' DA L 88 " ideal model delta sigma weight residual 106.00 102.90 3.10 6.00e-01 2.78e+00 2.67e+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 ... (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 - 0.095: 3843 0.095 - 0.191: 632 0.191 - 0.286: 83 0.286 - 0.382: 10 0.382 - 0.477: 1 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 -2.73 -2.25 -0.48 2.00e-01 2.50e+01 5.69e+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: 0.010 Normalize map: mean=0, sd=1: 2.200 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: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 29.290 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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= 0.610 Angle : 1.199 14.283 41212 Z= 0.737 Chirality : 0.073 0.477 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/Z covalent geometry : bond 0.01120 / 0.59 (30035) covalent geometry : angle 1.19895 / 0.74 (41212) hydrogen bonds : bond 0.32757 / 36.72 ( 789) hydrogen bonds : angle 11.04785 / 14.08 ( 2178) metal coordination : bond 0.34345 / 33.50 ( 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 : 1.166 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: 0.6597 (pp) REVERT: A 560 ASP cc_start: 0.7143 (m-30) cc_final: 0.6845 (t0) REVERT: A 562 GLN cc_start: 0.7171 (mm110) cc_final: 0.6897 (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: 0.7735 (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: 0.7160 (mmt) REVERT: F 35 ASN cc_start: 0.8103 (m-40) cc_final: 0.7899 (m-40) REVERT: F 287 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7703 (p90) REVERT: G 201 THR cc_start: 0.8456 (t) cc_final: 0.8113 (p) REVERT: H 102 ARG cc_start: 0.4394 (OUTLIER) cc_final: 0.3624 (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: 0.6019 (p0) REVERT: I 62 TYR cc_start: 0.8182 (p90) cc_final: 0.7935 (p90) outliers start: 58 outliers final: 22 residues processed: 676 average time/residue: 0.2009 time to fit residues: 208.0258 Evaluate side-chains 436 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 409 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 11 ARG 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: 9.9990 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... A 45 ASN A 120 HIS A 125 HIS A 226 HIS A 227 GLN A 420 HIS A 486 ASN A 562 GLN A 581 ASN B 6 ASN B 77 HIS B 299 HIS C 72 GLN C 77 HIS C 153 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS D 72 GLN D 77 HIS D 145 ASN D 174 ASN D 299 HIS D 349 HIS F 110 GLN F 145 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 349 HIS E 77 HIS ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 HIS G 72 GLN G 299 HIS ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 349 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN H 71 GLN H 105 GLN I 25 ASN I 46 HIS I 151 HIS I 153 HIS I 194 HIS I 214 ASN ** I 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 368 HIS J 80 GLN J 237 HIS J 296 HIS J 309 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.189024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146332 restraints weight = 37992.519| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.56 r_work: 0.3125 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 2.065 30041 Z= 0.428 Angle : 0.711 10.213 41212 Z= 0.386 Chirality : 0.046 0.271 4569 Planarity : 0.006 0.084 4876 Dihedral : 17.514 176.551 5113 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.87 % Allowed : 9.55 % Favored : 87.58 % 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: -3.59 (0.13), residues: 3275 helix: -2.75 (0.12), residues: 1046 sheet: -1.89 (0.21), residues: 558 loop : -2.26 (0.13), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 5 TYR 0.023 0.002 TYR D 275 PHE 0.017 0.002 PHE I 2 TRP 0.030 0.002 TRP I 203 HIS 0.012 0.001 HIS I 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (30035) covalent geometry : angle 0.71132 / 0.39 (41212) hydrogen bonds : bond 0.06245 / 6.76 ( 789) hydrogen bonds : angle 6.54574 / 7.91 ( 2178) metal coordination : bond 0.84309 / 84.30 ( 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 518 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 433 time to evaluate : 1.033 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 177 MET cc_start: 0.4218 (tpp) cc_final: 0.3637 (tpp) REVERT: A 181 LEU cc_start: 0.7070 (mt) cc_final: 0.6529 (pp) REVERT: A 190 ASN cc_start: 0.8072 (t0) cc_final: 0.7838 (t0) REVERT: A 452 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8515 (tp) REVERT: A 560 ASP cc_start: 0.7431 (m-30) cc_final: 0.6683 (t0) REVERT: A 619 TYR cc_start: 0.6486 (m-10) cc_final: 0.6017 (m-10) REVERT: B 110 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7394 (mm-40) REVERT: B 126 THR cc_start: 0.8423 (m) cc_final: 0.8080 (p) REVERT: C 39 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8461 (pp) REVERT: C 287 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.5740 (p90) REVERT: C 331 ILE cc_start: 0.8585 (pt) cc_final: 0.8336 (mt) REVERT: D 146 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8454 (p) REVERT: D 176 THR cc_start: 0.9106 (m) cc_final: 0.8832 (p) REVERT: D 287 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7545 (p90) REVERT: F 14 ASP cc_start: 0.8032 (t0) cc_final: 0.7727 (t70) REVERT: F 35 ASN cc_start: 0.8341 (m-40) cc_final: 0.8081 (m-40) REVERT: F 107 LYS cc_start: 0.8641 (tttm) cc_final: 0.8409 (mmmt) REVERT: F 210 ARG cc_start: 0.8321 (ttm110) cc_final: 0.7840 (ttm110) REVERT: F 215 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8433 (mm) REVERT: F 337 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8785 (tp) REVERT: E 192 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: E 287 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.6929 (p90) REVERT: G 1 MET cc_start: 0.7041 (ttm) cc_final: 0.6804 (ptm) REVERT: G 201 THR cc_start: 0.8747 (t) cc_final: 0.8432 (p) REVERT: H 23 LYS cc_start: 0.7128 (mttt) cc_final: 0.6764 (tptp) REVERT: H 102 ARG cc_start: 0.4809 (OUTLIER) cc_final: 0.3613 (tpt170) REVERT: H 110 LEU cc_start: 0.7768 (mp) cc_final: 0.7535 (mp) REVERT: H 134 ASP cc_start: 0.5492 (t70) cc_final: 0.4639 (t70) REVERT: H 169 MET cc_start: 0.4860 (tmt) cc_final: 0.2488 (mmm) REVERT: I 9 TYR cc_start: 0.4510 (m-80) cc_final: 0.4043 (m-80) REVERT: I 11 ASP cc_start: 0.6348 (p0) cc_final: 0.5830 (p0) REVERT: I 62 TYR cc_start: 0.8488 (p90) cc_final: 0.7726 (p90) REVERT: I 119 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.6040 (tp) REVERT: I 260 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6524 (mm-30) REVERT: I 365 TYR cc_start: 0.6389 (m-80) cc_final: 0.5941 (m-80) REVERT: J 258 GLU cc_start: 0.7859 (tp30) cc_final: 0.7576 (tp30) REVERT: J 313 GLN cc_start: 0.6840 (mt0) cc_final: 0.6202 (mp10) REVERT: J 342 MET cc_start: 0.3583 (mtm) cc_final: 0.3324 (ptp) REVERT: J 380 PHE cc_start: 0.7843 (m-80) cc_final: 0.7435 (m-80) outliers start: 85 outliers final: 40 residues processed: 501 average time/residue: 0.1943 time to fit residues: 151.2865 Evaluate side-chains 416 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 365 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 452 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 B residue 52 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 310 LEU 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 52 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 215 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 91 VAL 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 11 ARG Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 215 LEU 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 57 ILE 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 254 GLU Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 172 ARG Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 310 LEU 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 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 319 optimal weight: 0.1980 chunk 251 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 270 optimal weight: 0.0970 chunk 134 optimal weight: 0.5980 chunk 6 optimal weight: 7.9990 chunk 243 optimal weight: 4.9990 chunk 334 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 129 optimal weight: 0.0980 chunk 110 optimal weight: 0.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 299 HIS ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS F 110 GLN F 145 ASN F 214 HIS ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 HIS E 349 HIS ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 ASN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 237 HIS I 368 HIS J 324 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.190468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.147598 restraints weight = 37931.487| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 4.44 r_work: 0.3204 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 30041 Z= 0.130 Angle : 0.599 9.068 41212 Z= 0.328 Chirality : 0.042 0.192 4569 Planarity : 0.005 0.056 4876 Dihedral : 17.337 177.379 5098 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.97 % Allowed : 10.57 % Favored : 86.46 % 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: -2.91 (0.13), residues: 3275 helix: -1.92 (0.14), residues: 1059 sheet: -1.76 (0.22), residues: 507 loop : -1.95 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 5 TYR 0.020 0.002 TYR A 543 PHE 0.022 0.001 PHE J 251 TRP 0.018 0.001 TRP F 161 HIS 0.009 0.001 HIS I 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (30035) covalent geometry : angle 0.59939 / 0.33 (41212) hydrogen bonds : bond 0.04587 / 4.91 ( 789) hydrogen bonds : angle 5.81210 / 7.00 ( 2178) metal coordination : bond 0.05306 / 3.71 ( 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 491 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 403 time to evaluate : 0.954 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 177 MET cc_start: 0.4278 (tpp) cc_final: 0.3721 (tpt) REVERT: A 181 LEU cc_start: 0.6986 (mt) cc_final: 0.6577 (pp) REVERT: A 560 ASP cc_start: 0.7250 (m-30) cc_final: 0.6547 (t0) REVERT: A 583 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7051 (tp) REVERT: A 619 TYR cc_start: 0.6401 (m-10) cc_final: 0.6115 (m-80) REVERT: B 110 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7441 (mm-40) REVERT: B 126 THR cc_start: 0.8490 (m) cc_final: 0.8113 (p) REVERT: C 277 GLU cc_start: 0.8147 (mp0) cc_final: 0.7946 (pm20) REVERT: C 287 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.5801 (p90) REVERT: D 146 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8373 (p) REVERT: D 176 THR cc_start: 0.9055 (m) cc_final: 0.8816 (p) REVERT: D 287 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7322 (p90) REVERT: F 11 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8541 (ptt180) REVERT: F 210 ARG cc_start: 0.8248 (ttm110) cc_final: 0.7760 (ttm110) REVERT: F 215 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8488 (mm) REVERT: F 337 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8871 (tp) REVERT: E 192 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: E 287 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.6943 (p90) REVERT: E 291 ARG cc_start: 0.7631 (tpp80) cc_final: 0.7408 (ttm-80) REVERT: G 172 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8228 (ttp80) REVERT: G 183 ASN cc_start: 0.8402 (m-40) cc_final: 0.8138 (t0) REVERT: G 201 THR cc_start: 0.8651 (t) cc_final: 0.8285 (p) REVERT: H 23 LYS cc_start: 0.6922 (mttt) cc_final: 0.6623 (tptp) REVERT: H 102 ARG cc_start: 0.4608 (OUTLIER) cc_final: 0.3350 (tpt170) REVERT: H 110 LEU cc_start: 0.6867 (mp) cc_final: 0.6533 (mp) REVERT: H 120 ARG cc_start: 0.7534 (mtm-85) cc_final: 0.7326 (mtm-85) REVERT: H 134 ASP cc_start: 0.5286 (t70) cc_final: 0.4648 (t70) REVERT: I 7 LYS cc_start: 0.7811 (mtpp) cc_final: 0.7304 (pttt) REVERT: I 15 GLU cc_start: 0.6477 (mp0) cc_final: 0.6250 (pm20) REVERT: I 62 TYR cc_start: 0.8277 (p90) cc_final: 0.7361 (p90) REVERT: I 119 LEU cc_start: 0.6293 (OUTLIER) cc_final: 0.5975 (tp) REVERT: I 151 HIS cc_start: 0.6023 (p90) cc_final: 0.5223 (p90) REVERT: I 207 HIS cc_start: 0.6341 (m-70) cc_final: 0.5685 (t-170) REVERT: I 260 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6574 (mm-30) REVERT: I 365 TYR cc_start: 0.6040 (m-80) cc_final: 0.5641 (m-80) REVERT: J 244 PHE cc_start: 0.7087 (m-80) cc_final: 0.6335 (m-80) REVERT: J 258 GLU cc_start: 0.7670 (tp30) cc_final: 0.6730 (mm-30) REVERT: J 304 LEU cc_start: 0.6508 (mt) cc_final: 0.6292 (mt) REVERT: J 313 GLN cc_start: 0.6720 (mt0) cc_final: 0.6080 (mp10) REVERT: J 342 MET cc_start: 0.3444 (mtm) cc_final: 0.3142 (ptp) REVERT: J 368 HIS cc_start: 0.8193 (m-70) cc_final: 0.7963 (m-70) outliers start: 88 outliers final: 43 residues processed: 471 average time/residue: 0.1859 time to fit residues: 136.6836 Evaluate side-chains 404 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 349 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 44 GLU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 38 THR 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 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 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 215 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 57 ILE 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 254 GLU Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain G residue 172 ARG Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 287 PHE 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 102 ARG Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 140 TYR Chi-restraints excluded: chain I residue 208 GLU Chi-restraints excluded: chain J residue 259 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 101 optimal weight: 0.4980 chunk 161 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 210 optimal weight: 0.9990 chunk 228 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 GLN C 72 GLN C 311 GLN D 71 HIS 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 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.189027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.146671 restraints weight = 37634.328| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.42 r_work: 0.3131 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30041 Z= 0.130 Angle : 0.578 9.530 41212 Z= 0.311 Chirality : 0.042 0.234 4569 Planarity : 0.005 0.057 4876 Dihedral : 17.185 176.599 5095 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.34 % Allowed : 12.19 % Favored : 84.47 % 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: -2.48 (0.14), residues: 3275 helix: -1.41 (0.15), residues: 1052 sheet: -1.34 (0.22), residues: 517 loop : -1.87 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 5 TYR 0.024 0.001 TYR I 219 PHE 0.022 0.001 PHE J 251 TRP 0.017 0.001 TRP D 161 HIS 0.008 0.001 HIS I 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (30035) covalent geometry : angle 0.57843 / 0.31 (41212) hydrogen bonds : bond 0.04215 / 4.42 ( 789) hydrogen bonds : angle 5.47828 / 6.60 ( 2178) metal coordination : bond 0.01786 / 1.58 ( 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 467 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 368 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4451 (tpp) cc_final: 0.3905 (tpp) REVERT: A 181 LEU cc_start: 0.7080 (mt) cc_final: 0.6609 (pp) REVERT: A 560 ASP cc_start: 0.7565 (m-30) cc_final: 0.6765 (t0) REVERT: A 583 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7053 (tp) REVERT: B 27 ASP cc_start: 0.8103 (m-30) cc_final: 0.7882 (m-30) REVERT: B 28 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8466 (ttp-170) REVERT: B 126 THR cc_start: 0.8526 (m) cc_final: 0.8142 (p) REVERT: D 146 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8428 (p) REVERT: D 176 THR cc_start: 0.9090 (m) cc_final: 0.8886 (p) REVERT: D 210 ARG cc_start: 0.8190 (ttm110) cc_final: 0.7983 (ttp-170) REVERT: D 287 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7376 (p90) REVERT: F 107 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8639 (tttm) REVERT: F 210 ARG cc_start: 0.8402 (ttm110) cc_final: 0.7896 (ttm110) REVERT: F 215 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8504 (mm) REVERT: E 192 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: E 287 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.6980 (p90) REVERT: E 291 ARG cc_start: 0.7647 (tpp80) cc_final: 0.7445 (ttm-80) REVERT: G 73 VAL cc_start: 0.8777 (m) cc_final: 0.8555 (t) REVERT: G 172 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8259 (ttm-80) REVERT: G 183 ASN cc_start: 0.8338 (m-40) cc_final: 0.8135 (t0) REVERT: H 23 LYS cc_start: 0.6994 (mttt) cc_final: 0.6639 (tptp) REVERT: H 83 PHE cc_start: 0.4865 (OUTLIER) cc_final: 0.2687 (m-80) REVERT: H 102 ARG cc_start: 0.4419 (OUTLIER) cc_final: 0.3353 (tpt170) REVERT: H 123 GLU cc_start: 0.7257 (pp20) cc_final: 0.6865 (pp20) REVERT: H 169 MET cc_start: 0.6200 (tmm) cc_final: 0.3185 (mmm) REVERT: I 7 LYS cc_start: 0.7963 (mtpp) cc_final: 0.7452 (pttt) REVERT: I 29 ASP cc_start: 0.5262 (p0) cc_final: 0.4989 (t70) REVERT: I 62 TYR cc_start: 0.8448 (p90) cc_final: 0.7713 (p90) REVERT: I 119 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5989 (tt) REVERT: I 151 HIS cc_start: 0.6287 (p90) cc_final: 0.5403 (p90) REVERT: I 194 HIS cc_start: 0.2427 (t70) cc_final: 0.1970 (t70) REVERT: I 260 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6476 (mm-30) REVERT: I 323 MET cc_start: 0.2168 (ppp) cc_final: 0.1505 (pmm) REVERT: I 365 TYR cc_start: 0.6355 (m-80) cc_final: 0.5996 (m-80) REVERT: J 244 PHE cc_start: 0.7298 (m-80) cc_final: 0.6518 (m-80) REVERT: J 258 GLU cc_start: 0.7824 (tp30) cc_final: 0.6771 (mm-30) REVERT: J 304 LEU cc_start: 0.6768 (mt) cc_final: 0.6531 (mt) REVERT: J 309 ASN cc_start: 0.7742 (m-40) cc_final: 0.7019 (m110) REVERT: J 368 HIS cc_start: 0.8411 (m-70) cc_final: 0.8145 (m-70) outliers start: 99 outliers final: 58 residues processed: 444 average time/residue: 0.1920 time to fit residues: 133.7585 Evaluate side-chains 415 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 347 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 542 LEU Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 44 GLU 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 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 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 333 ASP Chi-restraints excluded: chain F residue 1 MET 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 204 LEU Chi-restraints excluded: chain F residue 215 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 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 226 VAL Chi-restraints excluded: chain E residue 254 GLU 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 204 LEU Chi-restraints excluded: chain G residue 217 THR 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 71 GLN Chi-restraints excluded: chain H residue 83 PHE 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 140 TYR Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 208 GLU Chi-restraints excluded: chain J residue 255 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 6 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 186 optimal weight: 0.3980 chunk 269 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 GLN C 311 GLN F 110 GLN F 299 HIS F 349 HIS ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS I 153 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.190439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147983 restraints weight = 37774.855| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.38 r_work: 0.3156 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 30041 Z= 0.111 Angle : 0.541 8.067 41212 Z= 0.291 Chirality : 0.040 0.187 4569 Planarity : 0.004 0.057 4876 Dihedral : 17.035 178.433 5088 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.07 % Allowed : 13.00 % Favored : 83.93 % 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: -2.14 (0.14), residues: 3275 helix: -1.03 (0.15), residues: 1060 sheet: -1.34 (0.22), residues: 540 loop : -1.67 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 5 TYR 0.020 0.001 TYR A 543 PHE 0.021 0.001 PHE J 251 TRP 0.020 0.001 TRP B 159 HIS 0.006 0.001 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (30035) covalent geometry : angle 0.54147 / 0.29 (41212) hydrogen bonds : bond 0.03932 / 3.99 ( 789) hydrogen bonds : angle 5.19789 / 6.23 ( 2178) metal coordination : bond 0.03501 / 3.47 ( 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 460 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 369 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4305 (tpp) cc_final: 0.3766 (tpp) REVERT: A 181 LEU cc_start: 0.7041 (mt) cc_final: 0.6567 (pp) REVERT: A 560 ASP cc_start: 0.7498 (m-30) cc_final: 0.6688 (t0) REVERT: A 583 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7883 (tp) REVERT: A 619 TYR cc_start: 0.6851 (m-80) cc_final: 0.6436 (m-80) REVERT: B 27 ASP cc_start: 0.8099 (m-30) cc_final: 0.7884 (m-30) REVERT: B 28 ARG cc_start: 0.8637 (ttp80) cc_final: 0.8408 (ttp-170) REVERT: B 126 THR cc_start: 0.8520 (m) cc_final: 0.8177 (p) REVERT: C 39 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8525 (pp) REVERT: C 287 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.5948 (p90) REVERT: D 146 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8357 (p) REVERT: D 210 ARG cc_start: 0.8245 (ttm110) cc_final: 0.8007 (ttp-170) REVERT: D 287 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7306 (p90) REVERT: F 107 LYS cc_start: 0.8938 (mmmt) cc_final: 0.8719 (pttp) REVERT: F 210 ARG cc_start: 0.8386 (ttm110) cc_final: 0.7841 (ttm110) REVERT: E 287 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7052 (p90) REVERT: G 172 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8285 (ttm-80) REVERT: H 23 LYS cc_start: 0.6909 (mttt) cc_final: 0.6479 (tptp) REVERT: H 102 ARG cc_start: 0.4392 (OUTLIER) cc_final: 0.3263 (tpt170) REVERT: H 156 SER cc_start: 0.4968 (p) cc_final: 0.4441 (t) REVERT: H 169 MET cc_start: 0.6231 (tmm) cc_final: 0.3233 (mmm) REVERT: I 7 LYS cc_start: 0.7948 (mtpp) cc_final: 0.7405 (pttt) REVERT: I 62 TYR cc_start: 0.8382 (p90) cc_final: 0.7697 (p90) REVERT: I 119 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5763 (tp) REVERT: I 194 HIS cc_start: 0.2919 (t70) cc_final: 0.2575 (t70) REVERT: I 260 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6522 (mm-30) REVERT: I 323 MET cc_start: 0.2210 (ppp) cc_final: 0.1632 (pmm) REVERT: J 244 PHE cc_start: 0.7310 (m-80) cc_final: 0.6591 (m-80) REVERT: J 258 GLU cc_start: 0.7895 (tp30) cc_final: 0.7352 (tp30) REVERT: J 264 GLU cc_start: 0.6163 (tp30) cc_final: 0.5913 (tp30) REVERT: J 304 LEU cc_start: 0.6572 (mt) cc_final: 0.6352 (mt) REVERT: J 309 ASN cc_start: 0.7545 (m-40) cc_final: 0.6872 (m110) outliers start: 91 outliers final: 52 residues processed: 441 average time/residue: 0.1944 time to fit residues: 133.5701 Evaluate side-chains 394 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 333 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 561 HIS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 334 MET 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 146 THR 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 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 190 ILE 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 F residue 1 MET 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 114 GLN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 280 GLU 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 204 LEU Chi-restraints excluded: chain E residue 254 GLU 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 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 140 TYR Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 208 GLU Chi-restraints excluded: chain J residue 255 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 4 optimal weight: 10.0000 chunk 277 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 225 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 317 optimal weight: 30.0000 chunk 301 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 311 GLN F 311 GLN F 349 HIS G 214 HIS ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN H 150 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.186790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.145327 restraints weight = 37391.056| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.41 r_work: 0.3075 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3414 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= 0.164 Angle : 0.575 7.589 41212 Z= 0.306 Chirality : 0.042 0.207 4569 Planarity : 0.005 0.061 4876 Dihedral : 16.928 177.474 5080 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.21 % Allowed : 13.47 % Favored : 83.32 % 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: -2.02 (0.14), residues: 3275 helix: -0.88 (0.15), residues: 1067 sheet: -1.19 (0.22), residues: 543 loop : -1.66 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 210 TYR 0.023 0.002 TYR D 275 PHE 0.021 0.002 PHE E 287 TRP 0.018 0.001 TRP D 161 HIS 0.014 0.001 HIS F 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (30035) covalent geometry : angle 0.57531 / 0.31 (41212) hydrogen bonds : bond 0.04148 / 4.17 ( 789) hydrogen bonds : angle 5.16683 / 6.18 ( 2178) metal coordination : bond 0.00299 / 0.21 ( 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 446 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 351 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4436 (tpp) cc_final: 0.3898 (tpp) REVERT: A 181 LEU cc_start: 0.7041 (mt) cc_final: 0.6564 (pp) REVERT: A 535 GLU cc_start: 0.6463 (mt-10) cc_final: 0.5734 (pm20) REVERT: A 560 ASP cc_start: 0.7552 (m-30) cc_final: 0.6684 (t0) REVERT: A 583 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7754 (tp) REVERT: A 619 TYR cc_start: 0.6952 (m-80) cc_final: 0.6342 (m-80) REVERT: B 27 ASP cc_start: 0.8088 (m-30) cc_final: 0.7852 (m-30) REVERT: B 28 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8444 (ttp-170) REVERT: C 39 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8609 (pp) REVERT: C 287 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.5935 (p90) REVERT: D 146 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8405 (p) REVERT: D 210 ARG cc_start: 0.8337 (ttm110) cc_final: 0.8100 (ttp-170) REVERT: D 287 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7357 (p90) REVERT: F 107 LYS cc_start: 0.9007 (mmmt) cc_final: 0.8773 (pttp) REVERT: F 210 ARG cc_start: 0.8417 (ttm110) cc_final: 0.7777 (ttm110) REVERT: E 287 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7132 (p90) REVERT: G 172 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8326 (ttm-80) REVERT: H 23 LYS cc_start: 0.6782 (mttt) cc_final: 0.6435 (tptp) REVERT: H 83 PHE cc_start: 0.4683 (OUTLIER) cc_final: 0.2550 (m-80) REVERT: H 102 ARG cc_start: 0.4526 (OUTLIER) cc_final: 0.3343 (tpt170) REVERT: H 156 SER cc_start: 0.5111 (p) cc_final: 0.4589 (t) REVERT: I 7 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7434 (pttt) REVERT: I 29 ASP cc_start: 0.6004 (t70) cc_final: 0.4986 (p0) REVERT: I 62 TYR cc_start: 0.8423 (p90) cc_final: 0.7717 (p90) REVERT: I 194 HIS cc_start: 0.2737 (t70) cc_final: 0.2364 (t70) REVERT: I 260 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6516 (mm-30) REVERT: I 323 MET cc_start: 0.2248 (ppp) cc_final: 0.1636 (pmm) REVERT: I 365 TYR cc_start: 0.6341 (m-80) cc_final: 0.6053 (m-80) REVERT: J 244 PHE cc_start: 0.7277 (m-80) cc_final: 0.6537 (m-80) REVERT: J 258 GLU cc_start: 0.7889 (tp30) cc_final: 0.7392 (tp30) REVERT: J 304 LEU cc_start: 0.6676 (mt) cc_final: 0.6453 (mt) REVERT: J 309 ASN cc_start: 0.7606 (m-40) cc_final: 0.6936 (m110) outliers start: 95 outliers final: 62 residues processed: 431 average time/residue: 0.1861 time to fit residues: 126.5869 Evaluate side-chains 407 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 336 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 564 MET 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 314 GLU 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 91 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 146 THR 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 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 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 333 ASP Chi-restraints excluded: chain F residue 1 MET 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 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 H residue 52 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 208 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 217 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 chunk 301 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 270 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN D 42 GLN F 311 GLN F 349 HIS ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS I 324 ASN I 345 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.187865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143822 restraints weight = 37662.834| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.52 r_work: 0.3110 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30041 Z= 0.136 Angle : 0.559 10.696 41212 Z= 0.297 Chirality : 0.041 0.200 4569 Planarity : 0.005 0.071 4876 Dihedral : 16.877 178.623 5080 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.90 % Allowed : 13.91 % Favored : 83.19 % 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: -1.93 (0.14), residues: 3275 helix: -0.74 (0.15), residues: 1079 sheet: -1.23 (0.22), residues: 561 loop : -1.62 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 210 TYR 0.022 0.001 TYR D 275 PHE 0.019 0.001 PHE I 40 TRP 0.016 0.001 TRP D 161 HIS 0.020 0.001 HIS F 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (30035) covalent geometry : angle 0.55893 / 0.30 (41212) hydrogen bonds : bond 0.04000 / 4.01 ( 789) hydrogen bonds : angle 5.09967 / 6.10 ( 2178) metal coordination : bond 0.00133 / 0.12 ( 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 434 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 348 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TYR cc_start: 0.8141 (t80) cc_final: 0.7656 (t80) REVERT: A 177 MET cc_start: 0.4470 (tpp) cc_final: 0.3956 (tpp) REVERT: A 181 LEU cc_start: 0.7050 (mt) cc_final: 0.6578 (pp) REVERT: A 535 GLU cc_start: 0.6574 (mt-10) cc_final: 0.5754 (pm20) REVERT: A 560 ASP cc_start: 0.7533 (m-30) cc_final: 0.6654 (t0) REVERT: A 583 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7768 (tp) REVERT: A 619 TYR cc_start: 0.6887 (m-80) cc_final: 0.6094 (m-80) REVERT: B 27 ASP cc_start: 0.8165 (m-30) cc_final: 0.7930 (m-30) REVERT: B 28 ARG cc_start: 0.8633 (ttp80) cc_final: 0.8398 (ttp-170) REVERT: B 98 ARG cc_start: 0.8012 (mmt180) cc_final: 0.7779 (mmm-85) REVERT: C 39 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8582 (pp) REVERT: C 287 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.5902 (p90) REVERT: D 146 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8367 (p) REVERT: D 210 ARG cc_start: 0.8335 (ttm110) cc_final: 0.8113 (ttp-170) REVERT: D 287 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7437 (p90) REVERT: F 35 ASN cc_start: 0.8252 (m-40) cc_final: 0.8030 (t0) REVERT: F 107 LYS cc_start: 0.9000 (mmmt) cc_final: 0.8759 (pttp) REVERT: F 210 ARG cc_start: 0.8410 (ttm110) cc_final: 0.7778 (ttm110) REVERT: E 287 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7079 (p90) REVERT: G 172 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8334 (ttm-80) REVERT: H 23 LYS cc_start: 0.6758 (mttt) cc_final: 0.6427 (tptp) REVERT: H 83 PHE cc_start: 0.4695 (OUTLIER) cc_final: 0.2581 (m-80) REVERT: H 102 ARG cc_start: 0.4247 (OUTLIER) cc_final: 0.3250 (tpt-90) REVERT: H 120 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7524 (mtm-85) REVERT: H 150 HIS cc_start: 0.7069 (t-90) cc_final: 0.6472 (m-70) REVERT: H 156 SER cc_start: 0.5067 (p) cc_final: 0.4525 (t) REVERT: I 7 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7437 (pttt) REVERT: I 29 ASP cc_start: 0.5676 (t70) cc_final: 0.4881 (p0) REVERT: I 62 TYR cc_start: 0.8433 (p90) cc_final: 0.7693 (p90) REVERT: I 260 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6518 (mm-30) REVERT: I 323 MET cc_start: 0.2258 (ppp) cc_final: 0.1702 (pmm) REVERT: I 365 TYR cc_start: 0.6317 (m-80) cc_final: 0.6045 (m-80) REVERT: J 258 GLU cc_start: 0.7938 (tp30) cc_final: 0.7469 (tp30) REVERT: J 264 GLU cc_start: 0.6167 (tp30) cc_final: 0.5881 (tp30) REVERT: J 304 LEU cc_start: 0.6651 (mt) cc_final: 0.6433 (mt) REVERT: J 309 ASN cc_start: 0.7602 (m-40) cc_final: 0.6920 (m110) outliers start: 86 outliers final: 60 residues processed: 420 average time/residue: 0.1923 time to fit residues: 126.9256 Evaluate side-chains 398 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 329 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 485 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 549 ASN 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 7 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 314 GLU 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 91 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 146 THR 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 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 F residue 1 MET Chi-restraints excluded: chain F residue 51 ASP 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 289 VAL 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 146 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 172 ARG 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 H residue 52 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 83 PHE 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 208 GLU Chi-restraints excluded: chain J residue 255 ILE Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 388 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 147 optimal weight: 0.0470 chunk 252 optimal weight: 2.9990 chunk 191 optimal weight: 0.0970 chunk 73 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 156 optimal weight: 0.0270 chunk 277 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 327 optimal weight: 0.8980 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 ASN A 599 ASN C 311 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.190955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.148043 restraints weight = 37786.753| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.31 r_work: 0.3168 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30041 Z= 0.102 Angle : 0.522 8.844 41212 Z= 0.280 Chirality : 0.040 0.186 4569 Planarity : 0.004 0.063 4876 Dihedral : 16.727 179.626 5078 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.43 % Allowed : 14.48 % Favored : 83.09 % 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: -1.66 (0.14), residues: 3275 helix: -0.39 (0.16), residues: 1070 sheet: -1.14 (0.23), residues: 537 loop : -1.53 (0.15), residues: 1668 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 0.020 0.001 PHE I 40 TRP 0.014 0.001 TRP G 161 HIS 0.009 0.001 HIS F 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (30035) covalent geometry : angle 0.52195 / 0.28 (41212) hydrogen bonds : bond 0.03569 / 3.56 ( 789) hydrogen bonds : angle 4.92472 / 5.93 ( 2178) metal coordination : bond 0.00114 / 0.14 ( 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 426 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 354 time to evaluate : 1.050 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: 0.7349 (mt0) cc_final: 0.6816 (mm-40) REVERT: A 123 TYR cc_start: 0.8127 (t80) cc_final: 0.7658 (t80) REVERT: A 177 MET cc_start: 0.4464 (tpp) cc_final: 0.4092 (tpp) REVERT: A 181 LEU cc_start: 0.7058 (mt) cc_final: 0.6612 (pp) REVERT: A 247 MET cc_start: 0.8236 (ttm) cc_final: 0.8025 (ttm) REVERT: A 535 GLU cc_start: 0.6567 (mt-10) cc_final: 0.5728 (pm20) REVERT: A 560 ASP cc_start: 0.7500 (m-30) cc_final: 0.6624 (t0) REVERT: A 568 VAL cc_start: 0.8815 (t) cc_final: 0.8577 (m) REVERT: A 583 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7630 (tp) REVERT: A 619 TYR cc_start: 0.6788 (m-80) cc_final: 0.6051 (m-80) REVERT: B 27 ASP cc_start: 0.8033 (m-30) cc_final: 0.7823 (m-30) REVERT: B 28 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8366 (ttp-170) REVERT: B 98 ARG cc_start: 0.7990 (mmt180) cc_final: 0.7680 (mmm-85) REVERT: C 39 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8507 (pp) REVERT: C 287 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.5903 (p90) REVERT: D 146 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8327 (p) REVERT: D 210 ARG cc_start: 0.8321 (ttm110) cc_final: 0.8117 (ttp-170) REVERT: D 287 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7359 (p90) REVERT: F 210 ARG cc_start: 0.8412 (ttm110) cc_final: 0.7843 (ttm110) REVERT: E 138 ASN cc_start: 0.8385 (p0) cc_final: 0.8159 (p0) REVERT: E 287 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.6974 (p90) REVERT: G 172 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8301 (ttm-80) REVERT: H 23 LYS cc_start: 0.6767 (mttt) cc_final: 0.6412 (tptp) REVERT: H 83 PHE cc_start: 0.4661 (OUTLIER) cc_final: 0.2782 (m-80) REVERT: H 102 ARG cc_start: 0.4465 (OUTLIER) cc_final: 0.3252 (tpt170) REVERT: H 120 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7379 (mtm-85) REVERT: H 123 GLU cc_start: 0.7486 (pp20) cc_final: 0.6997 (pp20) REVERT: H 134 ASP cc_start: 0.5758 (t70) cc_final: 0.5303 (t70) REVERT: H 150 HIS cc_start: 0.7132 (t-90) cc_final: 0.6419 (m90) REVERT: H 156 SER cc_start: 0.4849 (p) cc_final: 0.4321 (t) REVERT: H 169 MET cc_start: 0.6212 (tmm) cc_final: 0.2826 (mmm) REVERT: I 7 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7455 (pttt) REVERT: I 11 ASP cc_start: 0.6178 (p0) cc_final: 0.5891 (p0) REVERT: I 29 ASP cc_start: 0.5454 (t70) cc_final: 0.4771 (p0) REVERT: I 62 TYR cc_start: 0.8391 (p90) cc_final: 0.7672 (p90) REVERT: I 143 HIS cc_start: 0.6343 (OUTLIER) cc_final: 0.5534 (m-70) REVERT: I 260 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6515 (mm-30) REVERT: I 323 MET cc_start: 0.2128 (ppp) cc_final: 0.1637 (pmm) REVERT: I 365 TYR cc_start: 0.6327 (m-80) cc_final: 0.6069 (m-80) REVERT: J 244 PHE cc_start: 0.7158 (m-80) cc_final: 0.6904 (m-80) REVERT: J 258 GLU cc_start: 0.7709 (tp30) cc_final: 0.7331 (tp30) REVERT: J 304 LEU cc_start: 0.6718 (mt) cc_final: 0.6498 (mt) REVERT: J 309 ASN cc_start: 0.7506 (m-40) cc_final: 0.6813 (m110) outliers start: 72 outliers final: 49 residues processed: 413 average time/residue: 0.1888 time to fit residues: 123.3188 Evaluate side-chains 396 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 337 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 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 564 MET Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 7 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 310 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 GLU 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 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 190 ILE 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 256 SER Chi-restraints excluded: chain F residue 287 PHE 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 85 ILE Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 172 ARG Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 83 PHE 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 143 HIS Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain J residue 298 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 250 optimal weight: 0.9980 chunk 228 optimal weight: 0.3980 chunk 256 optimal weight: 4.9990 chunk 307 optimal weight: 30.0000 chunk 272 optimal weight: 0.8980 chunk 287 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 88 optimal weight: 0.4980 chunk 211 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 ASN A 222 GLN C 311 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN I 345 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.189156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.147393 restraints weight = 37744.688| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.29 r_work: 0.3123 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30041 Z= 0.124 Angle : 0.542 9.602 41212 Z= 0.287 Chirality : 0.041 0.181 4569 Planarity : 0.004 0.063 4876 Dihedral : 16.684 179.120 5078 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.36 % Allowed : 14.72 % Favored : 82.92 % 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: -1.56 (0.14), residues: 3275 helix: -0.27 (0.16), residues: 1071 sheet: -1.01 (0.22), residues: 561 loop : -1.53 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 210 TYR 0.021 0.001 TYR D 275 PHE 0.019 0.001 PHE I 40 TRP 0.015 0.001 TRP D 161 HIS 0.004 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (30035) covalent geometry : angle 0.54213 / 0.29 (41212) hydrogen bonds : bond 0.03691 / 3.69 ( 789) hydrogen bonds : angle 4.89293 / 5.86 ( 2178) metal coordination : bond 0.00409 / 0.54 ( 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 424 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 354 time to evaluate : 1.014 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: 0.7418 (mt0) cc_final: 0.6919 (mm-40) REVERT: A 123 TYR cc_start: 0.8196 (t80) cc_final: 0.7834 (t80) REVERT: A 177 MET cc_start: 0.4600 (tpp) cc_final: 0.4122 (tpp) REVERT: A 181 LEU cc_start: 0.7059 (mt) cc_final: 0.6597 (pp) REVERT: A 222 GLN cc_start: 0.8001 (mt0) cc_final: 0.7753 (mt0) REVERT: A 535 GLU cc_start: 0.6631 (mt-10) cc_final: 0.5709 (pm20) REVERT: A 560 ASP cc_start: 0.7625 (m-30) cc_final: 0.6748 (t0) REVERT: A 568 VAL cc_start: 0.8845 (t) cc_final: 0.8518 (m) REVERT: A 583 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7734 (tp) REVERT: A 619 TYR cc_start: 0.6863 (m-80) cc_final: 0.6106 (m-80) REVERT: B 27 ASP cc_start: 0.8083 (m-30) cc_final: 0.7880 (m-30) REVERT: B 28 ARG cc_start: 0.8622 (ttp80) cc_final: 0.8377 (ttp-170) REVERT: B 98 ARG cc_start: 0.7992 (mmt180) cc_final: 0.7693 (mmm-85) REVERT: C 39 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8538 (pp) REVERT: C 272 ASP cc_start: 0.9042 (t0) cc_final: 0.8833 (t0) REVERT: C 287 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.5955 (p90) REVERT: D 146 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8320 (p) REVERT: D 221 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.9015 (t) REVERT: D 287 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7360 (p90) REVERT: E 192 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: E 287 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7026 (p90) REVERT: G 172 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8303 (ttp80) REVERT: H 23 LYS cc_start: 0.6783 (mttt) cc_final: 0.6437 (tptp) REVERT: H 83 PHE cc_start: 0.4667 (OUTLIER) cc_final: 0.2789 (m-80) REVERT: H 102 ARG cc_start: 0.4246 (OUTLIER) cc_final: 0.3233 (tpt-90) REVERT: H 120 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7396 (mtm-85) REVERT: H 123 GLU cc_start: 0.7324 (pp20) cc_final: 0.6832 (pp20) REVERT: H 150 HIS cc_start: 0.7172 (t-90) cc_final: 0.6423 (m90) REVERT: H 156 SER cc_start: 0.4800 (p) cc_final: 0.4352 (t) REVERT: H 169 MET cc_start: 0.6159 (tmm) cc_final: 0.2894 (mmm) REVERT: I 7 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7509 (pttt) REVERT: I 29 ASP cc_start: 0.5486 (t70) cc_final: 0.4816 (p0) REVERT: I 62 TYR cc_start: 0.8452 (p90) cc_final: 0.7792 (p90) REVERT: I 143 HIS cc_start: 0.6461 (OUTLIER) cc_final: 0.5606 (m-70) REVERT: I 260 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6494 (mm-30) REVERT: I 323 MET cc_start: 0.2268 (ppp) cc_final: 0.1770 (pmm) REVERT: J 244 PHE cc_start: 0.7190 (m-80) cc_final: 0.6920 (m-80) REVERT: J 258 GLU cc_start: 0.7719 (tp30) cc_final: 0.7262 (tp30) REVERT: J 304 LEU cc_start: 0.7040 (mt) cc_final: 0.6792 (mt) REVERT: J 309 ASN cc_start: 0.7682 (m-40) cc_final: 0.6932 (m110) outliers start: 70 outliers final: 51 residues processed: 413 average time/residue: 0.1969 time to fit residues: 128.4407 Evaluate side-chains 402 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 339 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 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 564 MET Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 7 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 C residue 39 LEU Chi-restraints excluded: chain C residue 44 GLU 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 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 190 ILE Chi-restraints excluded: chain D residue 221 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 44 GLU 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 E residue 44 GLU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 192 GLU 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 226 VAL Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 71 GLN 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 72 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 143 HIS Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain J residue 298 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 51 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 146 optimal weight: 0.7980 chunk 260 optimal weight: 10.0000 chunk 156 optimal weight: 0.0770 chunk 283 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 225 optimal weight: 0.6980 chunk 338 optimal weight: 6.9990 chunk 179 optimal weight: 0.0060 chunk 257 optimal weight: 5.9990 overall best weight: 1.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 ASN C 311 GLN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.186987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145036 restraints weight = 37336.005| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.27 r_work: 0.3099 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30041 Z= 0.160 Angle : 0.580 10.632 41212 Z= 0.306 Chirality : 0.042 0.213 4569 Planarity : 0.005 0.068 4876 Dihedral : 16.679 178.695 5078 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.40 % Allowed : 14.89 % Favored : 82.71 % 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: -1.59 (0.14), residues: 3275 helix: -0.27 (0.16), residues: 1071 sheet: -1.04 (0.23), residues: 543 loop : -1.57 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 210 TYR 0.022 0.001 TYR D 275 PHE 0.022 0.002 PHE E 287 TRP 0.017 0.001 TRP D 161 HIS 0.006 0.001 HIS E 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (30035) covalent geometry : angle 0.58013 / 0.31 (41212) hydrogen bonds : bond 0.03959 / 3.98 ( 789) hydrogen bonds : angle 4.95991 / 5.92 ( 2178) metal coordination : bond 0.00223 / 0.22 ( 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 407 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 336 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.7364 (mt0) cc_final: 0.6824 (mm-40) REVERT: A 123 TYR cc_start: 0.8152 (t80) cc_final: 0.7857 (t80) REVERT: A 177 MET cc_start: 0.4603 (tpp) cc_final: 0.4114 (tpp) REVERT: A 181 LEU cc_start: 0.7005 (mt) cc_final: 0.6542 (pp) REVERT: A 222 GLN cc_start: 0.7975 (mt0) cc_final: 0.7715 (mt0) REVERT: A 535 GLU cc_start: 0.6758 (mt-10) cc_final: 0.5890 (pm20) REVERT: A 560 ASP cc_start: 0.7634 (m-30) cc_final: 0.6739 (t0) REVERT: A 583 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7751 (tp) REVERT: A 619 TYR cc_start: 0.6828 (m-80) cc_final: 0.6042 (m-80) REVERT: B 27 ASP cc_start: 0.8022 (m-30) cc_final: 0.7796 (m-30) REVERT: B 28 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8427 (ttp-170) REVERT: C 39 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8612 (pp) REVERT: C 287 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.5927 (p90) REVERT: D 146 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8337 (p) REVERT: D 287 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7458 (p90) REVERT: F 210 ARG cc_start: 0.8390 (ttm110) cc_final: 0.7795 (ttm110) REVERT: E 96 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7690 (mm-30) REVERT: E 192 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: E 287 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7116 (p90) REVERT: G 164 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7253 (tm-30) REVERT: G 172 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8241 (ttp80) REVERT: H 23 LYS cc_start: 0.6791 (mttt) cc_final: 0.6426 (tptp) REVERT: H 83 PHE cc_start: 0.4708 (OUTLIER) cc_final: 0.2819 (m-80) REVERT: H 102 ARG cc_start: 0.4300 (OUTLIER) cc_final: 0.3221 (tpt-90) REVERT: H 120 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7560 (mtm-85) REVERT: H 150 HIS cc_start: 0.7280 (t-90) cc_final: 0.6552 (m90) REVERT: I 7 LYS cc_start: 0.7995 (mtpp) cc_final: 0.7476 (pttm) REVERT: I 29 ASP cc_start: 0.5551 (t70) cc_final: 0.4845 (p0) REVERT: I 62 TYR cc_start: 0.8429 (p90) cc_final: 0.7776 (p90) REVERT: I 143 HIS cc_start: 0.6561 (OUTLIER) cc_final: 0.5570 (m-70) REVERT: I 260 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6544 (mm-30) REVERT: I 323 MET cc_start: 0.2287 (ppp) cc_final: 0.1815 (pmm) REVERT: J 244 PHE cc_start: 0.7172 (m-80) cc_final: 0.6900 (m-80) REVERT: J 304 LEU cc_start: 0.6884 (mt) cc_final: 0.6629 (mt) REVERT: J 309 ASN cc_start: 0.7765 (m-40) cc_final: 0.7501 (m-40) outliers start: 71 outliers final: 52 residues processed: 396 average time/residue: 0.1954 time to fit residues: 121.5360 Evaluate side-chains 395 residues out of total 2962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 331 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 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 564 MET Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 7 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 C residue 39 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 146 THR 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 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 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 192 GLU 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 228 THR 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 302 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 71 GLN 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 72 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 143 HIS Chi-restraints excluded: chain I residue 223 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 263 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 22 optimal weight: 0.0570 chunk 150 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 293 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 274 optimal weight: 0.0020 chunk 252 optimal weight: 3.9990 overall best weight: 0.7108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 ASN C 311 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 GLN J 252 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.187581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145757 restraints weight = 37612.142| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.33 r_work: 0.3118 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3897 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 : 0.537 10.536 41212 Z= 0.285 Chirality : 0.040 0.180 4569 Planarity : 0.004 0.063 4876 Dihedral : 16.646 179.865 5078 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.33 % Allowed : 15.26 % Favored : 82.41 % 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: -1.45 (0.14), residues: 3275 helix: -0.11 (0.16), residues: 1078 sheet: -1.02 (0.23), residues: 523 loop : -1.49 (0.15), residues: 1674 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 0.020 0.001 PHE I 40 TRP 0.015 0.001 TRP G 161 HIS 0.004 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (30035) covalent geometry : angle 0.53739 / 0.28 (41212) hydrogen bonds : bond 0.03597 / 3.60 ( 789) hydrogen bonds : angle 4.86242 / 5.83 ( 2178) metal coordination : bond 0.00134 / 0.09 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7136.29 seconds wall clock time: 123 minutes 0.09 seconds (7380.09 seconds total)