Starting phenix.real_space_refine on Fri Mar 6 07:58:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uvn_20908/03_2026/6uvn_20908.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uvn_20908/03_2026/6uvn_20908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uvn_20908/03_2026/6uvn_20908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uvn_20908/03_2026/6uvn_20908.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uvn_20908/03_2026/6uvn_20908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uvn_20908/03_2026/6uvn_20908.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 60 5.49 5 S 145 5.16 5 C 18542 2.51 5 N 5102 2.21 5 O 5636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29487 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1619 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "B" Number of atoms: 3921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3921 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 23, 'TRANS': 474} Chain breaks: 3 Chain: "G" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "F" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "E" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "H" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "D" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "C" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2495 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 16, 'TRANS': 291} Chain breaks: 2 Chain: "I" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3124 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain breaks: 2 Chain: "J" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3171 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 20, 'TRANS': 368} Chain breaks: 2 Chain: "M" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1275 Classifications: {'DNA': 2, 'RNA': 59} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 14, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 25, 'rna3p': 35} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 405 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'TRANS': 80} Chain breaks: 3 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'UNK:plan-1': 81} Unresolved non-hydrogen planarities: 81 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22533 SG CYS I 128 147.814 149.918 69.762 1.00117.96 S ATOM 22724 SG CYS I 150 146.594 150.159 66.366 1.00114.46 S ATOM 25657 SG CYS J 128 108.738 151.170 24.259 1.00139.86 S ATOM 25848 SG CYS J 150 111.025 151.827 27.144 1.00131.60 S Time building chain proxies: 7.03, per 1000 atoms: 0.24 Number of scatterers: 29487 At special positions: 0 Unit cell: (164.85, 175.35, 182.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 145 16.00 P 60 15.00 O 5636 8.00 N 5102 7.00 C 18542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS I 163 " - pdb=" SG CYS I 181 " distance=2.39 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: 2.55 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 401 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 128 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 150 " pdb="ZN ZN I 401 " - pdb=" ND1 HIS I 153 " pdb=" ZN J 401 " pdb="ZN ZN J 401 " - pdb=" ND1 HIS J 153 " pdb="ZN ZN J 401 " - pdb=" SG CYS J 128 " pdb="ZN ZN J 401 " - pdb=" SG CYS J 150 " 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6756 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 47 sheets defined 38.0% alpha, 16.2% beta 6 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 16 through 35 Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.710A pdb=" N ASP A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 105 through 108 Processing helix chain 'A' and resid 111 through 129 removed outlier: 3.850A pdb=" N ARG A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 9 Processing helix chain 'B' and resid 10 through 15 removed outlier: 4.659A pdb=" N ASP B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 15' Processing helix chain 'B' and resid 18 through 24 Processing helix chain 'B' and resid 36 through 47 removed outlier: 3.702A pdb=" N LEU B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 67 removed outlier: 3.789A pdb=" N LYS B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 77 Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.755A pdb=" N ARG B 82 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.703A pdb=" N PHE B 135 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.568A pdb=" N LEU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 153' Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 172 through 182 removed outlier: 3.878A pdb=" N ALA B 178 " --> pdb=" O CYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 223 through 228 removed outlier: 3.520A pdb=" N ARG B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.683A pdb=" N THR B 498 " --> pdb=" O ASP B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.755A pdb=" N LYS B 517 " --> pdb=" O ASP B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 532 removed outlier: 3.562A pdb=" N ALA B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 555 Processing helix chain 'B' and resid 582 through 586 removed outlier: 3.679A pdb=" N TYR B 586 " --> pdb=" O LEU B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 613 removed outlier: 3.716A pdb=" N ILE B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 removed outlier: 4.026A pdb=" N ALA G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 48 through 52' Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.508A pdb=" N LEU G 118 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU G 120 " --> pdb=" O VAL G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 141 removed outlier: 3.558A pdb=" N ILE G 139 " --> pdb=" O TYR G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 189 through 203 removed outlier: 3.591A pdb=" N MET G 196 " --> pdb=" O ALA G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 272 Processing helix chain 'G' and resid 308 through 314 Processing helix chain 'G' and resid 315 through 323 Processing helix chain 'G' and resid 330 through 347 Processing helix chain 'F' and resid 48 through 52 removed outlier: 4.030A pdb=" N ALA F 52 " --> pdb=" O ALA F 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 48 through 52' Processing helix chain 'F' and resid 64 through 70 removed outlier: 3.798A pdb=" N GLN F 70 " --> pdb=" O GLU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.538A pdb=" N LEU F 118 " --> pdb=" O THR F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 141 removed outlier: 3.534A pdb=" N ASN F 138 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE F 139 " --> pdb=" O TYR F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 186 Processing helix chain 'F' and resid 189 through 203 removed outlier: 3.671A pdb=" N MET F 196 " --> pdb=" O ALA F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 272 Processing helix chain 'F' and resid 308 through 314 Processing helix chain 'F' and resid 315 through 325 Processing helix chain 'F' and resid 330 through 347 Processing helix chain 'E' and resid 48 through 52 removed outlier: 4.027A pdb=" N ALA E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 52' Processing helix chain 'E' and resid 66 through 70 removed outlier: 3.522A pdb=" N ALA E 69 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 114 Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 128 through 141 removed outlier: 3.565A pdb=" N ASN E 138 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 186 Processing helix chain 'E' and resid 190 through 203 removed outlier: 4.090A pdb=" N MET E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 272 Processing helix chain 'E' and resid 308 through 314 Processing helix chain 'E' and resid 315 through 325 removed outlier: 3.649A pdb=" N ALA E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 347 Processing helix chain 'H' and resid 48 through 52 removed outlier: 4.222A pdb=" N ALA H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 48 through 52' Processing helix chain 'H' and resid 64 through 70 removed outlier: 3.805A pdb=" N GLN H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 126 Processing helix chain 'H' and resid 128 through 141 removed outlier: 3.523A pdb=" N THR H 133 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN H 138 " --> pdb=" O ARG H 134 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE H 139 " --> pdb=" O TYR H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 186 Processing helix chain 'H' and resid 189 through 201 Processing helix chain 'H' and resid 263 through 272 Processing helix chain 'H' and resid 308 through 314 Processing helix chain 'H' and resid 315 through 325 Processing helix chain 'H' and resid 330 through 347 Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.764A pdb=" N ALA D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 52' Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.555A pdb=" N LEU D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 141 removed outlier: 3.539A pdb=" N ILE D 139 " --> pdb=" O TYR D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 186 removed outlier: 3.806A pdb=" N PHE D 184 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS D 185 " --> pdb=" O ARG D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 203 removed outlier: 3.753A pdb=" N MET D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 272 Processing helix chain 'D' and resid 308 through 314 Processing helix chain 'D' and resid 315 through 325 Processing helix chain 'D' and resid 330 through 347 Processing helix chain 'C' and resid 108 through 126 removed outlier: 3.834A pdb=" N THR C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 141 removed outlier: 3.884A pdb=" N ASN C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 187 removed outlier: 3.529A pdb=" N ASN C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 308 through 314 removed outlier: 3.853A pdb=" N ILE C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 325 Processing helix chain 'C' and resid 330 through 347 Processing helix chain 'I' and resid 13 through 26 removed outlier: 3.995A pdb=" N LYS I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY I 26 " --> pdb=" O ALA I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 3.518A pdb=" N PHE I 33 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 52 removed outlier: 4.463A pdb=" N THR I 51 " --> pdb=" O ASN I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 59 removed outlier: 3.678A pdb=" N ILE I 59 " --> pdb=" O ILE I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 Processing helix chain 'I' and resid 128 through 136 Processing helix chain 'I' and resid 139 through 144 removed outlier: 3.626A pdb=" N TRP I 142 " --> pdb=" O SER I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 173 Processing helix chain 'I' and resid 194 through 205 removed outlier: 4.436A pdb=" N VAL I 200 " --> pdb=" O ALA I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 219 through 231 Processing helix chain 'I' and resid 236 through 244 removed outlier: 3.649A pdb=" N PHE I 240 " --> pdb=" O ASP I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 265 removed outlier: 3.743A pdb=" N HIS I 252 " --> pdb=" O PRO I 248 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 287 removed outlier: 3.522A pdb=" N PHE I 283 " --> pdb=" O LEU I 279 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE I 284 " --> pdb=" O GLY I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 Processing helix chain 'I' and resid 324 through 332 removed outlier: 3.512A pdb=" N VAL I 330 " --> pdb=" O LEU I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 345 Processing helix chain 'I' and resid 369 through 380 Processing helix chain 'I' and resid 387 through 392 removed outlier: 4.109A pdb=" N SER I 392 " --> pdb=" O SER I 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 26 removed outlier: 3.824A pdb=" N LYS J 24 " --> pdb=" O ARG J 20 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN J 25 " --> pdb=" O VAL J 21 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 44 removed outlier: 3.662A pdb=" N ILE J 44 " --> pdb=" O PHE J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 52 removed outlier: 4.331A pdb=" N THR J 51 " --> pdb=" O ASN J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 59 removed outlier: 3.529A pdb=" N ILE J 59 " --> pdb=" O ILE J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 82 Processing helix chain 'J' and resid 89 through 93 Processing helix chain 'J' and resid 128 through 136 Processing helix chain 'J' and resid 139 through 144 removed outlier: 3.535A pdb=" N TRP J 142 " --> pdb=" O SER J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 173 Processing helix chain 'J' and resid 194 through 205 removed outlier: 3.516A pdb=" N THR J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA J 205 " --> pdb=" O SER J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 231 removed outlier: 4.067A pdb=" N TRP J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY J 222 " --> pdb=" O SER J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 244 removed outlier: 3.575A pdb=" N PHE J 240 " --> pdb=" O ASP J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 265 removed outlier: 3.752A pdb=" N PHE J 251 " --> pdb=" O TRP J 247 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N HIS J 252 " --> pdb=" O PRO J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 287 removed outlier: 3.679A pdb=" N PHE J 283 " --> pdb=" O LEU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 309 Processing helix chain 'J' and resid 324 through 332 removed outlier: 4.438A pdb=" N VAL J 330 " --> pdb=" O LEU J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 345 Processing helix chain 'J' and resid 369 through 378 removed outlier: 3.636A pdb=" N LEU J 375 " --> pdb=" O ASP J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 386 through 390 Processing helix chain 'N' and resid 276 through 282 Processing helix chain 'N' and resid 284 through 300 removed outlier: 3.573A pdb=" N UNK N 288 " --> pdb=" O UNK N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 305 through 321 Processing helix chain 'N' and resid 334 through 346 Processing helix chain 'N' and resid 356 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 150 through 155 Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 146 removed outlier: 3.655A pdb=" N THR A 144 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 41 " --> pdb=" O THR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 5.683A pdb=" N GLU B 592 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR B 570 " --> pdb=" O GLU B 592 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE B 594 " --> pdb=" O VAL B 568 " (cutoff:3.500A) removed outlier: 15.380A pdb=" N SER B 566 " --> pdb=" O PRO B 627 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 568 " --> pdb=" O VAL B 625 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL B 625 " --> pdb=" O VAL B 568 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 139 through 142 Processing sheet with id=AA9, first strand: chain 'B' and resid 201 through 205 removed outlier: 4.185A pdb=" N LYS B 587 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 510 through 511 Processing sheet with id=AB2, first strand: chain 'B' and resid 510 through 511 removed outlier: 4.664A pdb=" N ASN B 392 " --> pdb=" O PHE B 479 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N PHE B 479 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER B 480 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL B 442 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE B 482 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE B 440 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN B 484 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE B 438 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 398 through 399 Processing sheet with id=AB4, first strand: chain 'G' and resid 105 through 106 Processing sheet with id=AB5, first strand: chain 'G' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 21 through 26 current: chain 'G' and resid 154 through 161 Processing sheet with id=AB6, first strand: chain 'G' and resid 32 through 33 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 87 through 97 current: chain 'G' and resid 251 through 254 Processing sheet with id=AB7, first strand: chain 'G' and resid 38 through 44 Processing sheet with id=AB8, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'F' and resid 105 through 106 Processing sheet with id=AC1, first strand: chain 'F' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 21 through 26 current: chain 'F' and resid 154 through 161 Processing sheet with id=AC2, first strand: chain 'F' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 87 through 97 current: chain 'F' and resid 251 through 254 Processing sheet with id=AC3, first strand: chain 'F' and resid 38 through 44 Processing sheet with id=AC4, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'E' and resid 105 through 106 Processing sheet with id=AC6, first strand: chain 'E' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 21 through 26 current: chain 'E' and resid 154 through 161 Processing sheet with id=AC7, first strand: chain 'E' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 87 through 97 current: chain 'E' and resid 251 through 254 Processing sheet with id=AC8, first strand: chain 'E' and resid 38 through 44 Processing sheet with id=AC9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'H' and resid 105 through 106 removed outlier: 3.595A pdb=" N LYS H 105 " --> pdb=" O ALA H 11 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 32 through 34 Processing sheet with id=AD3, first strand: chain 'H' and resid 32 through 34 removed outlier: 4.181A pdb=" N PHE H 23 " --> pdb=" O PRO H 260 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N VAL H 25 " --> pdb=" O ARG H 258 " (cutoff:3.500A) removed outlier: 13.589A pdb=" N ARG H 258 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 37 through 44 Processing sheet with id=AD5, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.543A pdb=" N GLN H 58 " --> pdb=" O ASP H 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 228 through 229 removed outlier: 4.563A pdb=" N VAL H 248 " --> pdb=" O VAL H 229 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 273 through 275 Processing sheet with id=AD8, first strand: chain 'D' and resid 105 through 106 Processing sheet with id=AD9, first strand: chain 'D' and resid 17 through 18 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 26 current: chain 'D' and resid 154 through 161 Processing sheet with id=AE1, first strand: chain 'D' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 87 through 97 current: chain 'D' and resid 251 through 254 Processing sheet with id=AE2, first strand: chain 'D' and resid 38 through 44 Processing sheet with id=AE3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'D' and resid 273 through 275 Processing sheet with id=AE5, first strand: chain 'C' and resid 105 through 106 Processing sheet with id=AE6, first strand: chain 'C' and resid 32 through 34 Processing sheet with id=AE7, first strand: chain 'C' and resid 32 through 34 removed outlier: 4.115A pdb=" N PHE C 23 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 10.779A pdb=" N VAL C 25 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 14.055A pdb=" N ARG C 258 " --> pdb=" O VAL C 25 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 273 through 275 Processing sheet with id=AE9, first strand: chain 'I' and resid 95 through 101 removed outlier: 6.422A pdb=" N THR I 97 " --> pdb=" O VAL I 109 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL I 109 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N MET I 99 " --> pdb=" O ALA I 107 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA I 107 " --> pdb=" O MET I 99 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR I 105 " --> pdb=" O TYR I 101 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 95 through 101 removed outlier: 6.845A pdb=" N THR J 97 " --> pdb=" O VAL J 109 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL J 109 " --> pdb=" O THR J 97 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N MET J 99 " --> pdb=" O ALA J 107 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA J 107 " --> pdb=" O MET J 99 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR J 105 " --> pdb=" O TYR J 101 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 322 through 323 1083 hydrogen bonds defined for protein. 2985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 5.86 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7220 1.33 - 1.45: 6879 1.45 - 1.57: 15926 1.57 - 1.69: 120 1.69 - 1.81: 206 Bond restraints: 30351 Sorted by residual: bond pdb=" CA ASP J 371 " pdb=" C ASP J 371 " ideal model delta sigma weight residual 1.523 1.468 0.054 1.41e-02 5.03e+03 1.49e+01 bond pdb=" N TYR C 278 " pdb=" CA TYR C 278 " ideal model delta sigma weight residual 1.456 1.487 -0.031 9.40e-03 1.13e+04 1.05e+01 bond pdb=" N VAL I 259 " pdb=" CA VAL I 259 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.14e+00 bond pdb=" C HIS C 217 " pdb=" N LEU C 218 " ideal model delta sigma weight residual 1.327 1.285 0.042 1.39e-02 5.18e+03 8.96e+00 bond pdb=" N VAL H 55 " pdb=" CA VAL H 55 " ideal model delta sigma weight residual 1.457 1.492 -0.036 1.19e-02 7.06e+03 8.93e+00 ... (remaining 30346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 40165 2.09 - 4.18: 1186 4.18 - 6.27: 96 6.27 - 8.37: 26 8.37 - 10.46: 10 Bond angle restraints: 41483 Sorted by residual: angle pdb=" N PRO B 391 " pdb=" CA PRO B 391 " pdb=" C PRO B 391 " ideal model delta sigma weight residual 113.47 122.01 -8.54 1.43e+00 4.89e-01 3.56e+01 angle pdb=" N LYS C 143 " pdb=" CA LYS C 143 " pdb=" C LYS C 143 " ideal model delta sigma weight residual 114.56 107.74 6.82 1.27e+00 6.20e-01 2.89e+01 angle pdb=" N THR B 413 " pdb=" CA THR B 413 " pdb=" C THR B 413 " ideal model delta sigma weight residual 111.71 105.56 6.15 1.15e+00 7.56e-01 2.86e+01 angle pdb=" N PRO I 290 " pdb=" CA PRO I 290 " pdb=" C PRO I 290 " ideal model delta sigma weight residual 112.47 102.01 10.46 2.06e+00 2.36e-01 2.58e+01 angle pdb=" N PRO J 290 " pdb=" CA PRO J 290 " pdb=" CB PRO J 290 " ideal model delta sigma weight residual 103.25 98.19 5.06 1.05e+00 9.07e-01 2.33e+01 ... (remaining 41478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.38: 17304 28.38 - 56.75: 706 56.75 - 85.13: 123 85.13 - 113.50: 9 113.50 - 141.88: 1 Dihedral angle restraints: 18143 sinusoidal: 7754 harmonic: 10389 Sorted by residual: dihedral pdb=" O4' U M 43 " pdb=" C1' U M 43 " pdb=" N1 U M 43 " pdb=" C2 U M 43 " ideal model delta sinusoidal sigma weight residual 200.00 58.12 141.88 1 1.50e+01 4.44e-03 7.62e+01 dihedral pdb=" O4' U M 42 " pdb=" C1' U M 42 " pdb=" N1 U M 42 " pdb=" C2 U M 42 " ideal model delta sinusoidal sigma weight residual -160.00 -64.32 -95.68 1 1.50e+01 4.44e-03 4.69e+01 dihedral pdb=" CA ASP D 296 " pdb=" C ASP D 296 " pdb=" N VAL D 297 " pdb=" CA VAL D 297 " ideal model delta harmonic sigma weight residual -180.00 -150.80 -29.20 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 18140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3681 0.062 - 0.123: 836 0.123 - 0.184: 78 0.184 - 0.246: 7 0.246 - 0.307: 6 Chirality restraints: 4608 Sorted by residual: chirality pdb=" CA LEU I 289 " pdb=" N LEU I 289 " pdb=" C LEU I 289 " pdb=" CB LEU I 289 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA PRO J 290 " pdb=" N PRO J 290 " pdb=" C PRO J 290 " pdb=" CB PRO J 290 " both_signs ideal model delta sigma weight residual False 2.72 3.00 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA ILE B 393 " pdb=" N ILE B 393 " pdb=" C ILE B 393 " pdb=" CB ILE B 393 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 4605 not shown) Planarity restraints: 5088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 50 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C SER H 50 " -0.060 2.00e-02 2.50e+03 pdb=" O SER H 50 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU H 51 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U M 33 " 0.041 2.00e-02 2.50e+03 2.02e-02 9.18e+00 pdb=" N1 U M 33 " -0.040 2.00e-02 2.50e+03 pdb=" C2 U M 33 " -0.008 2.00e-02 2.50e+03 pdb=" O2 U M 33 " -0.005 2.00e-02 2.50e+03 pdb=" N3 U M 33 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U M 33 " 0.008 2.00e-02 2.50e+03 pdb=" O4 U M 33 " 0.013 2.00e-02 2.50e+03 pdb=" C5 U M 33 " -0.005 2.00e-02 2.50e+03 pdb=" C6 U M 33 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS I 161 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C CYS I 161 " -0.047 2.00e-02 2.50e+03 pdb=" O CYS I 161 " 0.018 2.00e-02 2.50e+03 pdb=" N SER I 162 " 0.015 2.00e-02 2.50e+03 ... (remaining 5085 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1003 2.67 - 3.23: 30776 3.23 - 3.79: 49537 3.79 - 4.34: 68318 4.34 - 4.90: 109726 Nonbonded interactions: 259360 Sorted by model distance: nonbonded pdb=" O VAL H 55 " pdb=" OG SER H 56 " model vdw 2.114 3.040 nonbonded pdb=" OH TYR G 53 " pdb=" OD2 ASP F 308 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR F 53 " pdb=" OD2 ASP E 308 " model vdw 2.200 3.040 nonbonded pdb=" NH1 ARG E 289 " pdb=" OD1 ASN E 343 " model vdw 2.202 3.120 nonbonded pdb=" O TRP D 277 " pdb=" NH2 ARG D 301 " model vdw 2.204 3.120 ... (remaining 259355 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 4 through 43 or resid 73 through 353)) selection = (chain 'E' and (resid 4 through 43 or resid 73 through 353)) selection = (chain 'F' and (resid 4 through 43 or resid 73 through 353)) selection = (chain 'G' and (resid 4 through 43 or resid 73 through 353)) selection = (chain 'H' and (resid 4 through 43 or resid 73 through 353)) } ncs_group { reference = (chain 'I' and (resid 1 through 162 or resid 164 through 401)) selection = (chain 'J' and (resid 1 through 354 or resid 362 through 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.790 Find NCS groups from input model: 0.390 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: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 0.010 0.398 30358 Z= 0.472 Angle : 0.870 30.735 41485 Z= 0.496 Chirality : 0.050 0.307 4608 Planarity : 0.005 0.051 5088 Dihedral : 15.465 141.875 11384 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.09 % Favored : 91.77 % Rotamer: Outliers : 0.52 % Allowed : 7.49 % Favored : 91.98 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -3.87 (0.12), residues: 3413 helix: -2.45 (0.12), residues: 1141 sheet: -2.01 (0.21), residues: 555 loop : -2.85 (0.13), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 40 TYR 0.017 0.002 TYR J 390 PHE 0.028 0.002 PHE E 92 TRP 0.026 0.002 TRP F 277 HIS 0.005 0.001 HIS B 158 Details of bonding type rmsd covalent geometry : bond 0.00960 (30351) covalent geometry : angle 0.84335 (41483) SS BOND : bond 0.35860 ( 1) SS BOND : angle 30.65015 ( 2) hydrogen bonds : bond 0.16189 ( 1059) hydrogen bonds : angle 7.47119 ( 3013) metal coordination : bond 0.23135 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8148 (p) cc_final: 0.7887 (t) REVERT: B 21 ARG cc_start: 0.8228 (mmt-90) cc_final: 0.7876 (mmm-85) REVERT: B 221 MET cc_start: 0.7917 (ttt) cc_final: 0.7604 (ttt) REVERT: B 456 PHE cc_start: 0.7647 (t80) cc_final: 0.7335 (t80) REVERT: G 137 MET cc_start: 0.7314 (mtp) cc_final: 0.6918 (mtp) REVERT: G 349 MET cc_start: 0.7835 (mpp) cc_final: 0.7142 (mtm) REVERT: F 128 TRP cc_start: 0.7990 (m100) cc_final: 0.7766 (m100) REVERT: F 337 MET cc_start: 0.7397 (tpt) cc_final: 0.7185 (mmm) REVERT: F 349 MET cc_start: 0.7405 (mtm) cc_final: 0.7126 (mtp) REVERT: E 22 CYS cc_start: 0.7260 (m) cc_final: 0.6939 (m) REVERT: E 223 MET cc_start: 0.7302 (ttp) cc_final: 0.7033 (ttp) REVERT: H 116 VAL cc_start: 0.8464 (t) cc_final: 0.8178 (m) REVERT: H 223 MET cc_start: 0.7510 (ttp) cc_final: 0.7228 (ttm) REVERT: H 289 ARG cc_start: 0.7875 (mpt90) cc_final: 0.7190 (mmt-90) REVERT: C 75 GLN cc_start: 0.8461 (tt0) cc_final: 0.7887 (tm-30) REVERT: C 223 MET cc_start: 0.8192 (ttp) cc_final: 0.7888 (ttt) REVERT: C 331 GLN cc_start: 0.8203 (tp-100) cc_final: 0.7743 (tp-100) REVERT: J 15 GLU cc_start: 0.8216 (mp0) cc_final: 0.7804 (mp0) REVERT: J 287 ILE cc_start: 0.9085 (tp) cc_final: 0.8810 (tp) outliers start: 16 outliers final: 9 residues processed: 234 average time/residue: 0.2100 time to fit residues: 75.5577 Evaluate side-chains 156 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain I residue 181 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0370 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.0970 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 8.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 166 ASN A 178 ASN B 11 ASN B 120 HIS B 224 HIS B 392 ASN B 420 HIS B 446 HIS B 493 GLN B 562 GLN B 621 ASN B 626 GLN G 221 ASN G 250 GLN G 318 HIS G 335 ASN G 338 HIS G 352 HIS F 182 GLN F 250 GLN F 335 ASN F 338 HIS E 80 HIS E 182 GLN E 331 GLN E 335 ASN E 352 HIS H 74 HIS H 80 HIS H 182 GLN H 331 GLN H 335 ASN H 338 HIS H 343 ASN D 74 HIS D 182 GLN D 217 HIS D 335 ASN D 338 HIS D 352 HIS C 113 GLN C 314 GLN C 335 ASN C 338 HIS I 60 ASN I 225 HIS I 262 ASN I 381 GLN J 46 HIS J 47 ASN J 225 HIS J 381 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.075442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.059900 restraints weight = 96000.985| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.75 r_work: 0.3174 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30358 Z= 0.135 Angle : 0.615 13.422 41485 Z= 0.318 Chirality : 0.042 0.204 4608 Planarity : 0.005 0.073 5088 Dihedral : 13.731 140.966 4763 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.36 % Favored : 94.58 % Rotamer: Outliers : 1.63 % Allowed : 10.62 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -2.64 (0.13), residues: 3413 helix: -1.16 (0.14), residues: 1152 sheet: -1.31 (0.23), residues: 496 loop : -2.32 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 310 TYR 0.016 0.001 TYR A 83 PHE 0.014 0.001 PHE C 339 TRP 0.018 0.001 TRP H 162 HIS 0.004 0.001 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00301 (30351) covalent geometry : angle 0.61437 (41483) SS BOND : bond 0.01521 ( 1) SS BOND : angle 3.34170 ( 2) hydrogen bonds : bond 0.04009 ( 1059) hydrogen bonds : angle 5.40750 ( 3013) metal coordination : bond 0.00751 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8191 (p) REVERT: B 21 ARG cc_start: 0.8261 (mmt-90) cc_final: 0.7889 (mmm-85) REVERT: B 221 MET cc_start: 0.8299 (ttt) cc_final: 0.7980 (ttp) REVERT: G 137 MET cc_start: 0.7373 (mtp) cc_final: 0.7027 (mtp) REVERT: G 337 MET cc_start: 0.6716 (tpt) cc_final: 0.6347 (tpp) REVERT: G 353 LYS cc_start: 0.6458 (mppt) cc_final: 0.6025 (mmtt) REVERT: F 289 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7209 (mmt180) REVERT: F 337 MET cc_start: 0.7425 (tpt) cc_final: 0.7212 (mmm) REVERT: E 5 LYS cc_start: 0.8019 (pptt) cc_final: 0.7780 (tptp) REVERT: E 22 CYS cc_start: 0.8090 (m) cc_final: 0.7685 (m) REVERT: E 341 MET cc_start: 0.8390 (mmt) cc_final: 0.8182 (mmp) REVERT: H 223 MET cc_start: 0.8175 (ttp) cc_final: 0.7953 (ttm) REVERT: H 289 ARG cc_start: 0.7933 (mpt90) cc_final: 0.7217 (mmt-90) REVERT: H 341 MET cc_start: 0.7728 (mmt) cc_final: 0.7298 (mmm) REVERT: D 215 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8397 (p) REVERT: D 295 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7545 (mm-30) REVERT: C 223 MET cc_start: 0.8718 (ttp) cc_final: 0.8380 (ttt) REVERT: J 15 GLU cc_start: 0.8425 (mp0) cc_final: 0.7946 (mp0) outliers start: 50 outliers final: 24 residues processed: 232 average time/residue: 0.1817 time to fit residues: 68.7154 Evaluate side-chains 183 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 392 ASN Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 289 ARG Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 277 TRP Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain J residue 332 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 26 optimal weight: 9.9990 chunk 249 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 132 optimal weight: 0.0470 chunk 7 optimal weight: 0.9980 chunk 127 optimal weight: 0.2980 chunk 76 optimal weight: 0.7980 chunk 257 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 ASN D 80 HIS C 221 ASN C 293 HIS C 331 GLN I 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.076522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.061173 restraints weight = 95979.695| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.72 r_work: 0.3211 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30358 Z= 0.116 Angle : 0.570 12.972 41485 Z= 0.292 Chirality : 0.041 0.224 4608 Planarity : 0.004 0.061 5088 Dihedral : 13.501 137.498 4758 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.19 % Favored : 94.78 % Rotamer: Outliers : 2.18 % Allowed : 11.99 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.14), residues: 3413 helix: -0.40 (0.15), residues: 1142 sheet: -1.03 (0.23), residues: 506 loop : -2.04 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 310 TYR 0.015 0.001 TYR I 390 PHE 0.011 0.001 PHE H 230 TRP 0.012 0.001 TRP D 144 HIS 0.003 0.001 HIS H 338 Details of bonding type rmsd covalent geometry : bond 0.00261 (30351) covalent geometry : angle 0.56965 (41483) SS BOND : bond 0.00219 ( 1) SS BOND : angle 1.82358 ( 2) hydrogen bonds : bond 0.03439 ( 1059) hydrogen bonds : angle 4.92131 ( 3013) metal coordination : bond 0.00120 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 180 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 SER cc_start: 0.8643 (OUTLIER) cc_final: 0.8191 (p) REVERT: B 21 ARG cc_start: 0.8140 (mmt-90) cc_final: 0.7760 (mmm-85) REVERT: B 221 MET cc_start: 0.8304 (ttt) cc_final: 0.8076 (ttm) REVERT: G 137 MET cc_start: 0.7363 (mtp) cc_final: 0.7022 (mtp) REVERT: G 337 MET cc_start: 0.6684 (tpt) cc_final: 0.6359 (tpp) REVERT: G 353 LYS cc_start: 0.6498 (mppt) cc_final: 0.6280 (mmtt) REVERT: F 337 MET cc_start: 0.7477 (tpt) cc_final: 0.7248 (mmm) REVERT: E 5 LYS cc_start: 0.8063 (pptt) cc_final: 0.7763 (tptp) REVERT: E 22 CYS cc_start: 0.8111 (m) cc_final: 0.7702 (m) REVERT: E 341 MET cc_start: 0.8407 (mmt) cc_final: 0.8044 (mmp) REVERT: H 46 MET cc_start: 0.8166 (mmt) cc_final: 0.7912 (mmp) REVERT: H 223 MET cc_start: 0.8129 (ttp) cc_final: 0.7910 (ttm) REVERT: H 341 MET cc_start: 0.7730 (mmt) cc_final: 0.7275 (mmm) REVERT: D 295 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7637 (mm-30) REVERT: C 223 MET cc_start: 0.8776 (ttp) cc_final: 0.8470 (ttt) REVERT: I 123 HIS cc_start: 0.8413 (p90) cc_final: 0.8060 (p90) REVERT: I 323 MET cc_start: 0.8530 (ptp) cc_final: 0.8161 (ptp) REVERT: J 15 GLU cc_start: 0.8468 (mp0) cc_final: 0.7992 (mp0) REVERT: J 306 TYR cc_start: 0.8684 (t80) cc_final: 0.8454 (t80) outliers start: 67 outliers final: 36 residues processed: 237 average time/residue: 0.1710 time to fit residues: 67.7204 Evaluate side-chains 191 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 277 TRP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain C residue 299 CYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 145 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 290 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 324 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 HIS ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN B 486 ASN G 250 GLN E 221 ASN C 182 GLN J 80 GLN J 345 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.074164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.058644 restraints weight = 96161.727| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.70 r_work: 0.3133 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 30358 Z= 0.267 Angle : 0.647 11.744 41485 Z= 0.330 Chirality : 0.044 0.234 4608 Planarity : 0.005 0.061 5088 Dihedral : 13.497 137.408 4758 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.67 % Allowed : 13.78 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -1.81 (0.14), residues: 3413 helix: -0.25 (0.15), residues: 1146 sheet: -1.06 (0.23), residues: 506 loop : -1.91 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 213 TYR 0.025 0.002 TYR B 123 PHE 0.025 0.002 PHE H 92 TRP 0.015 0.002 TRP G 155 HIS 0.006 0.001 HIS B 571 Details of bonding type rmsd covalent geometry : bond 0.00617 (30351) covalent geometry : angle 0.64683 (41483) SS BOND : bond 0.00307 ( 1) SS BOND : angle 1.82836 ( 2) hydrogen bonds : bond 0.03727 ( 1059) hydrogen bonds : angle 4.98714 ( 3013) metal coordination : bond 0.00249 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 167 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 CYS cc_start: 0.8327 (t) cc_final: 0.7991 (m) REVERT: A 83 TYR cc_start: 0.8548 (m-80) cc_final: 0.8261 (m-80) REVERT: A 156 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8361 (p) REVERT: B 21 ARG cc_start: 0.8107 (mmt-90) cc_final: 0.7691 (mmm-85) REVERT: B 221 MET cc_start: 0.8370 (ttt) cc_final: 0.8092 (ttm) REVERT: G 137 MET cc_start: 0.7431 (mtp) cc_final: 0.7072 (mtp) REVERT: G 353 LYS cc_start: 0.6492 (mppt) cc_final: 0.6171 (mmtt) REVERT: F 337 MET cc_start: 0.7693 (tpt) cc_final: 0.7445 (mmm) REVERT: E 5 LYS cc_start: 0.8166 (pptt) cc_final: 0.7853 (tptp) REVERT: E 22 CYS cc_start: 0.8153 (m) cc_final: 0.7759 (m) REVERT: E 276 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7496 (p0) REVERT: E 341 MET cc_start: 0.8369 (mmt) cc_final: 0.8163 (mmm) REVERT: C 75 GLN cc_start: 0.8616 (tt0) cc_final: 0.8029 (tm-30) REVERT: C 331 GLN cc_start: 0.8325 (tp40) cc_final: 0.7866 (tp-100) REVERT: C 337 MET cc_start: 0.8790 (mmm) cc_final: 0.8516 (tpp) REVERT: J 15 GLU cc_start: 0.8447 (mp0) cc_final: 0.8044 (mp0) REVERT: J 18 PHE cc_start: 0.9332 (OUTLIER) cc_final: 0.8883 (m-80) outliers start: 82 outliers final: 58 residues processed: 233 average time/residue: 0.1648 time to fit residues: 64.8201 Evaluate side-chains 218 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 157 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 392 ASN Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 350 PHE Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 277 TRP Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain I residue 331 MET Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 343 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 142 optimal weight: 2.9990 chunk 319 optimal weight: 40.0000 chunk 61 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 335 optimal weight: 2.9990 chunk 246 optimal weight: 6.9990 chunk 245 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 205 optimal weight: 0.9980 chunk 311 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN H 343 ASN C 113 GLN ** J 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.075129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.059557 restraints weight = 96265.223| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.73 r_work: 0.3162 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30358 Z= 0.176 Angle : 0.587 11.775 41485 Z= 0.299 Chirality : 0.042 0.330 4608 Planarity : 0.005 0.059 5088 Dihedral : 13.429 138.319 4758 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.93 % Allowed : 14.76 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -1.57 (0.14), residues: 3413 helix: -0.03 (0.16), residues: 1144 sheet: -0.98 (0.23), residues: 540 loop : -1.78 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 213 TYR 0.016 0.001 TYR B 123 PHE 0.013 0.001 PHE H 92 TRP 0.014 0.001 TRP F 155 HIS 0.003 0.001 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.00408 (30351) covalent geometry : angle 0.58706 (41483) SS BOND : bond 0.00217 ( 1) SS BOND : angle 1.66076 ( 2) hydrogen bonds : bond 0.03409 ( 1059) hydrogen bonds : angle 4.84575 ( 3013) metal coordination : bond 0.00128 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 172 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 CYS cc_start: 0.8331 (t) cc_final: 0.7945 (m) REVERT: A 156 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8323 (p) REVERT: B 21 ARG cc_start: 0.8026 (mmt-90) cc_final: 0.7632 (mmm-85) REVERT: B 221 MET cc_start: 0.8335 (ttt) cc_final: 0.8060 (ttm) REVERT: G 137 MET cc_start: 0.7457 (mtp) cc_final: 0.6963 (mtp) REVERT: G 141 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7515 (p0) REVERT: G 337 MET cc_start: 0.6738 (tpt) cc_final: 0.6396 (tpp) REVERT: G 353 LYS cc_start: 0.6596 (mppt) cc_final: 0.6277 (mmtt) REVERT: F 337 MET cc_start: 0.7630 (tpt) cc_final: 0.7360 (mmm) REVERT: E 5 LYS cc_start: 0.8195 (pptt) cc_final: 0.7869 (tptp) REVERT: E 22 CYS cc_start: 0.8141 (m) cc_final: 0.7761 (m) REVERT: E 120 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7668 (mm-30) REVERT: H 61 LYS cc_start: 0.6744 (mmmt) cc_final: 0.5984 (mmtt) REVERT: H 196 MET cc_start: 0.8373 (ttt) cc_final: 0.8160 (ttp) REVERT: H 320 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7881 (mt) REVERT: H 341 MET cc_start: 0.7598 (mmt) cc_final: 0.7093 (mmm) REVERT: C 30 ASP cc_start: 0.8537 (t0) cc_final: 0.8225 (t0) REVERT: C 75 GLN cc_start: 0.8549 (tt0) cc_final: 0.8017 (tm-30) REVERT: C 337 MET cc_start: 0.8812 (mmm) cc_final: 0.8500 (tpp) REVERT: I 123 HIS cc_start: 0.8475 (p90) cc_final: 0.8177 (p90) REVERT: I 174 LEU cc_start: 0.8211 (mt) cc_final: 0.8009 (mp) REVERT: I 384 GLU cc_start: 0.8501 (pm20) cc_final: 0.8181 (pm20) REVERT: J 15 GLU cc_start: 0.8439 (mp0) cc_final: 0.8032 (mp0) REVERT: J 18 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8854 (m-80) outliers start: 90 outliers final: 64 residues processed: 246 average time/residue: 0.1622 time to fit residues: 67.4773 Evaluate side-chains 231 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 162 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 141 ASN Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 350 PHE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 277 TRP Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 343 ASN Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain I residue 331 MET Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 343 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 249 optimal weight: 0.8980 chunk 334 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 279 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN G 331 GLN H 343 ASN D 70 GLN I 381 GLN ** J 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.075724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.060218 restraints weight = 95633.256| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.74 r_work: 0.3179 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30358 Z= 0.147 Angle : 0.569 11.645 41485 Z= 0.289 Chirality : 0.041 0.351 4608 Planarity : 0.004 0.063 5088 Dihedral : 13.354 138.504 4758 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.29 % Allowed : 14.99 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -1.40 (0.14), residues: 3413 helix: 0.12 (0.16), residues: 1136 sheet: -0.82 (0.23), residues: 539 loop : -1.69 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 213 TYR 0.014 0.001 TYR J 390 PHE 0.013 0.001 PHE F 265 TRP 0.013 0.001 TRP H 155 HIS 0.003 0.001 HIS E 338 Details of bonding type rmsd covalent geometry : bond 0.00341 (30351) covalent geometry : angle 0.56877 (41483) SS BOND : bond 0.00181 ( 1) SS BOND : angle 1.58515 ( 2) hydrogen bonds : bond 0.03284 ( 1059) hydrogen bonds : angle 4.75334 ( 3013) metal coordination : bond 0.00116 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 174 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 CYS cc_start: 0.8275 (t) cc_final: 0.7913 (m) REVERT: A 156 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.8307 (p) REVERT: B 21 ARG cc_start: 0.8000 (mmt-90) cc_final: 0.7602 (mmm-85) REVERT: B 221 MET cc_start: 0.8330 (ttt) cc_final: 0.8055 (ttm) REVERT: B 487 PHE cc_start: 0.7877 (t80) cc_final: 0.7637 (t80) REVERT: B 573 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8361 (mt) REVERT: G 137 MET cc_start: 0.7451 (mtp) cc_final: 0.7016 (mtp) REVERT: G 141 ASN cc_start: 0.7882 (OUTLIER) cc_final: 0.7501 (p0) REVERT: G 353 LYS cc_start: 0.6585 (mppt) cc_final: 0.6267 (mmtt) REVERT: F 30 ASP cc_start: 0.7947 (m-30) cc_final: 0.7497 (m-30) REVERT: F 337 MET cc_start: 0.7626 (tpt) cc_final: 0.7359 (mmm) REVERT: E 5 LYS cc_start: 0.8232 (pptt) cc_final: 0.7877 (tptp) REVERT: E 22 CYS cc_start: 0.8123 (m) cc_final: 0.7745 (m) REVERT: E 120 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7742 (mm-30) REVERT: E 276 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7496 (p0) REVERT: H 61 LYS cc_start: 0.6736 (mmmt) cc_final: 0.6006 (mmtt) REVERT: H 141 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.7681 (p0) REVERT: H 334 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7547 (mm) REVERT: H 341 MET cc_start: 0.7641 (mmt) cc_final: 0.7102 (mmp) REVERT: C 30 ASP cc_start: 0.8528 (t0) cc_final: 0.8199 (t0) REVERT: C 75 GLN cc_start: 0.8500 (tt0) cc_final: 0.8079 (tm-30) REVERT: C 280 GLU cc_start: 0.6778 (pp20) cc_final: 0.6525 (pp20) REVERT: C 337 MET cc_start: 0.8778 (mmm) cc_final: 0.8456 (tpp) REVERT: I 123 HIS cc_start: 0.8469 (p90) cc_final: 0.8178 (p90) REVERT: I 384 GLU cc_start: 0.8531 (pm20) cc_final: 0.8180 (pm20) REVERT: J 15 GLU cc_start: 0.8439 (mp0) cc_final: 0.7925 (mp0) REVERT: J 18 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8866 (m-80) outliers start: 101 outliers final: 72 residues processed: 260 average time/residue: 0.1642 time to fit residues: 72.2750 Evaluate side-chains 240 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 160 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 141 ASN Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 350 PHE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 277 TRP Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 141 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain H residue 334 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain I residue 331 MET Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 343 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 123 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 258 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 292 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 268 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 ASN C 117 GLN I 262 ASN ** J 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.076191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.060687 restraints weight = 95872.605| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.74 r_work: 0.3193 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30358 Z= 0.139 Angle : 0.564 13.919 41485 Z= 0.285 Chirality : 0.041 0.366 4608 Planarity : 0.004 0.070 5088 Dihedral : 13.309 139.485 4758 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.03 % Allowed : 15.90 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -1.26 (0.14), residues: 3413 helix: 0.28 (0.16), residues: 1135 sheet: -0.77 (0.23), residues: 539 loop : -1.63 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 213 TYR 0.014 0.001 TYR J 390 PHE 0.012 0.001 PHE F 265 TRP 0.012 0.001 TRP H 155 HIS 0.004 0.001 HIS G 338 Details of bonding type rmsd covalent geometry : bond 0.00321 (30351) covalent geometry : angle 0.56422 (41483) SS BOND : bond 0.00154 ( 1) SS BOND : angle 1.46370 ( 2) hydrogen bonds : bond 0.03204 ( 1059) hydrogen bonds : angle 4.66607 ( 3013) metal coordination : bond 0.00107 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 171 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 CYS cc_start: 0.8312 (t) cc_final: 0.7911 (m) REVERT: A 83 TYR cc_start: 0.8467 (m-80) cc_final: 0.8161 (m-80) REVERT: A 156 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8308 (p) REVERT: B 21 ARG cc_start: 0.7979 (mmt-90) cc_final: 0.7610 (mmm-85) REVERT: B 161 TRP cc_start: 0.7606 (m100) cc_final: 0.6891 (m100) REVERT: B 177 MET cc_start: 0.7152 (mmm) cc_final: 0.6408 (mtt) REVERT: B 221 MET cc_start: 0.8322 (ttt) cc_final: 0.8045 (ttm) REVERT: B 573 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8347 (mt) REVERT: G 137 MET cc_start: 0.7445 (mtp) cc_final: 0.7011 (mtp) REVERT: G 141 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7485 (p0) REVERT: G 337 MET cc_start: 0.6690 (tpt) cc_final: 0.6338 (tpp) REVERT: G 353 LYS cc_start: 0.6610 (mppt) cc_final: 0.6305 (mppt) REVERT: F 30 ASP cc_start: 0.7958 (m-30) cc_final: 0.7510 (m-30) REVERT: F 337 MET cc_start: 0.7578 (tpt) cc_final: 0.7320 (mmm) REVERT: E 5 LYS cc_start: 0.8251 (pptt) cc_final: 0.7891 (tptp) REVERT: E 22 CYS cc_start: 0.8134 (m) cc_final: 0.7812 (m) REVERT: E 120 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7759 (mm-30) REVERT: E 141 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7741 (p0) REVERT: H 61 LYS cc_start: 0.6756 (mmmt) cc_final: 0.6014 (mmtt) REVERT: H 334 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7445 (mm) REVERT: H 341 MET cc_start: 0.7640 (mmt) cc_final: 0.7102 (mmm) REVERT: C 30 ASP cc_start: 0.8434 (t0) cc_final: 0.8115 (t0) REVERT: C 337 MET cc_start: 0.8750 (mmm) cc_final: 0.8420 (tpp) REVERT: I 123 HIS cc_start: 0.8492 (p90) cc_final: 0.8202 (p90) REVERT: I 384 GLU cc_start: 0.8498 (pm20) cc_final: 0.8191 (pm20) REVERT: J 15 GLU cc_start: 0.8421 (mp0) cc_final: 0.8033 (mp0) REVERT: J 18 PHE cc_start: 0.9336 (OUTLIER) cc_final: 0.8885 (m-80) REVERT: J 344 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8197 (tp30) outliers start: 93 outliers final: 71 residues processed: 250 average time/residue: 0.1703 time to fit residues: 71.4458 Evaluate side-chains 235 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 157 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 141 ASN Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 277 TRP Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 350 PHE Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 277 TRP Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 141 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 334 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 343 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 240 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 301 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 279 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.076526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.061021 restraints weight = 95717.892| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.75 r_work: 0.3204 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30358 Z= 0.130 Angle : 0.559 12.890 41485 Z= 0.281 Chirality : 0.041 0.384 4608 Planarity : 0.004 0.067 5088 Dihedral : 13.267 139.734 4758 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.00 % Allowed : 16.23 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -1.16 (0.14), residues: 3413 helix: 0.38 (0.16), residues: 1138 sheet: -0.72 (0.23), residues: 534 loop : -1.57 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 213 TYR 0.020 0.001 TYR I 49 PHE 0.013 0.001 PHE C 78 TRP 0.018 0.001 TRP B 142 HIS 0.003 0.001 HIS G 338 Details of bonding type rmsd covalent geometry : bond 0.00300 (30351) covalent geometry : angle 0.55914 (41483) SS BOND : bond 0.00105 ( 1) SS BOND : angle 1.50410 ( 2) hydrogen bonds : bond 0.03128 ( 1059) hydrogen bonds : angle 4.60680 ( 3013) metal coordination : bond 0.00089 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 164 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 CYS cc_start: 0.8249 (t) cc_final: 0.7851 (m) REVERT: A 82 GLN cc_start: 0.8527 (pp30) cc_final: 0.8283 (pp30) REVERT: A 83 TYR cc_start: 0.8399 (m-80) cc_final: 0.8089 (m-80) REVERT: A 156 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8309 (p) REVERT: B 21 ARG cc_start: 0.7898 (mmt-90) cc_final: 0.7394 (mmm-85) REVERT: B 177 MET cc_start: 0.7267 (mmm) cc_final: 0.6271 (mmm) REVERT: B 221 MET cc_start: 0.8313 (ttt) cc_final: 0.8038 (ttm) REVERT: B 573 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8355 (mt) REVERT: G 137 MET cc_start: 0.7425 (mtp) cc_final: 0.7004 (mtp) REVERT: G 141 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7467 (p0) REVERT: G 337 MET cc_start: 0.6649 (tpt) cc_final: 0.6335 (tpp) REVERT: G 353 LYS cc_start: 0.6649 (mppt) cc_final: 0.6339 (mppt) REVERT: F 30 ASP cc_start: 0.7953 (m-30) cc_final: 0.7536 (m-30) REVERT: F 337 MET cc_start: 0.7563 (tpt) cc_final: 0.7308 (mmm) REVERT: E 5 LYS cc_start: 0.8264 (pptt) cc_final: 0.7898 (tptp) REVERT: E 22 CYS cc_start: 0.8132 (m) cc_final: 0.7797 (m) REVERT: E 120 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7753 (mm-30) REVERT: E 141 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7540 (p0) REVERT: E 276 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7503 (p0) REVERT: H 61 LYS cc_start: 0.6813 (mmmt) cc_final: 0.6180 (mmtt) REVERT: H 334 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7499 (mm) REVERT: H 341 MET cc_start: 0.7615 (mmt) cc_final: 0.7082 (mmm) REVERT: C 30 ASP cc_start: 0.8421 (t0) cc_final: 0.8106 (t0) REVERT: C 337 MET cc_start: 0.8736 (mmm) cc_final: 0.8405 (tpp) REVERT: I 123 HIS cc_start: 0.8509 (p90) cc_final: 0.8218 (p90) REVERT: I 384 GLU cc_start: 0.8493 (pm20) cc_final: 0.8159 (pm20) REVERT: J 15 GLU cc_start: 0.8430 (mp0) cc_final: 0.7946 (mp0) REVERT: J 18 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.8899 (m-80) REVERT: J 344 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8121 (tp30) outliers start: 92 outliers final: 71 residues processed: 243 average time/residue: 0.1687 time to fit residues: 68.5160 Evaluate side-chains 241 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 162 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 141 ASN Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 277 TRP Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 350 PHE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 277 TRP Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 141 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain H residue 334 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 342 MET Chi-restraints excluded: chain J residue 343 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 62 optimal weight: 4.9990 chunk 313 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 305 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 316 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 264 optimal weight: 0.7980 chunk 345 optimal weight: 30.0000 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.075284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.059651 restraints weight = 95827.486| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.74 r_work: 0.3163 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30358 Z= 0.206 Angle : 0.605 12.846 41485 Z= 0.304 Chirality : 0.043 0.441 4608 Planarity : 0.005 0.066 5088 Dihedral : 13.293 140.022 4758 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.97 % Allowed : 16.29 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -1.20 (0.14), residues: 3413 helix: 0.30 (0.16), residues: 1139 sheet: -0.75 (0.23), residues: 530 loop : -1.56 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 434 TYR 0.024 0.002 TYR I 49 PHE 0.019 0.002 PHE H 210 TRP 0.021 0.001 TRP B 142 HIS 0.004 0.001 HIS G 338 Details of bonding type rmsd covalent geometry : bond 0.00480 (30351) covalent geometry : angle 0.60448 (41483) SS BOND : bond 0.00133 ( 1) SS BOND : angle 1.52462 ( 2) hydrogen bonds : bond 0.03355 ( 1059) hydrogen bonds : angle 4.71641 ( 3013) metal coordination : bond 0.00222 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 167 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 CYS cc_start: 0.8235 (t) cc_final: 0.7841 (m) REVERT: A 83 TYR cc_start: 0.8434 (m-80) cc_final: 0.8082 (m-80) REVERT: A 156 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8248 (p) REVERT: B 21 ARG cc_start: 0.7881 (mmt-90) cc_final: 0.7519 (mmm-85) REVERT: B 161 TRP cc_start: 0.7643 (m100) cc_final: 0.6999 (m100) REVERT: B 221 MET cc_start: 0.8341 (ttt) cc_final: 0.8068 (ttm) REVERT: B 487 PHE cc_start: 0.7886 (t80) cc_final: 0.7534 (t80) REVERT: B 573 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8388 (mt) REVERT: G 137 MET cc_start: 0.7427 (mtp) cc_final: 0.6953 (mtp) REVERT: G 141 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7489 (p0) REVERT: G 353 LYS cc_start: 0.6622 (mppt) cc_final: 0.6323 (mppt) REVERT: F 30 ASP cc_start: 0.7943 (m-30) cc_final: 0.7510 (m-30) REVERT: F 337 MET cc_start: 0.7601 (tpt) cc_final: 0.7329 (mmm) REVERT: E 5 LYS cc_start: 0.8279 (pptt) cc_final: 0.7905 (tptp) REVERT: E 22 CYS cc_start: 0.8172 (m) cc_final: 0.7757 (m) REVERT: E 120 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7757 (mm-30) REVERT: E 141 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7579 (p0) REVERT: H 334 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7408 (mm) REVERT: C 30 ASP cc_start: 0.8442 (t0) cc_final: 0.8132 (t0) REVERT: C 280 GLU cc_start: 0.6731 (pp20) cc_final: 0.6447 (pp20) REVERT: C 337 MET cc_start: 0.8784 (mmm) cc_final: 0.8437 (tpp) REVERT: I 384 GLU cc_start: 0.8494 (pm20) cc_final: 0.8180 (pm20) REVERT: J 15 GLU cc_start: 0.8404 (mp0) cc_final: 0.8036 (mp0) REVERT: J 18 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8919 (m-80) REVERT: J 344 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8065 (tp30) outliers start: 91 outliers final: 77 residues processed: 240 average time/residue: 0.1657 time to fit residues: 67.6100 Evaluate side-chains 247 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 163 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 141 ASN Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 277 TRP Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 350 PHE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 277 TRP Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 141 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain H residue 334 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain I residue 326 LEU Chi-restraints excluded: chain I residue 331 MET Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 342 MET Chi-restraints excluded: chain J residue 343 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 294 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 278 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 271 optimal weight: 0.0170 chunk 253 optimal weight: 0.0270 chunk 317 optimal weight: 20.0000 chunk 296 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 153 HIS ** J 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.076318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.060775 restraints weight = 95310.924| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.75 r_work: 0.3196 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.937 30358 Z= 0.396 Angle : 0.569 12.587 41485 Z= 0.286 Chirality : 0.042 0.427 4608 Planarity : 0.004 0.067 5088 Dihedral : 13.296 139.750 4758 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.70 % Allowed : 16.75 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -1.08 (0.14), residues: 3413 helix: 0.43 (0.16), residues: 1131 sheet: -0.71 (0.23), residues: 530 loop : -1.50 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 213 TYR 0.023 0.001 TYR I 49 PHE 0.015 0.001 PHE H 210 TRP 0.018 0.001 TRP B 142 HIS 0.003 0.001 HIS G 338 Details of bonding type rmsd covalent geometry : bond 0.00327 (30351) covalent geometry : angle 0.56890 (41483) SS BOND : bond 0.00080 ( 1) SS BOND : angle 1.45690 ( 2) hydrogen bonds : bond 0.03167 ( 1059) hydrogen bonds : angle 4.63278 ( 3013) metal coordination : bond 0.79059 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 166 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 CYS cc_start: 0.8245 (t) cc_final: 0.7843 (m) REVERT: A 156 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.8303 (p) REVERT: B 21 ARG cc_start: 0.7871 (mmt-90) cc_final: 0.7499 (mmm-85) REVERT: B 145 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7801 (pt0) REVERT: B 161 TRP cc_start: 0.7602 (m100) cc_final: 0.6994 (m100) REVERT: B 177 MET cc_start: 0.7098 (mmm) cc_final: 0.6608 (mtt) REVERT: B 221 MET cc_start: 0.8322 (ttt) cc_final: 0.8015 (ttm) REVERT: B 487 PHE cc_start: 0.7855 (t80) cc_final: 0.7525 (t80) REVERT: B 573 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8346 (mt) REVERT: G 137 MET cc_start: 0.7449 (mtp) cc_final: 0.6985 (mtp) REVERT: G 141 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7521 (p0) REVERT: F 30 ASP cc_start: 0.8045 (m-30) cc_final: 0.7662 (m-30) REVERT: F 337 MET cc_start: 0.7564 (tpt) cc_final: 0.7318 (mmm) REVERT: E 5 LYS cc_start: 0.8283 (pptt) cc_final: 0.7911 (tptp) REVERT: E 22 CYS cc_start: 0.8172 (m) cc_final: 0.7823 (m) REVERT: E 120 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: E 141 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7570 (p0) REVERT: H 334 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7444 (mm) REVERT: H 337 MET cc_start: 0.7813 (tpp) cc_final: 0.7008 (mpp) REVERT: H 341 MET cc_start: 0.7629 (mmt) cc_final: 0.7077 (mmm) REVERT: C 30 ASP cc_start: 0.8386 (t0) cc_final: 0.8106 (t70) REVERT: C 337 MET cc_start: 0.8727 (mmm) cc_final: 0.8383 (tpp) REVERT: I 123 HIS cc_start: 0.8481 (p90) cc_final: 0.8242 (p90) REVERT: I 384 GLU cc_start: 0.8493 (pm20) cc_final: 0.8100 (pm20) REVERT: J 15 GLU cc_start: 0.8415 (mp0) cc_final: 0.7935 (mp0) REVERT: J 18 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.8886 (m-80) REVERT: J 297 ASN cc_start: 0.8634 (t0) cc_final: 0.8095 (t0) REVERT: J 344 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8066 (tp30) outliers start: 83 outliers final: 73 residues processed: 234 average time/residue: 0.1680 time to fit residues: 66.6181 Evaluate side-chains 243 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 163 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 141 ASN Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 277 TRP Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 350 PHE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 141 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain H residue 334 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain I residue 326 LEU Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 342 MET Chi-restraints excluded: chain J residue 343 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 104 optimal weight: 0.8980 chunk 218 optimal weight: 0.5980 chunk 225 optimal weight: 1.9990 chunk 309 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 107 optimal weight: 0.0870 chunk 232 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 166 ASN ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.077161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.061717 restraints weight = 95371.991| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.74 r_work: 0.3224 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30358 Z= 0.117 Angle : 0.556 12.950 41485 Z= 0.279 Chirality : 0.041 0.440 4608 Planarity : 0.004 0.066 5088 Dihedral : 13.239 138.042 4758 Min Nonbonded Distance : 1.505 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.64 % Allowed : 16.98 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -1.00 (0.14), residues: 3413 helix: 0.52 (0.16), residues: 1137 sheet: -0.65 (0.24), residues: 526 loop : -1.48 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 213 TYR 0.018 0.001 TYR I 49 PHE 0.012 0.001 PHE F 265 TRP 0.017 0.001 TRP B 142 HIS 0.039 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00270 (30351) covalent geometry : angle 0.55583 (41483) SS BOND : bond 0.00077 ( 1) SS BOND : angle 1.37080 ( 2) hydrogen bonds : bond 0.03045 ( 1059) hydrogen bonds : angle 4.56574 ( 3013) metal coordination : bond 0.03302 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7408.41 seconds wall clock time: 127 minutes 54.62 seconds (7674.62 seconds total)