Starting phenix.real_space_refine on Mon Sep 14 08:49:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uvn_20908/09_2026/6uvn_20908.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uvn_20908/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6uvn_20908/09_2026/6uvn_20908.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uvn_20908/09_2026/6uvn_20908.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uvn_20908/09_2026/6uvn_20908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uvn_20908/09_2026/6uvn_20908.map" model { file = "/net/cci-nas-00/data/ceres_data/6uvn_20908/09_2026/6uvn_20908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uvn_20908/09_2026/6uvn_20908.cif" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'RNAv2': 59} Modifications used: {'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: 21 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 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: 6.56, per 1000 atoms: 0.22 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: 2.59 Conformation dependent library (CDL) restraints added in 1.2 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: 3.61 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: 5.85 Time building geometry restraints manager: 3.46 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: 39963 2.09 - 4.18: 1335 4.18 - 6.27: 145 6.27 - 8.37: 27 8.37 - 10.46: 10 Bond angle restraints: 41480 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 41475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15968 17.95 - 35.89: 1517 35.89 - 53.84: 281 53.84 - 71.78: 113 71.78 - 89.73: 38 Dihedral angle restraints: 17917 sinusoidal: 7528 harmonic: 10389 Sorted by residual: dihedral pdb=" C4' U M 9 " pdb=" C3' U M 9 " pdb=" C2' U M 9 " pdb=" C1' U M 9 " ideal model delta sinusoidal sigma weight residual 36.35 -41.08 77.43 1 3.10e+00 1.04e-01 7.81e+02 dihedral pdb=" C4' A M 3 " pdb=" C3' A M 3 " pdb=" C2' A M 3 " pdb=" C1' A M 3 " ideal model delta sinusoidal sigma weight residual 36.34 -39.03 75.37 1 3.10e+00 1.04e-01 7.47e+02 dihedral pdb=" C4' G M 15 " pdb=" C3' G M 15 " pdb=" C2' G M 15 " pdb=" C1' G M 15 " ideal model delta sinusoidal sigma weight residual 36.34 -38.55 74.89 1 3.10e+00 1.04e-01 7.39e+02 ... (remaining 17914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3689 0.065 - 0.130: 738 0.130 - 0.194: 92 0.194 - 0.259: 54 0.259 - 0.324: 35 Chirality restraints: 4608 Sorted by residual: chirality pdb=" P A M 45 " pdb=" OP1 A M 45 " pdb=" OP2 A M 45 " pdb=" O5' A M 45 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" C2' A M 6 " pdb=" C3' A M 6 " pdb=" O2' A M 6 " pdb=" C1' A M 6 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.49e+00 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 ... (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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.950 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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= 0.473 Angle : 0.909 30.735 41482 Z= 0.502 Chirality : 0.061 0.324 4608 Planarity : 0.005 0.051 5088 Dihedral : 15.391 89.726 11158 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/Z covalent geometry : bond 0.00963 / 0.45 (30351) covalent geometry : angle 0.88386 / 0.49 (41480) SS BOND : bond 0.35860 / 18.87 ( 1) SS BOND : angle 30.65015 / 17.10 ( 2) hydrogen bonds : bond 0.16189 / 10.82 ( 1059) hydrogen bonds : angle 7.47119 / 5.12 ( 3013) metal coordination : bond 0.23135 / 10.64 ( 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 : 1.102 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: 0.2308 time to fit residues: 83.5889 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 : 1.132 ------------------------------------------------------------------------------- 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... A 160 ASN A 166 ASN A 178 ASN B 120 HIS ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 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 335 ASN E 352 HIS H 74 HIS H 80 HIS H 182 GLN H 335 ASN H 338 HIS H 343 ASN D 182 GLN D 217 HIS D 335 ASN D 338 HIS D 352 HIS C 113 GLN C 314 GLN C 331 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 153 HIS ** J 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.075073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.059504 restraints weight = 95978.977| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.75 r_work: 0.3164 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 2.276 30358 Z= 0.470 Angle : 0.961 26.804 41482 Z= 0.424 Chirality : 0.072 0.986 4608 Planarity : 0.005 0.090 5088 Dihedral : 11.477 159.792 4537 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.77 % Favored : 94.17 % Rotamer: Outliers : 1.79 % Allowed : 10.92 % Favored : 87.29 % 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: -2.76 (0.13), residues: 3413 helix: -1.27 (0.14), residues: 1149 sheet: -1.44 (0.23), residues: 489 loop : -2.36 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 310 TYR 0.019 0.002 TYR A 83 PHE 0.014 0.002 PHE I 284 TRP 0.017 0.002 TRP H 162 HIS 0.005 0.001 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (30351) covalent geometry : angle 0.96126 / 0.42 (41480) SS BOND : bond 0.00251 / 0.13 ( 1) SS BOND : angle 2.93872 / 1.56 ( 2) hydrogen bonds : bond 0.04430 / 2.88 ( 1059) hydrogen bonds : angle 5.67328 / 3.91 ( 3013) metal coordination : bond 0.92946 / 30.99 ( 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 234 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 179 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8537 (pp30) cc_final: 0.8236 (pp30) REVERT: A 156 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8221 (p) REVERT: B 21 ARG cc_start: 0.8334 (mmt-90) cc_final: 0.7937 (mmm-85) REVERT: B 177 MET cc_start: 0.7556 (mmt) cc_final: 0.7330 (mmm) REVERT: B 191 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7535 (m) REVERT: B 221 MET cc_start: 0.8308 (ttt) cc_final: 0.8021 (ttp) REVERT: B 456 PHE cc_start: 0.7540 (t80) cc_final: 0.7208 (t80) REVERT: G 137 MET cc_start: 0.7344 (mtp) cc_final: 0.6989 (mtp) REVERT: G 337 MET cc_start: 0.6756 (tpt) cc_final: 0.6373 (tpp) REVERT: G 353 LYS cc_start: 0.6442 (mppt) cc_final: 0.5938 (mmtt) REVERT: F 337 MET cc_start: 0.7571 (tpt) cc_final: 0.7328 (mmm) REVERT: E 5 LYS cc_start: 0.7940 (pptt) cc_final: 0.7699 (tptp) REVERT: E 22 CYS cc_start: 0.8042 (m) cc_final: 0.7641 (m) REVERT: E 223 MET cc_start: 0.8144 (ttp) cc_final: 0.7728 (ttp) REVERT: E 341 MET cc_start: 0.8388 (mmt) cc_final: 0.8109 (mmm) REVERT: H 223 MET cc_start: 0.8196 (ttp) cc_final: 0.7948 (ttm) REVERT: C 101 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8841 (mmm-85) REVERT: C 223 MET cc_start: 0.8751 (ttp) cc_final: 0.8453 (ttt) REVERT: I 217 LYS cc_start: 0.8919 (ptmt) cc_final: 0.8717 (ptmm) REVERT: I 323 MET cc_start: 0.8517 (ptp) cc_final: 0.7788 (mpp) REVERT: J 15 GLU cc_start: 0.8438 (mp0) cc_final: 0.7939 (mp0) outliers start: 55 outliers final: 27 residues processed: 226 average time/residue: 0.1969 time to fit residues: 73.0649 Evaluate side-chains 181 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 191 VAL Chi-restraints excluded: chain B residue 392 ASN Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 253 THR 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 C residue 101 ARG Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 113 GLN 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 105 THR Chi-restraints excluded: chain J residue 271 SER 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: 10.0000 chunk 249 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 257 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 ASN B 224 HIS ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 250 GLN G 331 GLN F 74 HIS E 74 HIS E 221 ASN E 331 GLN H 331 GLN I 46 HIS J 80 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.073664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.057968 restraints weight = 96057.589| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.71 r_work: 0.3121 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 30358 Z= 0.304 Angle : 0.848 17.454 41482 Z= 0.395 Chirality : 0.065 0.969 4608 Planarity : 0.005 0.063 5088 Dihedral : 12.070 171.528 4536 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.77 % Favored : 93.20 % Rotamer: Outliers : 2.15 % Allowed : 12.97 % Favored : 84.88 % 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: -2.35 (0.14), residues: 3413 helix: -0.84 (0.15), residues: 1151 sheet: -1.27 (0.23), residues: 524 loop : -2.17 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 289 TYR 0.026 0.002 TYR B 123 PHE 0.026 0.002 PHE H 92 TRP 0.017 0.002 TRP G 155 HIS 0.026 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.30 (30351) covalent geometry : angle 0.84818 / 0.39 (41480) SS BOND : bond 0.00288 / 0.15 ( 1) SS BOND : angle 2.24918 / 1.19 ( 2) hydrogen bonds : bond 0.04219 / 2.73 ( 1059) hydrogen bonds : angle 5.39300 / 3.73 ( 3013) metal coordination : bond 0.02959 / 1.48 ( 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 232 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 166 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8617 (m-80) cc_final: 0.8394 (m-80) REVERT: A 98 TYR cc_start: 0.8361 (m-80) cc_final: 0.8085 (m-10) REVERT: A 156 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8220 (p) REVERT: B 21 ARG cc_start: 0.8253 (mmt-90) cc_final: 0.7818 (mmm-85) REVERT: B 177 MET cc_start: 0.7608 (mmt) cc_final: 0.7402 (mmm) REVERT: B 221 MET cc_start: 0.8332 (ttt) cc_final: 0.7952 (ttp) REVERT: G 137 MET cc_start: 0.7428 (mtp) cc_final: 0.7084 (mtp) REVERT: G 353 LYS cc_start: 0.6421 (mppt) cc_final: 0.5950 (mmtt) REVERT: F 337 MET cc_start: 0.7678 (tpt) cc_final: 0.7432 (mmm) REVERT: E 5 LYS cc_start: 0.8004 (pptt) cc_final: 0.7739 (tptp) REVERT: E 22 CYS cc_start: 0.8150 (m) cc_final: 0.7757 (m) REVERT: E 46 MET cc_start: 0.8233 (mmt) cc_final: 0.7866 (mmm) REVERT: E 223 MET cc_start: 0.8140 (ttp) cc_final: 0.7755 (ttp) REVERT: H 289 ARG cc_start: 0.7997 (mpt90) cc_final: 0.7284 (mmt-90) REVERT: C 12 TYR cc_start: 0.8794 (m-80) cc_final: 0.8563 (m-80) REVERT: C 130 GLU cc_start: 0.8205 (tp30) cc_final: 0.7966 (tp30) REVERT: C 223 MET cc_start: 0.8768 (ttp) cc_final: 0.8455 (ttt) REVERT: I 85 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8550 (pm20) REVERT: I 174 LEU cc_start: 0.8349 (mt) cc_final: 0.8059 (mp) REVERT: I 217 LYS cc_start: 0.8942 (ptmt) cc_final: 0.8725 (ptmm) REVERT: J 15 GLU cc_start: 0.8418 (mp0) cc_final: 0.7962 (mp0) outliers start: 66 outliers final: 42 residues processed: 224 average time/residue: 0.1773 time to fit residues: 67.1172 Evaluate side-chains 196 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 A residue 159 THR Chi-restraints excluded: chain B residue 98 ILE 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 196 MET 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 E residue 16 ILE 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 100 LEU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain C residue 94 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 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 85 GLU 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 331 MET Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 343 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 145 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 290 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 324 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 ASN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 ASN H 45 GLN D 80 HIS D 87 HIS C 113 GLN I 60 ASN J 225 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.075975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.060515 restraints weight = 95117.641| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.72 r_work: 0.3192 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30358 Z= 0.145 Angle : 0.716 15.934 41482 Z= 0.335 Chirality : 0.054 0.638 4608 Planarity : 0.005 0.062 5088 Dihedral : 11.988 168.617 4532 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.64 % Allowed : 13.42 % Favored : 83.94 % 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: -0.45 (0.15), residues: 1145 sheet: -1.10 (0.23), residues: 505 loop : -1.98 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 294 TYR 0.030 0.002 TYR C 319 PHE 0.011 0.001 PHE J 115 TRP 0.016 0.001 TRP H 162 HIS 0.007 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (30351) covalent geometry : angle 0.71620 / 0.33 (41480) SS BOND : bond 0.00172 / 0.09 ( 1) SS BOND : angle 1.80785 / 0.95 ( 2) hydrogen bonds : bond 0.03592 / 2.33 ( 1059) hydrogen bonds : angle 5.10426 / 3.54 ( 3013) metal coordination : bond 0.03002 / 1.24 ( 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 259 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 178 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8516 (pp30) cc_final: 0.8261 (pp30) REVERT: A 83 TYR cc_start: 0.8485 (m-80) cc_final: 0.8274 (m-80) REVERT: A 156 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8270 (p) REVERT: B 21 ARG cc_start: 0.8122 (mmt-90) cc_final: 0.7713 (mmm-85) REVERT: B 221 MET cc_start: 0.8308 (ttt) cc_final: 0.8039 (ttm) REVERT: G 137 MET cc_start: 0.7381 (mtp) cc_final: 0.7053 (mtp) REVERT: G 337 MET cc_start: 0.6733 (tpt) cc_final: 0.6389 (tpp) REVERT: G 353 LYS cc_start: 0.6466 (mppt) cc_final: 0.6036 (mmtt) REVERT: F 337 MET cc_start: 0.7570 (tpt) cc_final: 0.7343 (mmm) REVERT: E 5 LYS cc_start: 0.8076 (pptt) cc_final: 0.7767 (tptp) REVERT: E 22 CYS cc_start: 0.8090 (m) cc_final: 0.7724 (m) REVERT: E 223 MET cc_start: 0.8095 (ttp) cc_final: 0.7712 (ttp) REVERT: E 341 MET cc_start: 0.8419 (mmt) cc_final: 0.8089 (mmp) REVERT: H 341 MET cc_start: 0.7547 (mmp) cc_final: 0.7092 (mmm) REVERT: C 223 MET cc_start: 0.8743 (ttp) cc_final: 0.8453 (ttt) REVERT: I 174 LEU cc_start: 0.8160 (mt) cc_final: 0.7923 (mp) REVERT: I 323 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7893 (mpp) REVERT: J 15 GLU cc_start: 0.8527 (mp0) cc_final: 0.8062 (mp0) REVERT: J 18 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8841 (m-80) REVERT: J 254 ILE cc_start: 0.8530 (mm) cc_final: 0.8293 (mt) outliers start: 81 outliers final: 48 residues processed: 250 average time/residue: 0.1752 time to fit residues: 73.9602 Evaluate side-chains 207 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 156 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 56 ILE Chi-restraints excluded: chain A residue 156 SER 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 616 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 350 PHE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 113 GLN 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 H residue 169 VAL Chi-restraints excluded: chain H residue 212 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 C residue 320 ILE Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 114 VAL 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 323 MET Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 153 HIS Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 332 LEU 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: 3.9990 chunk 61 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 335 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 ASN J 345 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.074872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.059410 restraints weight = 96182.722| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.69 r_work: 0.3154 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30358 Z= 0.234 Angle : 0.748 14.653 41482 Z= 0.350 Chirality : 0.055 0.723 4608 Planarity : 0.005 0.064 5088 Dihedral : 12.077 173.358 4532 Min Nonbonded Distance : 1.582 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.10 % Allowed : 14.21 % Favored : 82.70 % 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: -1.84 (0.14), residues: 3413 helix: -0.28 (0.15), residues: 1145 sheet: -1.07 (0.24), residues: 506 loop : -1.93 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.021 0.002 TYR B 123 PHE 0.020 0.002 PHE H 92 TRP 0.015 0.002 TRP H 155 HIS 0.006 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (30351) covalent geometry : angle 0.74750 / 0.35 (41480) SS BOND : bond 0.00265 / 0.14 ( 1) SS BOND : angle 1.71390 / 0.91 ( 2) hydrogen bonds : bond 0.03695 / 2.39 ( 1059) hydrogen bonds : angle 5.05132 / 3.50 ( 3013) metal coordination : bond 0.01499 / 0.61 ( 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 259 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 164 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8541 (m-80) cc_final: 0.8261 (m-80) REVERT: A 156 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8206 (p) REVERT: B 21 ARG cc_start: 0.8115 (mmt-90) cc_final: 0.7707 (mmm-85) REVERT: B 221 MET cc_start: 0.8315 (ttt) cc_final: 0.8061 (ttm) REVERT: B 573 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8449 (mt) REVERT: G 137 MET cc_start: 0.7442 (mtp) cc_final: 0.7069 (mtp) REVERT: G 318 HIS cc_start: 0.7514 (OUTLIER) cc_final: 0.7015 (t-90) REVERT: G 353 LYS cc_start: 0.6508 (mppt) cc_final: 0.6096 (mmtt) REVERT: F 337 MET cc_start: 0.7651 (tpt) cc_final: 0.7377 (mmm) REVERT: E 5 LYS cc_start: 0.8130 (pptt) cc_final: 0.7814 (tptp) REVERT: E 22 CYS cc_start: 0.8123 (m) cc_final: 0.7727 (m) REVERT: E 223 MET cc_start: 0.8114 (ttp) cc_final: 0.7742 (ttp) REVERT: H 289 ARG cc_start: 0.7984 (mpt90) cc_final: 0.7739 (mpt180) REVERT: H 341 MET cc_start: 0.7512 (mmp) cc_final: 0.7004 (mmm) REVERT: C 12 TYR cc_start: 0.8725 (m-80) cc_final: 0.8487 (m-80) REVERT: C 337 MET cc_start: 0.8805 (mmm) cc_final: 0.8539 (tpp) REVERT: I 323 MET cc_start: 0.8564 (ptp) cc_final: 0.7819 (mpp) REVERT: J 15 GLU cc_start: 0.8465 (mp0) cc_final: 0.7914 (mp0) REVERT: J 18 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.8851 (m-80) REVERT: J 254 ILE cc_start: 0.8574 (mm) cc_final: 0.8338 (mt) outliers start: 95 outliers final: 67 residues processed: 245 average time/residue: 0.1762 time to fit residues: 72.5226 Evaluate side-chains 223 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 152 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 56 ILE 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 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 595 ILE 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 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 G residue 318 HIS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 350 PHE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 113 GLN 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 H residue 76 VAL 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 343 ASN Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 94 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 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 114 VAL 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 J residue 18 PHE Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 153 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 249 optimal weight: 0.8980 chunk 334 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 279 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.074850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.059312 restraints weight = 95176.227| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.71 r_work: 0.3155 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30358 Z= 0.226 Angle : 0.736 14.126 41482 Z= 0.346 Chirality : 0.054 0.683 4608 Planarity : 0.005 0.071 5088 Dihedral : 12.052 173.824 4532 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.39 % Allowed : 15.15 % Favored : 81.46 % 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: -1.73 (0.14), residues: 3413 helix: -0.19 (0.15), residues: 1139 sheet: -1.01 (0.24), residues: 506 loop : -1.86 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.018 0.002 TYR B 123 PHE 0.015 0.002 PHE H 92 TRP 0.015 0.002 TRP H 155 HIS 0.007 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.23 (30351) covalent geometry : angle 0.73609 / 0.35 (41480) SS BOND : bond 0.00246 / 0.13 ( 1) SS BOND : angle 1.68235 / 0.89 ( 2) hydrogen bonds : bond 0.03612 / 2.34 ( 1059) hydrogen bonds : angle 5.01575 / 3.48 ( 3013) metal coordination : bond 0.01725 / 0.73 ( 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 268 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 164 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8542 (m-80) cc_final: 0.8239 (m-80) REVERT: A 156 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8219 (p) REVERT: B 21 ARG cc_start: 0.8075 (mmt-90) cc_final: 0.7670 (mmm-85) REVERT: B 221 MET cc_start: 0.8280 (ttt) cc_final: 0.7953 (ttp) REVERT: B 553 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8085 (tt) REVERT: B 573 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8421 (mt) REVERT: G 137 MET cc_start: 0.7440 (mtp) cc_final: 0.6972 (mtp) REVERT: G 141 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7544 (p0) REVERT: G 318 HIS cc_start: 0.7547 (OUTLIER) cc_final: 0.7032 (t-90) REVERT: G 337 MET cc_start: 0.6738 (tpt) cc_final: 0.6377 (tpp) REVERT: G 353 LYS cc_start: 0.6485 (mppt) cc_final: 0.6093 (mmtt) REVERT: F 337 MET cc_start: 0.7586 (tpt) cc_final: 0.7316 (mmm) REVERT: E 5 LYS cc_start: 0.8165 (pptt) cc_final: 0.7843 (tptp) REVERT: E 22 CYS cc_start: 0.8183 (m) cc_final: 0.7803 (m) REVERT: E 223 MET cc_start: 0.8123 (ttp) cc_final: 0.7741 (ttp) REVERT: E 276 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7471 (p0) REVERT: H 141 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.7709 (p0) REVERT: H 289 ARG cc_start: 0.8055 (mpt90) cc_final: 0.7611 (mmt-90) REVERT: H 320 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7918 (mt) REVERT: D 295 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7587 (mm-30) REVERT: C 12 TYR cc_start: 0.8715 (m-80) cc_final: 0.8471 (m-80) REVERT: C 337 MET cc_start: 0.8822 (mmm) cc_final: 0.8559 (mmm) REVERT: I 174 LEU cc_start: 0.8195 (mt) cc_final: 0.7951 (mp) REVERT: I 323 MET cc_start: 0.8623 (ptp) cc_final: 0.7944 (mpp) REVERT: I 384 GLU cc_start: 0.8568 (pm20) cc_final: 0.8203 (pm20) REVERT: J 15 GLU cc_start: 0.8474 (mp0) cc_final: 0.7933 (mp0) REVERT: J 18 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8855 (m-80) REVERT: J 254 ILE cc_start: 0.8556 (mm) cc_final: 0.8312 (mt) outliers start: 104 outliers final: 82 residues processed: 246 average time/residue: 0.1688 time to fit residues: 70.3445 Evaluate side-chains 248 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 157 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 553 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 595 ILE 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 196 MET Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain G residue 318 HIS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 88 ILE 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 344 LEU Chi-restraints excluded: chain F residue 350 PHE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 120 GLU 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 323 LEU 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 204 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 94 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 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 333 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 119 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 J residue 18 PHE Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 153 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 123 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 258 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 159 optimal weight: 0.9990 chunk 292 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 268 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 ASN I 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.076151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.060736 restraints weight = 95212.056| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.71 r_work: 0.3195 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30358 Z= 0.144 Angle : 0.692 13.565 41482 Z= 0.323 Chirality : 0.050 0.495 4608 Planarity : 0.005 0.069 5088 Dihedral : 11.930 172.358 4532 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.00 % Allowed : 15.97 % Favored : 81.04 % 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: -0.04 (0.15), residues: 1153 sheet: -0.94 (0.24), residues: 515 loop : -1.78 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 294 TYR 0.015 0.001 TYR I 390 PHE 0.012 0.001 PHE G 230 TRP 0.014 0.001 TRP F 155 HIS 0.008 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (30351) covalent geometry : angle 0.69165 / 0.32 (41480) SS BOND : bond 0.00135 / 0.07 ( 1) SS BOND : angle 1.53437 / 0.81 ( 2) hydrogen bonds : bond 0.03347 / 2.17 ( 1059) hydrogen bonds : angle 4.88883 / 3.39 ( 3013) metal coordination : bond 0.01662 / 0.70 ( 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 261 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 169 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8168 (p) REVERT: B 21 ARG cc_start: 0.8029 (mmt-90) cc_final: 0.7647 (mmm-85) REVERT: B 573 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8369 (mt) REVERT: G 137 MET cc_start: 0.7418 (mtp) cc_final: 0.7005 (mtp) REVERT: G 141 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7548 (p0) REVERT: G 337 MET cc_start: 0.6682 (tpt) cc_final: 0.6361 (tpp) REVERT: G 353 LYS cc_start: 0.6515 (mppt) cc_final: 0.6133 (mmtt) REVERT: F 337 MET cc_start: 0.7543 (tpt) cc_final: 0.7292 (mmm) REVERT: E 5 LYS cc_start: 0.8183 (pptt) cc_final: 0.7860 (tptp) REVERT: E 22 CYS cc_start: 0.8152 (m) cc_final: 0.7784 (m) REVERT: E 173 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6715 (p0) REVERT: E 223 MET cc_start: 0.8080 (ttp) cc_final: 0.7707 (ttp) REVERT: E 276 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7378 (p0) REVERT: E 323 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7346 (mp) REVERT: H 289 ARG cc_start: 0.7980 (mpt90) cc_final: 0.7732 (mpt180) REVERT: H 320 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7878 (mt) REVERT: H 341 MET cc_start: 0.7569 (mmp) cc_final: 0.7091 (mmm) REVERT: D 295 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7656 (mm-30) REVERT: C 30 ASP cc_start: 0.8568 (t0) cc_final: 0.8263 (t0) REVERT: C 337 MET cc_start: 0.8769 (mmm) cc_final: 0.8525 (mmm) REVERT: I 384 GLU cc_start: 0.8503 (pm20) cc_final: 0.8165 (pm20) REVERT: J 15 GLU cc_start: 0.8470 (mp0) cc_final: 0.7935 (mp0) REVERT: J 18 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8864 (m-80) outliers start: 92 outliers final: 70 residues processed: 243 average time/residue: 0.1730 time to fit residues: 71.7198 Evaluate side-chains 231 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 153 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 156 SER 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 497 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 595 ILE 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 196 MET Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 223 MET 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 76 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 350 PHE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 173 ASP 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 323 LEU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 51 LEU 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 320 ILE Chi-restraints excluded: chain D residue 196 MET 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 C residue 305 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain I residue 45 ASP 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 323 MET Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 153 HIS 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 342 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 240 optimal weight: 0.0170 chunk 230 optimal weight: 2.9990 chunk 301 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 279 optimal weight: 0.0970 chunk 13 optimal weight: 0.0770 chunk 182 optimal weight: 1.9990 overall best weight: 0.6376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.077067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.061610 restraints weight = 95113.741| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.72 r_work: 0.3225 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30358 Z= 0.123 Angle : 0.669 12.099 41482 Z= 0.313 Chirality : 0.049 0.422 4608 Planarity : 0.004 0.069 5088 Dihedral : 11.875 171.517 4532 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.74 % Allowed : 16.65 % Favored : 80.61 % 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: -1.37 (0.14), residues: 3413 helix: 0.14 (0.16), residues: 1153 sheet: -0.77 (0.23), residues: 524 loop : -1.70 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 213 TYR 0.015 0.001 TYR I 390 PHE 0.013 0.001 PHE G 230 TRP 0.016 0.001 TRP H 162 HIS 0.007 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (30351) covalent geometry : angle 0.66921 / 0.31 (41480) SS BOND : bond 0.00133 / 0.07 ( 1) SS BOND : angle 1.49554 / 0.79 ( 2) hydrogen bonds : bond 0.03239 / 2.10 ( 1059) hydrogen bonds : angle 4.75370 / 3.30 ( 3013) metal coordination : bond 0.01650 / 0.69 ( 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 266 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 182 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 CYS cc_start: 0.8271 (t) cc_final: 0.7933 (m) REVERT: A 83 TYR cc_start: 0.8440 (m-80) cc_final: 0.8141 (m-80) REVERT: A 156 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8135 (p) REVERT: B 21 ARG cc_start: 0.7993 (mmt-90) cc_final: 0.7627 (mmm-85) REVERT: B 177 MET cc_start: 0.7113 (mmm) cc_final: 0.6448 (mtt) REVERT: B 487 PHE cc_start: 0.7818 (t80) cc_final: 0.7603 (t80) REVERT: B 573 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8352 (mt) REVERT: G 137 MET cc_start: 0.7422 (mtp) cc_final: 0.7036 (mtp) REVERT: G 141 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7522 (p0) REVERT: G 337 MET cc_start: 0.6665 (tpt) cc_final: 0.6313 (tpp) REVERT: G 341 MET cc_start: 0.7541 (mmt) cc_final: 0.7120 (mmm) REVERT: G 353 LYS cc_start: 0.6571 (mppt) cc_final: 0.6221 (mmtt) REVERT: F 30 ASP cc_start: 0.7942 (m-30) cc_final: 0.7483 (m-30) REVERT: F 297 VAL cc_start: 0.7512 (OUTLIER) cc_final: 0.7259 (p) REVERT: F 337 MET cc_start: 0.7557 (tpt) cc_final: 0.7313 (mmm) REVERT: E 5 LYS cc_start: 0.8193 (pptt) cc_final: 0.7875 (tptp) REVERT: E 22 CYS cc_start: 0.8101 (m) cc_final: 0.7781 (m) REVERT: E 46 MET cc_start: 0.8278 (mmt) cc_final: 0.7946 (mmm) REVERT: E 223 MET cc_start: 0.8027 (ttp) cc_final: 0.7646 (ttp) REVERT: E 276 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7432 (p0) REVERT: E 323 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7382 (mp) REVERT: H 61 LYS cc_start: 0.7049 (mmmt) cc_final: 0.6391 (mmtt) REVERT: H 141 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.8030 (p0) REVERT: H 334 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7550 (mm) REVERT: H 337 MET cc_start: 0.7646 (tpp) cc_final: 0.7298 (ttp) REVERT: H 341 MET cc_start: 0.7615 (mmp) cc_final: 0.7172 (mmm) REVERT: C 30 ASP cc_start: 0.8515 (t0) cc_final: 0.8196 (t0) REVERT: C 280 GLU cc_start: 0.6733 (pp20) cc_final: 0.6506 (pp20) REVERT: C 337 MET cc_start: 0.8737 (mmm) cc_final: 0.8425 (tpp) REVERT: I 35 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: I 49 TYR cc_start: 0.7690 (t80) cc_final: 0.7324 (t80) REVERT: I 123 HIS cc_start: 0.8470 (p90) cc_final: 0.8147 (p90) REVERT: I 384 GLU cc_start: 0.8509 (pm20) cc_final: 0.8181 (pm20) REVERT: J 15 GLU cc_start: 0.8469 (mp0) cc_final: 0.7933 (mp0) REVERT: J 18 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8843 (m-80) outliers start: 84 outliers final: 61 residues processed: 252 average time/residue: 0.1813 time to fit residues: 76.7903 Evaluate side-chains 230 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 159 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 156 SER 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 595 ILE 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 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 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 111 VAL Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 121 LEU 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 323 LEU Chi-restraints excluded: chain H residue 25 VAL 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 126 ILE 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 42 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 106 CYS 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 305 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 153 HIS 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 342 MET 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: 4.9990 chunk 162 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 305 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 316 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 264 optimal weight: 0.9980 chunk 345 optimal weight: 30.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.075556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.059987 restraints weight = 95161.770| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.72 r_work: 0.3178 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30358 Z= 0.220 Angle : 0.719 12.406 41482 Z= 0.337 Chirality : 0.052 0.517 4608 Planarity : 0.005 0.080 5088 Dihedral : 11.931 173.634 4532 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.90 % Allowed : 16.68 % Favored : 80.42 % 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: -1.37 (0.14), residues: 3413 helix: 0.16 (0.16), residues: 1143 sheet: -0.85 (0.23), residues: 522 loop : -1.67 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.021 0.002 TYR B 123 PHE 0.021 0.002 PHE C 78 TRP 0.013 0.002 TRP J 221 HIS 0.007 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (30351) covalent geometry : angle 0.71908 / 0.34 (41480) SS BOND : bond 0.00162 / 0.09 ( 1) SS BOND : angle 1.46472 / 0.77 ( 2) hydrogen bonds : bond 0.03446 / 2.24 ( 1059) hydrogen bonds : angle 4.81197 / 3.34 ( 3013) metal coordination : bond 0.01465 / 0.62 ( 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 250 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 161 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 CYS cc_start: 0.8398 (t) cc_final: 0.7983 (m) REVERT: A 83 TYR cc_start: 0.8503 (m-80) cc_final: 0.8186 (m-80) REVERT: A 156 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8204 (p) REVERT: B 21 ARG cc_start: 0.8000 (mmt-90) cc_final: 0.7607 (mmm-85) REVERT: B 177 MET cc_start: 0.7313 (mmm) cc_final: 0.6576 (mtt) REVERT: B 487 PHE cc_start: 0.7929 (t80) cc_final: 0.7660 (t80) REVERT: B 573 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8422 (mt) REVERT: G 137 MET cc_start: 0.7454 (mtp) cc_final: 0.7015 (mtp) REVERT: G 141 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7500 (p0) REVERT: G 353 LYS cc_start: 0.6590 (mppt) cc_final: 0.6181 (mmtt) REVERT: F 30 ASP cc_start: 0.8029 (m-30) cc_final: 0.7568 (m-30) REVERT: F 196 MET cc_start: 0.7544 (ttm) cc_final: 0.7278 (ttm) REVERT: F 205 ASP cc_start: 0.8200 (t0) cc_final: 0.7993 (t70) REVERT: F 337 MET cc_start: 0.7576 (tpt) cc_final: 0.7307 (mmm) REVERT: E 5 LYS cc_start: 0.8225 (pptt) cc_final: 0.7870 (tptp) REVERT: E 22 CYS cc_start: 0.8169 (m) cc_final: 0.7798 (m) REVERT: E 46 MET cc_start: 0.8269 (mmt) cc_final: 0.7944 (mmm) REVERT: E 120 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: E 173 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6815 (p0) REVERT: E 223 MET cc_start: 0.8099 (ttp) cc_final: 0.7726 (ttp) REVERT: E 276 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7444 (p0) REVERT: E 323 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7476 (mp) REVERT: H 61 LYS cc_start: 0.6975 (mmmt) cc_final: 0.6287 (mmtt) REVERT: H 141 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.7675 (p0) REVERT: H 334 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7542 (mm) REVERT: H 337 MET cc_start: 0.7682 (tpp) cc_final: 0.7315 (ttp) REVERT: H 341 MET cc_start: 0.7548 (mmp) cc_final: 0.7021 (mmm) REVERT: C 30 ASP cc_start: 0.8537 (t0) cc_final: 0.8238 (t0) REVERT: C 337 MET cc_start: 0.8783 (mmm) cc_final: 0.8445 (tpp) REVERT: I 123 HIS cc_start: 0.8477 (p90) cc_final: 0.8171 (p90) REVERT: I 384 GLU cc_start: 0.8499 (pm20) cc_final: 0.8187 (pm20) REVERT: J 15 GLU cc_start: 0.8456 (mp0) cc_final: 0.7957 (mp0) REVERT: J 18 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8877 (m-80) outliers start: 89 outliers final: 72 residues processed: 232 average time/residue: 0.1745 time to fit residues: 68.7667 Evaluate side-chains 238 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 156 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 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 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 223 MET Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain G residue 328 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE 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 111 VAL Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 173 ASP 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 323 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 76 VAL 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 126 ILE Chi-restraints excluded: chain D residue 196 MET 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 C residue 305 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain I residue 105 THR 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 J residue 18 PHE Chi-restraints excluded: chain J residue 153 HIS 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 342 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 294 optimal weight: 0.0670 chunk 104 optimal weight: 0.8980 chunk 278 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 271 optimal weight: 0.3980 chunk 253 optimal weight: 0.9990 chunk 317 optimal weight: 10.0000 chunk 296 optimal weight: 0.0470 chunk 10 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.077471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.062103 restraints weight = 94688.338| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.72 r_work: 0.3237 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30358 Z= 0.120 Angle : 0.668 12.594 41482 Z= 0.313 Chirality : 0.048 0.344 4608 Planarity : 0.005 0.073 5088 Dihedral : 11.880 170.451 4532 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.28 % Allowed : 17.50 % Favored : 80.22 % 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: -1.22 (0.14), residues: 3413 helix: 0.28 (0.16), residues: 1147 sheet: -0.73 (0.23), residues: 530 loop : -1.59 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 288 TYR 0.016 0.001 TYR I 390 PHE 0.020 0.001 PHE C 78 TRP 0.019 0.001 TRP J 221 HIS 0.007 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (30351) covalent geometry : angle 0.66840 / 0.31 (41480) SS BOND : bond 0.00088 / 0.05 ( 1) SS BOND : angle 1.41322 / 0.74 ( 2) hydrogen bonds : bond 0.03188 / 2.07 ( 1059) hydrogen bonds : angle 4.70054 / 3.26 ( 3013) metal coordination : bond 0.01609 / 0.67 ( 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 237 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 167 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 CYS cc_start: 0.8340 (t) cc_final: 0.7949 (m) REVERT: A 82 GLN cc_start: 0.8441 (pp30) cc_final: 0.8213 (pp30) REVERT: A 83 TYR cc_start: 0.8398 (m-80) cc_final: 0.8072 (m-80) REVERT: A 156 SER cc_start: 0.8639 (OUTLIER) cc_final: 0.8244 (p) REVERT: B 21 ARG cc_start: 0.7920 (mmt-90) cc_final: 0.7551 (mmm-85) REVERT: B 177 MET cc_start: 0.7146 (mmm) cc_final: 0.6449 (mtt) REVERT: B 487 PHE cc_start: 0.7866 (t80) cc_final: 0.7634 (t80) REVERT: B 573 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8354 (mt) REVERT: G 137 MET cc_start: 0.7403 (mtp) cc_final: 0.6989 (mtp) REVERT: G 141 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7505 (p0) REVERT: G 353 LYS cc_start: 0.6570 (mppt) cc_final: 0.6207 (mmtt) REVERT: F 30 ASP cc_start: 0.7954 (m-30) cc_final: 0.7497 (m-30) REVERT: F 162 TRP cc_start: 0.7559 (t60) cc_final: 0.7285 (t60) REVERT: F 337 MET cc_start: 0.7439 (tpt) cc_final: 0.7205 (mmm) REVERT: E 5 LYS cc_start: 0.8230 (pptt) cc_final: 0.7891 (tptp) REVERT: E 22 CYS cc_start: 0.8097 (m) cc_final: 0.7773 (m) REVERT: E 46 MET cc_start: 0.8245 (mmt) cc_final: 0.7951 (mmm) REVERT: E 120 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7742 (mm-30) REVERT: E 173 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6766 (p0) REVERT: E 223 MET cc_start: 0.8022 (ttp) cc_final: 0.7624 (ttp) REVERT: E 276 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7423 (p0) REVERT: E 323 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7471 (mt) REVERT: H 61 LYS cc_start: 0.6939 (mmmt) cc_final: 0.6262 (mmtt) REVERT: H 141 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.8011 (p0) REVERT: H 341 MET cc_start: 0.7614 (mmp) cc_final: 0.7184 (mmm) REVERT: C 30 ASP cc_start: 0.8524 (t0) cc_final: 0.8197 (t0) REVERT: C 337 MET cc_start: 0.8713 (mmm) cc_final: 0.8381 (tpp) REVERT: I 123 HIS cc_start: 0.8489 (p90) cc_final: 0.8163 (p90) REVERT: I 384 GLU cc_start: 0.8495 (pm20) cc_final: 0.8158 (pm20) REVERT: J 15 GLU cc_start: 0.8441 (mp0) cc_final: 0.7932 (mp0) REVERT: J 18 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.8852 (m-80) REVERT: J 306 TYR cc_start: 0.8664 (t80) cc_final: 0.8448 (t80) outliers start: 70 outliers final: 55 residues processed: 228 average time/residue: 0.1787 time to fit residues: 68.6736 Evaluate side-chains 223 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 159 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 156 SER Chi-restraints excluded: chain B residue 98 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 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 277 TRP Chi-restraints excluded: chain F residue 290 PHE 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 121 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 173 ASP 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 323 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain H residue 25 VAL 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 D residue 126 ILE 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 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 305 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 345 ILE 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 J residue 18 PHE Chi-restraints excluded: chain J residue 153 HIS 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 342 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 104 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 309 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 6 optimal weight: 0.0670 chunk 113 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 232 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 HIS ** B 196 ASN ** 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 = 0.3711 r_free = 0.3711 target = 0.076711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.061277 restraints weight = 95266.751| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.73 r_work: 0.3211 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30358 Z= 0.156 Angle : 0.678 12.304 41482 Z= 0.318 Chirality : 0.049 0.393 4608 Planarity : 0.005 0.066 5088 Dihedral : 11.843 171.774 4532 Min Nonbonded Distance : 1.634 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.28 % Allowed : 17.43 % Favored : 80.29 % 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: -1.18 (0.14), residues: 3413 helix: 0.30 (0.16), residues: 1143 sheet: -0.68 (0.24), residues: 512 loop : -1.57 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.024 0.001 TYR I 306 PHE 0.013 0.001 PHE G 230 TRP 0.023 0.001 TRP J 221 HIS 0.007 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (30351) covalent geometry : angle 0.67766 / 0.32 (41480) SS BOND : bond 0.00108 / 0.06 ( 1) SS BOND : angle 1.37514 / 0.72 ( 2) hydrogen bonds : bond 0.03250 / 2.11 ( 1059) hydrogen bonds : angle 4.69240 / 3.26 ( 3013) metal coordination : bond 0.01477 / 0.62 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7857.80 seconds wall clock time: 135 minutes 48.55 seconds (8148.55 seconds total)