Starting phenix.real_space_refine on Fri Mar 15 09:32:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/03_2024/6ip1_9697.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/03_2024/6ip1_9697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/03_2024/6ip1_9697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/03_2024/6ip1_9697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/03_2024/6ip1_9697.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/03_2024/6ip1_9697.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.016 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: 4 Type Number sf(0) Gaussians S 83 5.16 5 C 7037 2.51 5 N 1901 2.21 5 O 2224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 47": "NH1" <-> "NH2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C ASP 70": "OD1" <-> "OD2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E ARG 47": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 47": "NH1" <-> "NH2" Residue "G ARG 19": "NH1" <-> "NH2" Residue "G ARG 47": "NH1" <-> "NH2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H ARG 47": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11245 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "B" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 509 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "C" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 520 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "D" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 495 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "E" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2303 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 288} Chain: "F" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2303 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 288} Chain: "G" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2303 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 288} Chain: "H" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2303 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 288} Time building chain proxies: 6.15, per 1000 atoms: 0.55 Number of scatterers: 11245 At special positions: 0 Unit cell: (117.589, 116.282, 118.895, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 83 16.00 O 2224 8.00 N 1901 7.00 C 7037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.68 Conformation dependent library (CDL) restraints added in 2.2 seconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 86.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 28 through 83 removed outlier: 3.855A pdb=" N THR A 35 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 228 removed outlier: 4.266A pdb=" N ARG B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 252 removed outlier: 4.238A pdb=" N ASN B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 249 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 37 removed outlier: 3.593A pdb=" N ARG C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 67 removed outlier: 3.685A pdb=" N ASP C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 47 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 60 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 77 removed outlier: 4.032A pdb=" N ALA C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU C 75 " --> pdb=" O MET C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'D' and resid 142 through 201 removed outlier: 3.752A pdb=" N GLN D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS D 162 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET D 167 " --> pdb=" O MET D 163 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 171 " --> pdb=" O MET D 167 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 20 removed outlier: 3.548A pdb=" N ALA E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS E 20 " --> pdb=" O GLU E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 27 removed outlier: 3.567A pdb=" N PHE E 27 " --> pdb=" O SER E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 55 removed outlier: 4.237A pdb=" N GLU E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA E 48 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS E 53 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET E 54 " --> pdb=" O ASN E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 75 removed outlier: 3.998A pdb=" N SER E 63 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN E 67 " --> pdb=" O SER E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 90 removed outlier: 3.643A pdb=" N ALA E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N CYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP E 87 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.621A pdb=" N LYS E 94 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 113 removed outlier: 3.603A pdb=" N ASN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS E 103 " --> pdb=" O GLU E 99 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU E 109 " --> pdb=" O MET E 105 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR E 111 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 134 removed outlier: 3.515A pdb=" N ILE E 130 " --> pdb=" O SER E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 155 removed outlier: 3.608A pdb=" N ALA E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 175 removed outlier: 3.879A pdb=" N ASN E 162 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS E 167 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA E 172 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN E 174 " --> pdb=" O GLY E 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 175 " --> pdb=" O TYR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 194 removed outlier: 4.054A pdb=" N ASP E 183 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 212 removed outlier: 3.820A pdb=" N TYR E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 232 removed outlier: 4.459A pdb=" N PHE E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 Processing helix chain 'E' and resid 239 through 252 removed outlier: 3.766A pdb=" N LYS E 245 " --> pdb=" O CYS E 241 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA E 250 " --> pdb=" O LYS E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 268 removed outlier: 3.718A pdb=" N GLU E 261 " --> pdb=" O ASP E 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR E 266 " --> pdb=" O ALA E 262 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER E 268 " --> pdb=" O LYS E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 295 removed outlier: 3.533A pdb=" N THR E 278 " --> pdb=" O GLN E 274 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN E 288 " --> pdb=" O LYS E 284 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY E 289 " --> pdb=" O LYS E 285 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP E 290 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 20 removed outlier: 3.547A pdb=" N ALA F 17 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 removed outlier: 3.567A pdb=" N PHE F 27 " --> pdb=" O SER F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 55 removed outlier: 4.237A pdb=" N GLU F 43 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE F 44 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA F 48 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE F 52 " --> pdb=" O ALA F 48 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET F 54 " --> pdb=" O ASN F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 75 removed outlier: 3.997A pdb=" N SER F 63 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN F 67 " --> pdb=" O SER F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 90 removed outlier: 3.643A pdb=" N ALA F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N CYS F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 95 removed outlier: 3.622A pdb=" N LYS F 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 113 removed outlier: 3.604A pdb=" N ASN F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU F 109 " --> pdb=" O MET F 105 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR F 111 " --> pdb=" O ALA F 107 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 134 removed outlier: 3.515A pdb=" N ILE F 130 " --> pdb=" O SER F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 155 removed outlier: 3.607A pdb=" N ALA F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP F 150 " --> pdb=" O GLU F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 175 removed outlier: 3.879A pdb=" N ASN F 162 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS F 164 " --> pdb=" O SER F 160 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS F 167 " --> pdb=" O LYS F 163 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 172 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN F 174 " --> pdb=" O GLY F 170 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 175 " --> pdb=" O TYR F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 194 removed outlier: 4.053A pdb=" N ASP F 183 " --> pdb=" O GLN F 179 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE F 184 " --> pdb=" O LYS F 180 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP F 194 " --> pdb=" O THR F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 212 removed outlier: 3.819A pdb=" N TYR F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 232 removed outlier: 4.459A pdb=" N PHE F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 239 through 252 removed outlier: 3.766A pdb=" N LYS F 245 " --> pdb=" O CYS F 241 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA F 250 " --> pdb=" O LYS F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 268 removed outlier: 3.718A pdb=" N GLU F 261 " --> pdb=" O ASP F 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 295 removed outlier: 3.533A pdb=" N THR F 278 " --> pdb=" O GLN F 274 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN F 288 " --> pdb=" O LYS F 284 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY F 289 " --> pdb=" O LYS F 285 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP F 290 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 20 removed outlier: 3.549A pdb=" N ALA G 17 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS G 20 " --> pdb=" O GLU G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 27 removed outlier: 3.567A pdb=" N PHE G 27 " --> pdb=" O SER G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 55 removed outlier: 4.237A pdb=" N GLU G 43 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE G 44 " --> pdb=" O GLU G 40 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR G 45 " --> pdb=" O ALA G 41 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA G 48 " --> pdb=" O ILE G 44 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS G 53 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET G 54 " --> pdb=" O ASN G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 75 removed outlier: 3.998A pdb=" N SER G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN G 67 " --> pdb=" O SER G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 90 removed outlier: 3.997A pdb=" N ASP G 87 " --> pdb=" O THR G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 95 removed outlier: 3.621A pdb=" N LYS G 94 " --> pdb=" O ALA G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 113 removed outlier: 3.604A pdb=" N ASN G 102 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS G 103 " --> pdb=" O GLU G 99 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU G 109 " --> pdb=" O MET G 105 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE G 110 " --> pdb=" O ARG G 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP G 113 " --> pdb=" O GLU G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 134 removed outlier: 3.514A pdb=" N ILE G 130 " --> pdb=" O SER G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 155 removed outlier: 3.608A pdb=" N ALA G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 175 removed outlier: 3.879A pdb=" N ASN G 162 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS G 163 " --> pdb=" O SER G 159 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS G 164 " --> pdb=" O SER G 160 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS G 167 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA G 172 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN G 174 " --> pdb=" O GLY G 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU G 175 " --> pdb=" O TYR G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 194 removed outlier: 4.054A pdb=" N ASP G 183 " --> pdb=" O GLN G 179 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE G 184 " --> pdb=" O LYS G 180 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP G 194 " --> pdb=" O THR G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 212 removed outlier: 3.700A pdb=" N LYS G 208 " --> pdb=" O ASP G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 232 removed outlier: 4.459A pdb=" N PHE G 232 " --> pdb=" O TYR G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 238 Processing helix chain 'G' and resid 239 through 252 removed outlier: 3.766A pdb=" N LYS G 245 " --> pdb=" O CYS G 241 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA G 250 " --> pdb=" O LYS G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 268 removed outlier: 3.718A pdb=" N GLU G 261 " --> pdb=" O ASP G 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR G 266 " --> pdb=" O ALA G 262 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER G 268 " --> pdb=" O LYS G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 295 removed outlier: 3.533A pdb=" N THR G 278 " --> pdb=" O GLN G 274 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN G 288 " --> pdb=" O LYS G 284 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY G 289 " --> pdb=" O LYS G 285 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP G 290 " --> pdb=" O THR G 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.548A pdb=" N ALA H 17 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU H 18 " --> pdb=" O LEU H 14 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS H 20 " --> pdb=" O GLU H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 27 removed outlier: 3.567A pdb=" N PHE H 27 " --> pdb=" O SER H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 55 removed outlier: 4.237A pdb=" N GLU H 43 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE H 44 " --> pdb=" O GLU H 40 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA H 48 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET H 54 " --> pdb=" O ASN H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 75 removed outlier: 3.998A pdb=" N SER H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN H 67 " --> pdb=" O SER H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 90 removed outlier: 3.643A pdb=" N ALA H 81 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N CYS H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP H 87 " --> pdb=" O THR H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 95 removed outlier: 3.620A pdb=" N LYS H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 113 removed outlier: 3.604A pdb=" N ASN H 102 " --> pdb=" O GLN H 98 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS H 103 " --> pdb=" O GLU H 99 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU H 109 " --> pdb=" O MET H 105 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE H 110 " --> pdb=" O ARG H 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP H 113 " --> pdb=" O GLU H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 134 removed outlier: 3.514A pdb=" N ILE H 130 " --> pdb=" O SER H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 155 removed outlier: 3.608A pdb=" N ALA H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP H 150 " --> pdb=" O GLU H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 175 removed outlier: 3.879A pdb=" N ASN H 162 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS H 163 " --> pdb=" O SER H 159 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS H 164 " --> pdb=" O SER H 160 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS H 167 " --> pdb=" O LYS H 163 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA H 172 " --> pdb=" O VAL H 168 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN H 174 " --> pdb=" O GLY H 170 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 175 " --> pdb=" O TYR H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 194 removed outlier: 4.054A pdb=" N ASP H 183 " --> pdb=" O GLN H 179 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE H 184 " --> pdb=" O LYS H 180 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP H 194 " --> pdb=" O THR H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 212 removed outlier: 3.820A pdb=" N TYR H 205 " --> pdb=" O SER H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 232 removed outlier: 4.459A pdb=" N PHE H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 238 Processing helix chain 'H' and resid 239 through 252 removed outlier: 3.766A pdb=" N LYS H 245 " --> pdb=" O CYS H 241 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA H 250 " --> pdb=" O LYS H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 268 removed outlier: 3.718A pdb=" N GLU H 261 " --> pdb=" O ASP H 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR H 266 " --> pdb=" O ALA H 262 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER H 268 " --> pdb=" O LYS H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 295 removed outlier: 3.533A pdb=" N THR H 278 " --> pdb=" O GLN H 274 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN H 288 " --> pdb=" O LYS H 284 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY H 289 " --> pdb=" O LYS H 285 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP H 290 " --> pdb=" O THR H 286 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 2046 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3669 1.34 - 1.46: 1657 1.46 - 1.57: 5952 1.57 - 1.69: 0 1.69 - 1.81: 134 Bond restraints: 11412 Sorted by residual: bond pdb=" N LYS C 69 " pdb=" CA LYS C 69 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N ASP A 57 " pdb=" CA ASP A 57 " ideal model delta sigma weight residual 1.459 1.434 0.025 1.18e-02 7.18e+03 4.50e+00 bond pdb=" CA LEU F 197 " pdb=" C LEU F 197 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.28e-02 6.10e+03 4.40e+00 bond pdb=" C TRP A 89 " pdb=" O TRP A 89 " ideal model delta sigma weight residual 1.231 1.271 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" N ASP A 44 " pdb=" CA ASP A 44 " ideal model delta sigma weight residual 1.459 1.437 0.022 1.17e-02 7.31e+03 3.50e+00 ... (remaining 11407 not shown) Histogram of bond angle deviations from ideal: 95.63 - 103.29: 75 103.29 - 110.95: 3608 110.95 - 118.61: 5311 118.61 - 126.27: 6207 126.27 - 133.93: 120 Bond angle restraints: 15321 Sorted by residual: angle pdb=" N LYS C 69 " pdb=" CA LYS C 69 " pdb=" C LYS C 69 " ideal model delta sigma weight residual 111.07 116.12 -5.05 1.07e+00 8.73e-01 2.23e+01 angle pdb=" N ASP C 70 " pdb=" CA ASP C 70 " pdb=" C ASP C 70 " ideal model delta sigma weight residual 111.28 106.52 4.76 1.09e+00 8.42e-01 1.91e+01 angle pdb=" N ASP A 57 " pdb=" CA ASP A 57 " pdb=" C ASP A 57 " ideal model delta sigma weight residual 111.03 106.21 4.82 1.11e+00 8.12e-01 1.88e+01 angle pdb=" C ALA E 17 " pdb=" N GLU E 18 " pdb=" CA GLU E 18 " ideal model delta sigma weight residual 122.07 128.25 -6.18 1.43e+00 4.89e-01 1.87e+01 angle pdb=" C ALA F 17 " pdb=" N GLU F 18 " pdb=" CA GLU F 18 " ideal model delta sigma weight residual 122.07 128.18 -6.11 1.43e+00 4.89e-01 1.83e+01 ... (remaining 15316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 6485 15.99 - 31.99: 424 31.99 - 47.98: 115 47.98 - 63.97: 3 63.97 - 79.97: 4 Dihedral angle restraints: 7031 sinusoidal: 2824 harmonic: 4207 Sorted by residual: dihedral pdb=" CA VAL C 36 " pdb=" C VAL C 36 " pdb=" N GLU C 37 " pdb=" CA GLU C 37 " ideal model delta harmonic sigma weight residual 180.00 151.74 28.26 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ALA A 81 " pdb=" C ALA A 81 " pdb=" N ALA A 82 " pdb=" CA ALA A 82 " ideal model delta harmonic sigma weight residual 180.00 155.21 24.79 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA PHE F 232 " pdb=" C PHE F 232 " pdb=" N PRO F 233 " pdb=" CA PRO F 233 " ideal model delta harmonic sigma weight residual 180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 7028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1087 0.048 - 0.095: 482 0.095 - 0.143: 64 0.143 - 0.190: 29 0.190 - 0.238: 5 Chirality restraints: 1667 Sorted by residual: chirality pdb=" CB VAL C 36 " pdb=" CA VAL C 36 " pdb=" CG1 VAL C 36 " pdb=" CG2 VAL C 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE E 216 " pdb=" N ILE E 216 " pdb=" C ILE E 216 " pdb=" CB ILE E 216 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE G 216 " pdb=" N ILE G 216 " pdb=" C ILE G 216 " pdb=" CB ILE G 216 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1664 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO F 196 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.21e+00 pdb=" C PRO F 196 " 0.050 2.00e-02 2.50e+03 pdb=" O PRO F 196 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU F 197 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 233 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C PRO F 233 " -0.045 2.00e-02 2.50e+03 pdb=" O PRO F 233 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA F 234 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 233 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C PRO E 233 " 0.045 2.00e-02 2.50e+03 pdb=" O PRO E 233 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA E 234 " -0.015 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 6 2.04 - 2.75: 1825 2.75 - 3.47: 16634 3.47 - 4.18: 26466 4.18 - 4.90: 44221 Nonbonded interactions: 89152 Sorted by model distance: nonbonded pdb=" CB LYS C 69 " pdb=" CE1 HIS G 79 " model vdw 1.321 3.660 nonbonded pdb=" O MET C 64 " pdb=" CG2 ILE C 67 " model vdw 1.541 3.460 nonbonded pdb=" CA MET C 64 " pdb=" CG2 ILE C 67 " model vdw 1.752 3.890 nonbonded pdb=" C MET C 64 " pdb=" CG2 ILE C 67 " model vdw 1.768 3.690 nonbonded pdb=" CB LYS C 69 " pdb=" ND1 HIS G 79 " model vdw 1.910 3.520 ... (remaining 89147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.580 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.620 Find NCS groups from input model: 0.660 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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 : 0.006 0.050 11412 Z= 0.363 Angle : 1.025 9.555 15321 Z= 0.570 Chirality : 0.053 0.238 1667 Planarity : 0.005 0.030 1998 Dihedral : 11.709 79.966 4295 Min Nonbonded Distance : 1.321 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.34 % Allowed : 5.50 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.85 (0.15), residues: 1404 helix: -3.86 (0.09), residues: 1073 sheet: None (None), residues: 0 loop : -2.85 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP F 275 HIS 0.012 0.003 HIS H 251 PHE 0.029 0.004 PHE F 85 TYR 0.027 0.003 TYR H 45 ARG 0.010 0.001 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 657 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8179 (m-30) cc_final: 0.7771 (t0) REVERT: B 203 ILE cc_start: 0.8103 (mm) cc_final: 0.7561 (pt) REVERT: B 226 GLN cc_start: 0.8572 (tt0) cc_final: 0.8294 (tt0) REVERT: B 242 ASP cc_start: 0.7416 (t70) cc_final: 0.7178 (t70) REVERT: C 34 GLN cc_start: 0.8655 (tp40) cc_final: 0.8429 (tp40) REVERT: C 56 GLN cc_start: 0.8428 (mm110) cc_final: 0.8191 (mt0) REVERT: E 57 ASN cc_start: 0.8430 (t0) cc_final: 0.8155 (t0) REVERT: E 58 TRP cc_start: 0.8676 (m-90) cc_final: 0.7843 (m-90) REVERT: E 75 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7636 (tp) REVERT: E 104 LEU cc_start: 0.8871 (mt) cc_final: 0.8607 (mt) REVERT: E 122 LYS cc_start: 0.8866 (tttp) cc_final: 0.8406 (tppt) REVERT: E 125 ILE cc_start: 0.8615 (pp) cc_final: 0.8240 (mt) REVERT: E 227 LYS cc_start: 0.8577 (mttm) cc_final: 0.8026 (tptt) REVERT: E 278 THR cc_start: 0.8490 (p) cc_final: 0.8110 (t) REVERT: F 67 GLN cc_start: 0.8085 (mt0) cc_final: 0.7657 (mt0) REVERT: F 78 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8589 (mtpt) REVERT: F 87 ASP cc_start: 0.8699 (m-30) cc_final: 0.8365 (m-30) REVERT: F 135 LEU cc_start: 0.8856 (mt) cc_final: 0.8282 (mt) REVERT: F 175 LEU cc_start: 0.8259 (mm) cc_final: 0.7981 (tt) REVERT: F 203 LYS cc_start: 0.8262 (pptt) cc_final: 0.7973 (pttp) REVERT: F 268 SER cc_start: 0.8636 (p) cc_final: 0.8307 (m) REVERT: F 276 LEU cc_start: 0.9036 (tm) cc_final: 0.8585 (tm) REVERT: F 279 MET cc_start: 0.7967 (mmt) cc_final: 0.7759 (mmt) REVERT: F 288 GLN cc_start: 0.8289 (mt0) cc_final: 0.7926 (mt0) REVERT: G 71 LEU cc_start: 0.8336 (mt) cc_final: 0.7640 (mt) REVERT: G 93 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7752 (mttt) REVERT: G 175 LEU cc_start: 0.8805 (mm) cc_final: 0.8231 (mt) REVERT: G 239 ARG cc_start: 0.7408 (tpt90) cc_final: 0.7032 (tpt170) REVERT: G 267 ASP cc_start: 0.8694 (p0) cc_final: 0.8025 (t70) REVERT: H 9 GLU cc_start: 0.7757 (tp30) cc_final: 0.7453 (tp30) REVERT: H 54 MET cc_start: 0.8481 (tpp) cc_final: 0.8256 (mtm) REVERT: H 99 GLU cc_start: 0.7932 (tp30) cc_final: 0.7557 (mp0) REVERT: H 106 ARG cc_start: 0.7680 (mtp85) cc_final: 0.7218 (mtm180) REVERT: H 125 ILE cc_start: 0.8414 (pp) cc_final: 0.8099 (pt) REVERT: H 138 ILE cc_start: 0.9031 (mm) cc_final: 0.8492 (mt) REVERT: H 146 GLU cc_start: 0.7578 (tt0) cc_final: 0.7301 (tp30) REVERT: H 166 LEU cc_start: 0.8344 (tt) cc_final: 0.8125 (tt) REVERT: H 175 LEU cc_start: 0.7788 (mm) cc_final: 0.7496 (mm) REVERT: H 222 LYS cc_start: 0.7666 (ttmt) cc_final: 0.7362 (ptmt) outliers start: 4 outliers final: 0 residues processed: 657 average time/residue: 0.2706 time to fit residues: 238.9663 Evaluate side-chains 394 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 188 ASN E 50 ASN E 76 GLN E 98 GLN E 187 GLN E 191 ASN F 23 ASN F 25 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN G 162 ASN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN H 147 GLN ** H 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11412 Z= 0.283 Angle : 0.813 9.528 15321 Z= 0.436 Chirality : 0.044 0.186 1667 Planarity : 0.004 0.040 1998 Dihedral : 6.504 59.528 1530 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 5.76 % Allowed : 18.46 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.19), residues: 1404 helix: -1.90 (0.13), residues: 1115 sheet: None (None), residues: 0 loop : -2.52 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 275 HIS 0.010 0.002 HIS E 213 PHE 0.025 0.003 PHE F 85 TYR 0.039 0.002 TYR B 235 ARG 0.004 0.001 ARG F 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 436 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8781 (tt0) REVERT: A 61 SER cc_start: 0.8562 (p) cc_final: 0.8050 (t) REVERT: A 65 ASP cc_start: 0.8663 (m-30) cc_final: 0.8077 (t0) REVERT: A 78 GLU cc_start: 0.8778 (pp20) cc_final: 0.7824 (tp30) REVERT: B 203 ILE cc_start: 0.8284 (mm) cc_final: 0.8026 (pt) REVERT: B 229 MET cc_start: 0.8113 (mtm) cc_final: 0.7737 (ttm) REVERT: C 34 GLN cc_start: 0.8650 (tp40) cc_final: 0.8251 (tp40) REVERT: D 184 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7757 (mtpt) REVERT: D 191 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7360 (mtp85) REVERT: E 57 ASN cc_start: 0.8391 (t0) cc_final: 0.8009 (t0) REVERT: E 116 ARG cc_start: 0.7346 (mpp80) cc_final: 0.7117 (mtm180) REVERT: E 164 CYS cc_start: 0.8635 (m) cc_final: 0.7838 (t) REVERT: E 175 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8063 (tt) REVERT: E 227 LYS cc_start: 0.8724 (mttm) cc_final: 0.8220 (tptt) REVERT: F 11 MET cc_start: 0.7836 (ppp) cc_final: 0.7570 (ppp) REVERT: F 24 SER cc_start: 0.7521 (m) cc_final: 0.6985 (t) REVERT: F 51 MET cc_start: 0.7700 (tpp) cc_final: 0.6739 (tpp) REVERT: F 54 MET cc_start: 0.8810 (mmm) cc_final: 0.8414 (tpp) REVERT: F 67 GLN cc_start: 0.7939 (mt0) cc_final: 0.7558 (tm-30) REVERT: F 80 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: F 87 ASP cc_start: 0.8508 (m-30) cc_final: 0.7990 (m-30) REVERT: F 101 ILE cc_start: 0.9007 (pp) cc_final: 0.8788 (pp) REVERT: F 125 ILE cc_start: 0.8450 (pp) cc_final: 0.8078 (mt) REVERT: F 140 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7655 (mtmm) REVERT: F 175 LEU cc_start: 0.8669 (mm) cc_final: 0.8057 (tt) REVERT: F 244 MET cc_start: 0.7092 (ttm) cc_final: 0.6794 (ttm) REVERT: F 266 TYR cc_start: 0.8459 (t80) cc_final: 0.8136 (t80) REVERT: F 268 SER cc_start: 0.8311 (p) cc_final: 0.7852 (m) REVERT: F 271 ARG cc_start: 0.7485 (tpt-90) cc_final: 0.6701 (tpp-160) REVERT: G 45 TYR cc_start: 0.6861 (t80) cc_final: 0.6448 (t80) REVERT: G 93 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7944 (mttt) REVERT: G 105 MET cc_start: 0.8622 (tpp) cc_final: 0.8353 (tpp) REVERT: G 113 ASP cc_start: 0.7789 (p0) cc_final: 0.7100 (t0) REVERT: G 264 LYS cc_start: 0.8321 (tptp) cc_final: 0.7621 (tptp) REVERT: G 267 ASP cc_start: 0.8775 (p0) cc_final: 0.8412 (p0) REVERT: H 25 GLN cc_start: 0.6756 (mp10) cc_final: 0.6521 (mp10) REVERT: H 76 GLN cc_start: 0.8165 (mp10) cc_final: 0.7385 (tm-30) REVERT: H 103 CYS cc_start: 0.8180 (p) cc_final: 0.7845 (p) REVERT: H 106 ARG cc_start: 0.7965 (mtp85) cc_final: 0.7365 (mtm180) REVERT: H 150 ASP cc_start: 0.8532 (t0) cc_final: 0.8027 (t0) REVERT: H 153 LYS cc_start: 0.8909 (mtpp) cc_final: 0.8369 (mtpt) REVERT: H 159 SER cc_start: 0.8443 (p) cc_final: 0.8229 (p) REVERT: H 204 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: H 222 LYS cc_start: 0.7201 (ttmt) cc_final: 0.6904 (tttt) outliers start: 68 outliers final: 40 residues processed: 467 average time/residue: 0.2556 time to fit residues: 162.0499 Evaluate side-chains 412 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 367 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 204 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 113 optimal weight: 0.0010 chunk 126 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN C 77 ASN D 175 ASN D 188 ASN E 50 ASN ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.6093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11412 Z= 0.208 Angle : 0.718 13.074 15321 Z= 0.377 Chirality : 0.042 0.177 1667 Planarity : 0.003 0.044 1998 Dihedral : 6.086 65.864 1528 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 6.10 % Allowed : 21.93 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.21), residues: 1404 helix: -0.91 (0.15), residues: 1127 sheet: None (None), residues: 0 loop : -2.49 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 275 HIS 0.008 0.002 HIS E 79 PHE 0.019 0.002 PHE F 85 TYR 0.034 0.002 TYR B 235 ARG 0.004 0.000 ARG G 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 406 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8832 (ptm160) cc_final: 0.8629 (ptm160) REVERT: A 65 ASP cc_start: 0.8364 (m-30) cc_final: 0.7907 (t0) REVERT: A 68 ASP cc_start: 0.7266 (t0) cc_final: 0.6950 (t0) REVERT: A 70 LEU cc_start: 0.9448 (tp) cc_final: 0.8957 (tt) REVERT: A 78 GLU cc_start: 0.8795 (pp20) cc_final: 0.7855 (tp30) REVERT: B 193 SER cc_start: 0.8666 (p) cc_final: 0.8349 (t) REVERT: B 199 HIS cc_start: 0.6851 (t70) cc_final: 0.6413 (t-170) REVERT: B 203 ILE cc_start: 0.8220 (mm) cc_final: 0.7970 (pt) REVERT: B 210 ARG cc_start: 0.8014 (mmm160) cc_final: 0.7720 (ttm-80) REVERT: B 229 MET cc_start: 0.8126 (mtm) cc_final: 0.7816 (ttm) REVERT: C 34 GLN cc_start: 0.8438 (tp40) cc_final: 0.8072 (tp40) REVERT: D 184 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7901 (mtpt) REVERT: D 186 ASP cc_start: 0.7624 (m-30) cc_final: 0.7265 (m-30) REVERT: E 40 GLU cc_start: 0.7777 (tp30) cc_final: 0.7451 (tp30) REVERT: E 57 ASN cc_start: 0.8311 (t0) cc_final: 0.7999 (t0) REVERT: E 98 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7716 (tp-100) REVERT: E 164 CYS cc_start: 0.8736 (m) cc_final: 0.7863 (t) REVERT: E 227 LYS cc_start: 0.8650 (mttm) cc_final: 0.8162 (tptt) REVERT: F 11 MET cc_start: 0.7814 (ppp) cc_final: 0.7529 (ppp) REVERT: F 24 SER cc_start: 0.7494 (m) cc_final: 0.7164 (t) REVERT: F 51 MET cc_start: 0.7869 (tpp) cc_final: 0.6968 (tpp) REVERT: F 54 MET cc_start: 0.8668 (mmm) cc_final: 0.8415 (tpp) REVERT: F 66 CYS cc_start: 0.8626 (t) cc_final: 0.7793 (p) REVERT: F 67 GLN cc_start: 0.7672 (mt0) cc_final: 0.7158 (tp40) REVERT: F 80 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7522 (m-30) REVERT: F 87 ASP cc_start: 0.8733 (m-30) cc_final: 0.8327 (m-30) REVERT: F 101 ILE cc_start: 0.9030 (pp) cc_final: 0.8792 (pp) REVERT: F 125 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8232 (mt) REVERT: F 140 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7678 (mtmm) REVERT: F 158 ASN cc_start: 0.9250 (p0) cc_final: 0.8832 (p0) REVERT: F 171 TYR cc_start: 0.7971 (m-80) cc_final: 0.6884 (m-80) REVERT: F 175 LEU cc_start: 0.8696 (mm) cc_final: 0.8029 (tt) REVERT: F 226 GLN cc_start: 0.8146 (tp40) cc_final: 0.7889 (tp-100) REVERT: F 263 VAL cc_start: 0.8908 (t) cc_final: 0.8688 (m) REVERT: F 268 SER cc_start: 0.8352 (p) cc_final: 0.7254 (m) REVERT: F 279 MET cc_start: 0.8501 (mmm) cc_final: 0.8249 (mmt) REVERT: G 93 LYS cc_start: 0.8302 (mtpt) cc_final: 0.8043 (mttt) REVERT: G 105 MET cc_start: 0.8527 (tpp) cc_final: 0.8056 (tpp) REVERT: G 106 ARG cc_start: 0.7033 (ttm110) cc_final: 0.6772 (ttm110) REVERT: G 113 ASP cc_start: 0.7890 (p0) cc_final: 0.6991 (t0) REVERT: G 125 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8338 (pt) REVERT: G 152 TYR cc_start: 0.9155 (OUTLIER) cc_final: 0.8696 (m-10) REVERT: G 158 ASN cc_start: 0.5205 (m110) cc_final: 0.4992 (m110) REVERT: G 163 LYS cc_start: 0.8474 (mtmt) cc_final: 0.7879 (mttm) REVERT: G 179 GLN cc_start: 0.8404 (tp-100) cc_final: 0.7598 (tt0) REVERT: G 239 ARG cc_start: 0.7375 (tpt170) cc_final: 0.6823 (tpt170) REVERT: G 267 ASP cc_start: 0.8632 (p0) cc_final: 0.8370 (p0) REVERT: H 76 GLN cc_start: 0.8120 (mp10) cc_final: 0.7345 (tm-30) REVERT: H 105 MET cc_start: 0.8670 (tpt) cc_final: 0.8335 (tpt) REVERT: H 125 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8232 (mt) REVERT: H 140 LYS cc_start: 0.8336 (mttt) cc_final: 0.8048 (mtmt) REVERT: H 204 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: H 222 LYS cc_start: 0.7254 (ttmt) cc_final: 0.7008 (tttt) REVERT: H 271 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.6687 (ttt180) outliers start: 72 outliers final: 34 residues processed: 442 average time/residue: 0.2566 time to fit residues: 154.9586 Evaluate side-chains 400 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 359 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 228 TYR Chi-restraints excluded: chain H residue 243 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN C 66 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 175 ASN D 188 ASN E 50 ASN E 254 GLN ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 HIS ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.6636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11412 Z= 0.260 Angle : 0.746 11.459 15321 Z= 0.392 Chirality : 0.043 0.184 1667 Planarity : 0.004 0.045 1998 Dihedral : 6.054 67.736 1528 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 6.44 % Allowed : 23.45 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.22), residues: 1404 helix: -0.54 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -2.39 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 275 HIS 0.009 0.002 HIS E 123 PHE 0.022 0.002 PHE H 85 TYR 0.035 0.002 TYR B 235 ARG 0.005 0.000 ARG D 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 379 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.8517 (tp40) cc_final: 0.8315 (tm-30) REVERT: A 44 ASP cc_start: 0.8512 (t0) cc_final: 0.8088 (t0) REVERT: A 70 LEU cc_start: 0.9311 (tp) cc_final: 0.8925 (tt) REVERT: B 193 SER cc_start: 0.8828 (p) cc_final: 0.8503 (t) REVERT: B 199 HIS cc_start: 0.6731 (t70) cc_final: 0.6247 (t-170) REVERT: B 203 ILE cc_start: 0.8326 (mm) cc_final: 0.7659 (pt) REVERT: B 206 GLU cc_start: 0.8455 (pp20) cc_final: 0.8209 (pp20) REVERT: B 215 MET cc_start: 0.8321 (ppp) cc_final: 0.8004 (ppp) REVERT: B 217 MET cc_start: 0.6886 (mmp) cc_final: 0.6557 (mmp) REVERT: B 229 MET cc_start: 0.8152 (mtm) cc_final: 0.7735 (ttm) REVERT: C 34 GLN cc_start: 0.8272 (tp40) cc_final: 0.7973 (tp40) REVERT: C 38 GLU cc_start: 0.8749 (tp30) cc_final: 0.8525 (tp30) REVERT: D 184 LYS cc_start: 0.8296 (mtpt) cc_final: 0.7862 (mtpt) REVERT: E 50 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8483 (t0) REVERT: E 57 ASN cc_start: 0.8655 (t0) cc_final: 0.8310 (t0) REVERT: E 98 GLN cc_start: 0.8098 (tp-100) cc_final: 0.7805 (tp-100) REVERT: E 122 LYS cc_start: 0.9242 (tppt) cc_final: 0.8991 (tppt) REVERT: E 164 CYS cc_start: 0.8729 (m) cc_final: 0.7660 (t) REVERT: E 175 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8487 (tt) REVERT: E 200 TYR cc_start: 0.8003 (m-80) cc_final: 0.7698 (m-80) REVERT: E 227 LYS cc_start: 0.8711 (mttm) cc_final: 0.8213 (tptt) REVERT: F 11 MET cc_start: 0.7795 (ppp) cc_final: 0.7568 (ppp) REVERT: F 24 SER cc_start: 0.7721 (m) cc_final: 0.7211 (t) REVERT: F 51 MET cc_start: 0.8002 (tpp) cc_final: 0.7086 (tpp) REVERT: F 54 MET cc_start: 0.8597 (mmm) cc_final: 0.8375 (tpp) REVERT: F 80 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7573 (m-30) REVERT: F 87 ASP cc_start: 0.8728 (m-30) cc_final: 0.8293 (m-30) REVERT: F 158 ASN cc_start: 0.9216 (p0) cc_final: 0.8976 (p0) REVERT: F 171 TYR cc_start: 0.8223 (m-80) cc_final: 0.7096 (m-80) REVERT: F 175 LEU cc_start: 0.8844 (mm) cc_final: 0.8263 (tt) REVERT: F 193 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6763 (tpt) REVERT: F 218 MET cc_start: 0.3970 (OUTLIER) cc_final: 0.3625 (mtm) REVERT: F 268 SER cc_start: 0.8388 (p) cc_final: 0.7659 (m) REVERT: G 11 MET cc_start: 0.7445 (tmm) cc_final: 0.7032 (mmp) REVERT: G 105 MET cc_start: 0.8514 (tpp) cc_final: 0.8108 (tpp) REVERT: G 106 ARG cc_start: 0.7045 (ttm110) cc_final: 0.6817 (ttm110) REVERT: G 113 ASP cc_start: 0.7876 (p0) cc_final: 0.6796 (t0) REVERT: G 152 TYR cc_start: 0.9218 (OUTLIER) cc_final: 0.8572 (m-10) REVERT: G 163 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8015 (mttp) REVERT: G 222 LYS cc_start: 0.7623 (ttmt) cc_final: 0.7117 (ttpt) REVERT: G 239 ARG cc_start: 0.7240 (tpt170) cc_final: 0.6959 (tpt170) REVERT: H 51 MET cc_start: 0.8329 (mtm) cc_final: 0.7586 (ttm) REVERT: H 76 GLN cc_start: 0.8021 (mp10) cc_final: 0.7130 (tm-30) REVERT: H 125 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8397 (mt) REVERT: H 146 GLU cc_start: 0.8082 (tt0) cc_final: 0.7679 (tm-30) REVERT: H 153 LYS cc_start: 0.8887 (mtpp) cc_final: 0.8629 (mtpt) REVERT: H 204 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7828 (m-30) REVERT: H 218 MET cc_start: 0.4709 (tpp) cc_final: 0.4497 (tpt) REVERT: H 222 LYS cc_start: 0.6913 (ttmt) cc_final: 0.6484 (ptmt) REVERT: H 249 GLU cc_start: 0.7792 (tm-30) cc_final: 0.6445 (tm-30) REVERT: H 271 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.6934 (ttt180) outliers start: 76 outliers final: 50 residues processed: 413 average time/residue: 0.2414 time to fit residues: 136.9764 Evaluate side-chains 409 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 351 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain E residue 50 ASN Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 228 TYR Chi-restraints excluded: chain H residue 276 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN C 66 GLN D 152 GLN D 175 ASN D 188 ASN E 50 ASN F 23 ASN ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.7002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11412 Z= 0.187 Angle : 0.698 15.470 15321 Z= 0.359 Chirality : 0.041 0.193 1667 Planarity : 0.003 0.048 1998 Dihedral : 5.911 69.281 1528 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 5.67 % Allowed : 25.49 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.23), residues: 1404 helix: -0.22 (0.16), residues: 1137 sheet: None (None), residues: 0 loop : -2.65 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 275 HIS 0.015 0.002 HIS G 79 PHE 0.015 0.002 PHE E 235 TYR 0.038 0.001 TYR B 235 ARG 0.005 0.000 ARG F 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 389 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8376 (t0) cc_final: 0.7897 (t0) REVERT: A 65 ASP cc_start: 0.8205 (m-30) cc_final: 0.7670 (t0) REVERT: A 70 LEU cc_start: 0.9096 (tp) cc_final: 0.8816 (tt) REVERT: B 193 SER cc_start: 0.8808 (p) cc_final: 0.8481 (t) REVERT: B 195 ILE cc_start: 0.7023 (mm) cc_final: 0.6735 (tp) REVERT: B 203 ILE cc_start: 0.8018 (mm) cc_final: 0.7571 (pt) REVERT: B 206 GLU cc_start: 0.8157 (pp20) cc_final: 0.7679 (pp20) REVERT: B 210 ARG cc_start: 0.7930 (mmm160) cc_final: 0.7561 (ttm-80) REVERT: B 215 MET cc_start: 0.8290 (ppp) cc_final: 0.7996 (ppp) REVERT: B 229 MET cc_start: 0.8046 (mtm) cc_final: 0.7769 (ttm) REVERT: C 38 GLU cc_start: 0.8690 (tp30) cc_final: 0.8402 (tp30) REVERT: C 66 GLN cc_start: 0.8305 (mt0) cc_final: 0.8101 (mt0) REVERT: D 184 LYS cc_start: 0.8076 (mtpt) cc_final: 0.7781 (mtpt) REVERT: E 40 GLU cc_start: 0.7782 (tp30) cc_final: 0.7551 (tp30) REVERT: E 57 ASN cc_start: 0.8418 (t0) cc_final: 0.8011 (t0) REVERT: E 98 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7859 (tp-100) REVERT: E 122 LYS cc_start: 0.9313 (tppt) cc_final: 0.8995 (tppt) REVERT: E 164 CYS cc_start: 0.8719 (m) cc_final: 0.7606 (t) REVERT: E 175 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8430 (tt) REVERT: E 227 LYS cc_start: 0.8707 (mttm) cc_final: 0.8197 (tptt) REVERT: F 11 MET cc_start: 0.7706 (ppp) cc_final: 0.7443 (ppp) REVERT: F 24 SER cc_start: 0.7631 (m) cc_final: 0.7276 (t) REVERT: F 51 MET cc_start: 0.7857 (tpp) cc_final: 0.7110 (tpp) REVERT: F 87 ASP cc_start: 0.8723 (m-30) cc_final: 0.8283 (m-30) REVERT: F 103 CYS cc_start: 0.8716 (m) cc_final: 0.8513 (m) REVERT: F 158 ASN cc_start: 0.9193 (p0) cc_final: 0.8964 (p0) REVERT: F 175 LEU cc_start: 0.8824 (mm) cc_final: 0.8271 (tt) REVERT: F 193 MET cc_start: 0.7168 (mmt) cc_final: 0.6754 (mmm) REVERT: F 218 MET cc_start: 0.3826 (OUTLIER) cc_final: 0.3534 (mtm) REVERT: F 226 GLN cc_start: 0.7975 (tp40) cc_final: 0.7692 (tp-100) REVERT: F 268 SER cc_start: 0.8659 (p) cc_final: 0.7828 (m) REVERT: G 79 HIS cc_start: 0.6442 (t-170) cc_final: 0.6228 (t-170) REVERT: G 85 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8493 (m-10) REVERT: G 105 MET cc_start: 0.8463 (tpp) cc_final: 0.7915 (tpp) REVERT: G 106 ARG cc_start: 0.6918 (ttm110) cc_final: 0.6565 (ttm110) REVERT: G 113 ASP cc_start: 0.7807 (p0) cc_final: 0.6647 (t0) REVERT: G 126 SER cc_start: 0.9359 (m) cc_final: 0.9142 (t) REVERT: G 152 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.8480 (m-10) REVERT: G 163 LYS cc_start: 0.8522 (mtmt) cc_final: 0.7992 (mttp) REVERT: G 222 LYS cc_start: 0.7608 (ttmt) cc_final: 0.6914 (ttpt) REVERT: G 227 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8562 (mmtt) REVERT: H 76 GLN cc_start: 0.7743 (mp10) cc_final: 0.6848 (tm-30) REVERT: H 87 ASP cc_start: 0.8081 (t70) cc_final: 0.7805 (t70) REVERT: H 125 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8380 (mt) REVERT: H 146 GLU cc_start: 0.8138 (tt0) cc_final: 0.7719 (tm-30) REVERT: H 204 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: H 248 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6941 (mm) REVERT: H 271 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.6887 (ttt180) REVERT: H 284 LYS cc_start: 0.8994 (tttm) cc_final: 0.8736 (tttm) outliers start: 67 outliers final: 35 residues processed: 421 average time/residue: 0.2592 time to fit residues: 150.6264 Evaluate side-chains 397 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 355 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 248 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN D 175 ASN D 188 ASN E 50 ASN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 GLN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.7359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11412 Z= 0.277 Angle : 0.777 15.536 15321 Z= 0.401 Chirality : 0.044 0.205 1667 Planarity : 0.004 0.052 1998 Dihedral : 6.020 71.502 1528 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 6.94 % Allowed : 25.83 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.23), residues: 1404 helix: -0.26 (0.15), residues: 1149 sheet: None (None), residues: 0 loop : -2.52 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 58 HIS 0.010 0.002 HIS E 123 PHE 0.019 0.002 PHE H 214 TYR 0.040 0.002 TYR B 235 ARG 0.012 0.001 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 369 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8638 (t0) cc_final: 0.8019 (t0) REVERT: A 70 LEU cc_start: 0.9182 (tp) cc_final: 0.8882 (tt) REVERT: B 193 SER cc_start: 0.8958 (p) cc_final: 0.8604 (t) REVERT: B 203 ILE cc_start: 0.7995 (mm) cc_final: 0.7383 (pt) REVERT: B 215 MET cc_start: 0.8242 (ppp) cc_final: 0.7827 (ppp) REVERT: B 216 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: B 217 MET cc_start: 0.6808 (mmp) cc_final: 0.6594 (mmp) REVERT: B 229 MET cc_start: 0.8158 (mtm) cc_final: 0.7819 (ttm) REVERT: C 41 ASP cc_start: 0.8468 (p0) cc_final: 0.8209 (p0) REVERT: C 75 GLU cc_start: 0.7504 (tp30) cc_final: 0.7280 (tp30) REVERT: D 163 MET cc_start: 0.8395 (ttp) cc_final: 0.8181 (ttm) REVERT: D 184 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7796 (mtpt) REVERT: D 186 ASP cc_start: 0.7527 (m-30) cc_final: 0.7296 (m-30) REVERT: E 45 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7284 (t80) REVERT: E 50 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8565 (t0) REVERT: E 57 ASN cc_start: 0.8648 (t0) cc_final: 0.8252 (t0) REVERT: E 98 GLN cc_start: 0.8138 (tp-100) cc_final: 0.7908 (tp-100) REVERT: E 122 LYS cc_start: 0.9362 (tppt) cc_final: 0.9012 (tppt) REVERT: E 164 CYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8227 (m) REVERT: E 267 ASP cc_start: 0.7703 (p0) cc_final: 0.7447 (t0) REVERT: F 11 MET cc_start: 0.7995 (ppp) cc_final: 0.7766 (ppp) REVERT: F 24 SER cc_start: 0.7737 (m) cc_final: 0.7202 (t) REVERT: F 51 MET cc_start: 0.7960 (tpp) cc_final: 0.7737 (tpt) REVERT: F 87 ASP cc_start: 0.8774 (m-30) cc_final: 0.8373 (m-30) REVERT: F 103 CYS cc_start: 0.8878 (m) cc_final: 0.8617 (m) REVERT: F 175 LEU cc_start: 0.8918 (mm) cc_final: 0.8346 (tt) REVERT: F 218 MET cc_start: 0.3946 (OUTLIER) cc_final: 0.3657 (mtm) REVERT: F 271 ARG cc_start: 0.7806 (tpt-90) cc_final: 0.7397 (tpp-160) REVERT: F 279 MET cc_start: 0.8566 (mmm) cc_final: 0.8081 (mmt) REVERT: G 11 MET cc_start: 0.7503 (tmm) cc_final: 0.6959 (mmp) REVERT: G 51 MET cc_start: 0.8395 (tpp) cc_final: 0.8078 (tpp) REVERT: G 93 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8559 (mmmm) REVERT: G 105 MET cc_start: 0.8507 (tpp) cc_final: 0.8026 (tpp) REVERT: G 106 ARG cc_start: 0.7005 (ttm110) cc_final: 0.6745 (ttm110) REVERT: G 113 ASP cc_start: 0.7911 (p0) cc_final: 0.6795 (t0) REVERT: G 126 SER cc_start: 0.9417 (m) cc_final: 0.9201 (t) REVERT: G 152 TYR cc_start: 0.9202 (OUTLIER) cc_final: 0.8408 (m-10) REVERT: G 163 LYS cc_start: 0.8673 (mtmt) cc_final: 0.8111 (mttp) REVERT: G 222 LYS cc_start: 0.7620 (ttmt) cc_final: 0.7006 (ttpt) REVERT: G 227 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8664 (mmtt) REVERT: G 259 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7703 (t80) REVERT: H 51 MET cc_start: 0.8436 (mtm) cc_final: 0.7604 (ttm) REVERT: H 87 ASP cc_start: 0.8074 (t70) cc_final: 0.7766 (t70) REVERT: H 125 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8468 (mt) REVERT: H 146 GLU cc_start: 0.8222 (tt0) cc_final: 0.7766 (tm-30) REVERT: H 153 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8692 (mtpt) REVERT: H 204 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8039 (m-30) REVERT: H 219 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8084 (pp) REVERT: H 248 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6947 (mm) REVERT: H 271 ARG cc_start: 0.8397 (mmm-85) cc_final: 0.7095 (ttt180) REVERT: H 284 LYS cc_start: 0.9019 (tttm) cc_final: 0.8814 (tttm) outliers start: 82 outliers final: 54 residues processed: 410 average time/residue: 0.2564 time to fit residues: 144.6869 Evaluate side-chains 411 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 346 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 45 TYR Chi-restraints excluded: chain E residue 50 ASN Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 164 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 131 TYR Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 228 TYR Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 276 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN B 213 HIS ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 188 ASN E 50 ASN ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.7622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11412 Z= 0.269 Angle : 0.775 14.767 15321 Z= 0.401 Chirality : 0.043 0.259 1667 Planarity : 0.004 0.057 1998 Dihedral : 6.055 73.298 1528 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 6.86 % Allowed : 27.01 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.23), residues: 1404 helix: -0.19 (0.16), residues: 1149 sheet: None (None), residues: 0 loop : -2.35 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 58 HIS 0.016 0.002 HIS G 79 PHE 0.023 0.002 PHE G 85 TYR 0.041 0.002 TYR B 235 ARG 0.009 0.001 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 365 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8483 (t0) cc_final: 0.7962 (t0) REVERT: A 70 LEU cc_start: 0.9183 (tp) cc_final: 0.8851 (tt) REVERT: B 193 SER cc_start: 0.8973 (p) cc_final: 0.8657 (t) REVERT: B 203 ILE cc_start: 0.7965 (mm) cc_final: 0.7455 (pt) REVERT: B 216 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: B 229 MET cc_start: 0.8053 (mtm) cc_final: 0.7750 (ttm) REVERT: B 232 ARG cc_start: 0.8225 (ttp-110) cc_final: 0.7988 (ttm-80) REVERT: B 245 GLU cc_start: 0.7997 (tp30) cc_final: 0.7608 (tp30) REVERT: C 34 GLN cc_start: 0.8190 (tp40) cc_final: 0.7880 (tp40) REVERT: C 75 GLU cc_start: 0.7466 (tp30) cc_final: 0.7240 (tp30) REVERT: D 186 ASP cc_start: 0.7500 (m-30) cc_final: 0.7222 (m-30) REVERT: E 45 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7284 (t80) REVERT: E 50 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8602 (t0) REVERT: E 57 ASN cc_start: 0.8666 (t0) cc_final: 0.8240 (t0) REVERT: E 98 GLN cc_start: 0.8187 (tp-100) cc_final: 0.7964 (tp-100) REVERT: E 122 LYS cc_start: 0.9399 (tppt) cc_final: 0.9032 (tppt) REVERT: E 164 CYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8229 (m) REVERT: E 267 ASP cc_start: 0.7586 (p0) cc_final: 0.7360 (t0) REVERT: F 11 MET cc_start: 0.7965 (ppp) cc_final: 0.7763 (ppp) REVERT: F 24 SER cc_start: 0.7728 (m) cc_final: 0.7186 (t) REVERT: F 87 ASP cc_start: 0.8726 (m-30) cc_final: 0.8332 (m-30) REVERT: F 162 ASN cc_start: 0.8587 (t0) cc_final: 0.8377 (t0) REVERT: F 175 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8385 (tt) REVERT: F 218 MET cc_start: 0.3651 (OUTLIER) cc_final: 0.3266 (mtm) REVERT: F 279 MET cc_start: 0.8574 (mmm) cc_final: 0.8125 (mmt) REVERT: G 11 MET cc_start: 0.7455 (tmm) cc_final: 0.7012 (mmp) REVERT: G 51 MET cc_start: 0.8300 (tpp) cc_final: 0.7898 (tpp) REVERT: G 93 LYS cc_start: 0.8806 (mmmm) cc_final: 0.8583 (mmmm) REVERT: G 94 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.6936 (mtpt) REVERT: G 105 MET cc_start: 0.8543 (tpp) cc_final: 0.8036 (tpp) REVERT: G 106 ARG cc_start: 0.6885 (ttm110) cc_final: 0.6674 (ttm110) REVERT: G 113 ASP cc_start: 0.7733 (p0) cc_final: 0.6648 (t0) REVERT: G 126 SER cc_start: 0.9407 (m) cc_final: 0.9201 (t) REVERT: G 152 TYR cc_start: 0.9169 (OUTLIER) cc_final: 0.8321 (m-10) REVERT: G 163 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8121 (mttp) REVERT: G 222 LYS cc_start: 0.7657 (ttmt) cc_final: 0.7046 (ttpt) REVERT: G 227 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8661 (mmtt) REVERT: G 259 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.7523 (t80) REVERT: H 51 MET cc_start: 0.8447 (mtm) cc_final: 0.7615 (ttm) REVERT: H 87 ASP cc_start: 0.8101 (t70) cc_final: 0.7793 (t70) REVERT: H 125 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8457 (mt) REVERT: H 146 GLU cc_start: 0.8197 (tt0) cc_final: 0.7738 (tm-30) REVERT: H 193 MET cc_start: 0.7381 (tpp) cc_final: 0.6966 (tpp) REVERT: H 204 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: H 248 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7068 (mm) REVERT: H 271 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.6994 (ttt180) outliers start: 81 outliers final: 56 residues processed: 405 average time/residue: 0.2409 time to fit residues: 134.7526 Evaluate side-chains 414 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 346 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 45 TYR Chi-restraints excluded: chain E residue 50 ASN Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 164 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 131 TYR Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 228 TYR Chi-restraints excluded: chain H residue 248 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN B 236 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN E 187 GLN ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.7819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11412 Z= 0.226 Angle : 0.759 14.309 15321 Z= 0.391 Chirality : 0.043 0.211 1667 Planarity : 0.003 0.059 1998 Dihedral : 6.027 73.938 1528 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 6.01 % Allowed : 29.13 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.23), residues: 1404 helix: -0.09 (0.16), residues: 1149 sheet: None (None), residues: 0 loop : -2.32 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 275 HIS 0.012 0.002 HIS G 79 PHE 0.029 0.002 PHE G 85 TYR 0.041 0.002 TYR B 235 ARG 0.008 0.001 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 369 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8588 (t0) cc_final: 0.8239 (t0) REVERT: A 66 ARG cc_start: 0.8290 (mmp-170) cc_final: 0.7863 (mtp85) REVERT: A 70 LEU cc_start: 0.8898 (tp) cc_final: 0.8552 (tt) REVERT: B 193 SER cc_start: 0.8960 (p) cc_final: 0.8675 (t) REVERT: B 203 ILE cc_start: 0.7896 (mm) cc_final: 0.7400 (pt) REVERT: B 229 MET cc_start: 0.7998 (mtm) cc_final: 0.7728 (ttm) REVERT: C 32 MET cc_start: 0.8435 (tpp) cc_final: 0.8026 (tmm) REVERT: C 34 GLN cc_start: 0.8314 (tp40) cc_final: 0.8001 (tp40) REVERT: C 75 GLU cc_start: 0.7438 (tp30) cc_final: 0.7136 (tp30) REVERT: D 184 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7837 (mtpt) REVERT: E 44 ILE cc_start: 0.8410 (tp) cc_final: 0.8069 (pt) REVERT: E 45 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.6902 (t80) REVERT: E 50 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8652 (t0) REVERT: E 57 ASN cc_start: 0.8571 (t0) cc_final: 0.8149 (t0) REVERT: E 98 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7880 (tp-100) REVERT: E 122 LYS cc_start: 0.9354 (tppt) cc_final: 0.8992 (tppt) REVERT: E 164 CYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8186 (m) REVERT: E 267 ASP cc_start: 0.7673 (p0) cc_final: 0.7384 (t70) REVERT: F 24 SER cc_start: 0.7681 (m) cc_final: 0.7326 (t) REVERT: F 51 MET cc_start: 0.7239 (tpt) cc_final: 0.6810 (tpt) REVERT: F 87 ASP cc_start: 0.8737 (m-30) cc_final: 0.8356 (m-30) REVERT: F 162 ASN cc_start: 0.8599 (t0) cc_final: 0.8349 (t0) REVERT: F 175 LEU cc_start: 0.8931 (mm) cc_final: 0.8402 (tt) REVERT: F 218 MET cc_start: 0.3460 (OUTLIER) cc_final: 0.3138 (mtm) REVERT: F 279 MET cc_start: 0.8547 (mmm) cc_final: 0.8120 (mmt) REVERT: G 11 MET cc_start: 0.7289 (tmm) cc_final: 0.6995 (mmp) REVERT: G 51 MET cc_start: 0.8380 (tpp) cc_final: 0.7938 (tpp) REVERT: G 75 LEU cc_start: 0.9224 (tt) cc_final: 0.8633 (mp) REVERT: G 94 LYS cc_start: 0.7329 (mtmm) cc_final: 0.7118 (mmtp) REVERT: G 105 MET cc_start: 0.8512 (tpp) cc_final: 0.8058 (tpp) REVERT: G 106 ARG cc_start: 0.6876 (ttm110) cc_final: 0.6635 (ttm110) REVERT: G 113 ASP cc_start: 0.7812 (p0) cc_final: 0.6765 (t0) REVERT: G 126 SER cc_start: 0.9377 (m) cc_final: 0.9173 (t) REVERT: G 152 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8446 (m-10) REVERT: G 163 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8087 (mttp) REVERT: H 51 MET cc_start: 0.8470 (mtm) cc_final: 0.7595 (ttm) REVERT: H 87 ASP cc_start: 0.8097 (t70) cc_final: 0.7707 (t70) REVERT: H 125 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8424 (mt) REVERT: H 146 GLU cc_start: 0.8204 (tt0) cc_final: 0.7708 (tm-30) REVERT: H 193 MET cc_start: 0.7274 (tpp) cc_final: 0.6868 (tpp) REVERT: H 204 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: H 213 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6914 (m170) REVERT: H 271 ARG cc_start: 0.8200 (mmm-85) cc_final: 0.6962 (ttt180) outliers start: 71 outliers final: 48 residues processed: 410 average time/residue: 0.2368 time to fit residues: 133.5145 Evaluate side-chains 405 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 349 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 45 TYR Chi-restraints excluded: chain E residue 50 ASN Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 164 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 45 TYR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 131 TYR Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 HIS Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 228 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 0.0770 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN D 152 GLN E 50 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.8025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11412 Z= 0.206 Angle : 0.770 13.464 15321 Z= 0.393 Chirality : 0.043 0.223 1667 Planarity : 0.003 0.062 1998 Dihedral : 5.967 74.150 1528 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 5.08 % Allowed : 30.06 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.23), residues: 1404 helix: 0.06 (0.16), residues: 1137 sheet: None (None), residues: 0 loop : -2.31 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 275 HIS 0.011 0.002 HIS G 79 PHE 0.023 0.002 PHE G 85 TYR 0.031 0.001 TYR B 235 ARG 0.006 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 363 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8478 (t0) cc_final: 0.8137 (t0) REVERT: A 66 ARG cc_start: 0.8115 (mmp-170) cc_final: 0.7644 (mtp85) REVERT: A 70 LEU cc_start: 0.8778 (tp) cc_final: 0.8493 (tt) REVERT: B 193 SER cc_start: 0.8936 (p) cc_final: 0.8684 (t) REVERT: B 203 ILE cc_start: 0.7911 (mm) cc_final: 0.7468 (pt) REVERT: B 222 LEU cc_start: 0.8799 (tt) cc_final: 0.8372 (mt) REVERT: B 229 MET cc_start: 0.7906 (mtm) cc_final: 0.7688 (ttm) REVERT: B 231 ASP cc_start: 0.7941 (t0) cc_final: 0.7475 (t0) REVERT: C 32 MET cc_start: 0.8438 (tpp) cc_final: 0.8073 (tmm) REVERT: C 34 GLN cc_start: 0.8114 (tp40) cc_final: 0.7819 (tp40) REVERT: C 66 GLN cc_start: 0.8357 (mt0) cc_final: 0.7898 (mm-40) REVERT: C 75 GLU cc_start: 0.7423 (tp30) cc_final: 0.7127 (tp30) REVERT: D 184 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7821 (mtpt) REVERT: E 44 ILE cc_start: 0.8269 (tp) cc_final: 0.7932 (pt) REVERT: E 57 ASN cc_start: 0.8477 (t0) cc_final: 0.8118 (t0) REVERT: E 76 GLN cc_start: 0.8447 (mp10) cc_final: 0.7562 (pp30) REVERT: E 84 CYS cc_start: 0.8846 (p) cc_final: 0.8574 (p) REVERT: E 98 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7952 (tp-100) REVERT: E 122 LYS cc_start: 0.9267 (tppt) cc_final: 0.8960 (tppt) REVERT: E 164 CYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8135 (m) REVERT: E 218 MET cc_start: 0.5581 (tpp) cc_final: 0.3409 (mmt) REVERT: E 227 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8330 (tptp) REVERT: F 24 SER cc_start: 0.7618 (m) cc_final: 0.7283 (t) REVERT: F 45 TYR cc_start: 0.7513 (t80) cc_final: 0.6755 (t80) REVERT: F 51 MET cc_start: 0.7309 (tpt) cc_final: 0.6836 (tpt) REVERT: F 66 CYS cc_start: 0.8780 (t) cc_final: 0.7584 (p) REVERT: F 83 THR cc_start: 0.8180 (t) cc_final: 0.7857 (t) REVERT: F 140 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7781 (mtmm) REVERT: F 155 GLU cc_start: 0.7087 (tm-30) cc_final: 0.5826 (tm-30) REVERT: F 171 TYR cc_start: 0.8151 (m-80) cc_final: 0.7512 (m-80) REVERT: F 175 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8350 (tt) REVERT: F 179 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7569 (tp40) REVERT: F 226 GLN cc_start: 0.7919 (tp-100) cc_final: 0.7666 (mm-40) REVERT: F 279 MET cc_start: 0.8503 (mmm) cc_final: 0.8133 (mmt) REVERT: G 51 MET cc_start: 0.8316 (tpp) cc_final: 0.7892 (tpp) REVERT: G 75 LEU cc_start: 0.9253 (tt) cc_final: 0.8718 (mp) REVERT: G 79 HIS cc_start: 0.6997 (t-170) cc_final: 0.6580 (t-170) REVERT: G 93 LYS cc_start: 0.8807 (mmmm) cc_final: 0.8560 (mmmt) REVERT: G 94 LYS cc_start: 0.7386 (mtmm) cc_final: 0.6990 (mmtt) REVERT: G 105 MET cc_start: 0.8449 (tpp) cc_final: 0.8036 (tpp) REVERT: G 106 ARG cc_start: 0.6738 (ttm110) cc_final: 0.6486 (ttm110) REVERT: G 113 ASP cc_start: 0.7701 (p0) cc_final: 0.6622 (t0) REVERT: G 152 TYR cc_start: 0.9272 (OUTLIER) cc_final: 0.8398 (m-10) REVERT: G 162 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7317 (m-40) REVERT: G 222 LYS cc_start: 0.7460 (ttmt) cc_final: 0.7016 (tttt) REVERT: G 265 GLU cc_start: 0.8223 (pp20) cc_final: 0.7476 (tm-30) REVERT: H 11 MET cc_start: 0.6736 (tpt) cc_final: 0.6392 (tpt) REVERT: H 51 MET cc_start: 0.8451 (mtm) cc_final: 0.7615 (ttm) REVERT: H 87 ASP cc_start: 0.8066 (t70) cc_final: 0.7737 (t70) REVERT: H 125 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8413 (mt) REVERT: H 146 GLU cc_start: 0.8175 (tt0) cc_final: 0.7685 (tm-30) REVERT: H 193 MET cc_start: 0.7238 (tpp) cc_final: 0.6794 (tpp) REVERT: H 204 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8282 (m-30) REVERT: H 213 HIS cc_start: 0.7131 (OUTLIER) cc_final: 0.6695 (m170) REVERT: H 271 ARG cc_start: 0.8182 (mmm-85) cc_final: 0.6794 (ttt180) outliers start: 60 outliers final: 41 residues processed: 394 average time/residue: 0.2504 time to fit residues: 134.4397 Evaluate side-chains 396 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 346 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 164 CYS Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 179 GLN Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain G residue 45 TYR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 131 TYR Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 HIS Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 228 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 6.9990 chunk 63 optimal weight: 0.0470 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 128 optimal weight: 0.0020 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 85 optimal weight: 0.0970 chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.6288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.8099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 11412 Z= 0.291 Angle : 1.114 59.200 15321 Z= 0.638 Chirality : 0.044 0.261 1667 Planarity : 0.006 0.161 1998 Dihedral : 6.048 74.189 1528 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.12 % Favored : 91.81 % Rotamer: Outliers : 4.74 % Allowed : 30.48 % Favored : 64.78 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1404 helix: 0.04 (0.16), residues: 1137 sheet: None (None), residues: 0 loop : -2.30 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 275 HIS 0.009 0.002 HIS G 79 PHE 0.019 0.002 PHE G 85 TYR 0.024 0.001 TYR B 235 ARG 0.011 0.001 ARG F 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 349 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8471 (t0) cc_final: 0.8146 (t0) REVERT: A 66 ARG cc_start: 0.8103 (mmp-170) cc_final: 0.7639 (mtp85) REVERT: A 70 LEU cc_start: 0.8819 (tp) cc_final: 0.8537 (tt) REVERT: B 193 SER cc_start: 0.8947 (p) cc_final: 0.8681 (t) REVERT: B 203 ILE cc_start: 0.7915 (mm) cc_final: 0.7468 (pt) REVERT: B 222 LEU cc_start: 0.8804 (tt) cc_final: 0.8434 (mt) REVERT: B 229 MET cc_start: 0.7845 (mtm) cc_final: 0.7628 (ttm) REVERT: B 231 ASP cc_start: 0.7873 (t0) cc_final: 0.7477 (t0) REVERT: C 34 GLN cc_start: 0.8147 (tp40) cc_final: 0.7799 (tp40) REVERT: C 66 GLN cc_start: 0.8309 (mt0) cc_final: 0.7905 (mm-40) REVERT: C 75 GLU cc_start: 0.7429 (tp30) cc_final: 0.7106 (tp30) REVERT: D 184 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7828 (mtpt) REVERT: D 196 ASN cc_start: 0.7761 (p0) cc_final: 0.7475 (p0) REVERT: E 57 ASN cc_start: 0.8469 (t0) cc_final: 0.8104 (t0) REVERT: E 84 CYS cc_start: 0.8836 (p) cc_final: 0.8560 (p) REVERT: E 98 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7948 (tp-100) REVERT: E 122 LYS cc_start: 0.9265 (tppt) cc_final: 0.8953 (tppt) REVERT: E 164 CYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8133 (m) REVERT: E 218 MET cc_start: 0.5562 (tpp) cc_final: 0.3388 (mmt) REVERT: F 24 SER cc_start: 0.7616 (m) cc_final: 0.7279 (t) REVERT: F 45 TYR cc_start: 0.7504 (t80) cc_final: 0.6752 (t80) REVERT: F 51 MET cc_start: 0.7289 (tpt) cc_final: 0.6887 (tpt) REVERT: F 66 CYS cc_start: 0.8769 (t) cc_final: 0.7580 (p) REVERT: F 140 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7780 (mtmm) REVERT: F 155 GLU cc_start: 0.7091 (tm-30) cc_final: 0.5826 (tm-30) REVERT: F 171 TYR cc_start: 0.8141 (m-80) cc_final: 0.7508 (m-80) REVERT: F 175 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8354 (tt) REVERT: F 226 GLN cc_start: 0.7840 (tp-100) cc_final: 0.7634 (mm-40) REVERT: F 279 MET cc_start: 0.8485 (mmm) cc_final: 0.8146 (mmt) REVERT: G 51 MET cc_start: 0.8308 (tpp) cc_final: 0.7881 (tpp) REVERT: G 75 LEU cc_start: 0.9264 (tt) cc_final: 0.8636 (mp) REVERT: G 79 HIS cc_start: 0.6986 (t-170) cc_final: 0.6569 (t-170) REVERT: G 93 LYS cc_start: 0.8799 (mmmm) cc_final: 0.8562 (mmmt) REVERT: G 94 LYS cc_start: 0.7397 (mtmm) cc_final: 0.6992 (mmtt) REVERT: G 105 MET cc_start: 0.8446 (tpp) cc_final: 0.8035 (tpp) REVERT: G 106 ARG cc_start: 0.6730 (ttm110) cc_final: 0.6479 (ttm110) REVERT: G 113 ASP cc_start: 0.7702 (p0) cc_final: 0.6620 (t0) REVERT: G 152 TYR cc_start: 0.9275 (OUTLIER) cc_final: 0.8403 (m-10) REVERT: H 11 MET cc_start: 0.6737 (tpt) cc_final: 0.6390 (tpt) REVERT: H 51 MET cc_start: 0.8435 (mtm) cc_final: 0.7616 (ttm) REVERT: H 87 ASP cc_start: 0.8094 (t70) cc_final: 0.7662 (t70) REVERT: H 125 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8411 (mt) REVERT: H 146 GLU cc_start: 0.8181 (tt0) cc_final: 0.7682 (tm-30) REVERT: H 193 MET cc_start: 0.7233 (tpp) cc_final: 0.6774 (tpp) REVERT: H 213 HIS cc_start: 0.6997 (OUTLIER) cc_final: 0.6696 (m170) REVERT: H 244 MET cc_start: 0.8435 (tmm) cc_final: 0.8195 (tmm) REVERT: H 271 ARG cc_start: 0.8174 (mmm-85) cc_final: 0.6797 (ttt180) outliers start: 56 outliers final: 44 residues processed: 374 average time/residue: 0.2476 time to fit residues: 127.4407 Evaluate side-chains 395 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 345 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 50 ASN Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 164 CYS Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain G residue 45 TYR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 131 TYR Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 HIS Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 228 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.1980 chunk 102 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 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 = 0.4054 r_free = 0.4054 target = 0.153266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.132922 restraints weight = 24879.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.136323 restraints weight = 13799.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.138617 restraints weight = 8891.860| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.8101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 11412 Z= 0.342 Angle : 1.216 59.198 15321 Z= 0.713 Chirality : 0.045 0.347 1667 Planarity : 0.005 0.113 1998 Dihedral : 6.036 74.212 1528 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.12 % Favored : 91.81 % Rotamer: Outliers : 4.91 % Allowed : 30.14 % Favored : 64.94 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.23), residues: 1404 helix: 0.03 (0.16), residues: 1137 sheet: None (None), residues: 0 loop : -2.30 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 275 HIS 0.007 0.002 HIS G 79 PHE 0.015 0.001 PHE G 207 TYR 0.020 0.001 TYR B 235 ARG 0.009 0.001 ARG F 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2942.24 seconds wall clock time: 53 minutes 43.57 seconds (3223.57 seconds total)