Starting phenix.real_space_refine (version: dev) on Mon Feb 20 03:15:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/02_2023/6ip1_9697.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/02_2023/6ip1_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_9697/02_2023/6ip1_9697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/02_2023/6ip1_9697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/02_2023/6ip1_9697.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/02_2023/6ip1_9697.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 7.01, per 1000 atoms: 0.62 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: 4.71 Conformation dependent library (CDL) restraints added in 1.6 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: 0.46 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: 3.03 Time building geometry restraints manager: 5.05 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 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. 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: 0.190 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: 0.000 Extract box with map and model: 2.100 Check model and map are aligned: 0.170 Process input model: 31.980 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 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 % 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 *********************** 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 : 1.304 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: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 657 average time/residue: 0.2768 time to fit residues: 243.7023 Evaluate side-chains 377 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 1.384 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 58 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 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: 2.9990 chunk 81 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN D 175 ASN D 188 ASN E 50 ASN E 98 GLN 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** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 11412 Z= 0.276 Angle : 0.823 10.569 15321 Z= 0.437 Chirality : 0.044 0.183 1667 Planarity : 0.004 0.040 1998 Dihedral : 6.387 59.590 1528 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 5.67 % 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: -3.27 (0.19), residues: 1404 helix: -1.87 (0.13), residues: 1116 sheet: None (None), residues: 0 loop : -2.50 (0.35), residues: 288 *********************** 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 499 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 432 time to evaluate : 1.542 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 outliers start: 67 outliers final: 38 residues processed: 465 average time/residue: 0.2656 time to fit residues: 166.2473 Evaluate side-chains 395 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 357 time to evaluate : 1.325 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.1114 time to fit residues: 9.5872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 137 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN E 76 GLN E 187 GLN E 191 ASN F 50 ASN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7560 moved from start: 0.6324 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= 0.234 Angle : 0.754 13.229 15321 Z= 0.395 Chirality : 0.043 0.178 1667 Planarity : 0.003 0.043 1998 Dihedral : 6.161 66.444 1528 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer Outliers : 4.49 % 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: -2.03 (0.21), residues: 1404 helix: -0.90 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -2.56 (0.36), residues: 276 *********************** 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 440 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 387 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 24 residues processed: 411 average time/residue: 0.2570 time to fit residues: 144.0828 Evaluate side-chains 360 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 336 time to evaluate : 1.328 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1318 time to fit residues: 7.1097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN D 152 GLN D 159 ASN D 169 ASN D 177 GLN D 188 ASN E 254 GLN F 23 ASN ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 HIS ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.6829 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= 0.193 Angle : 0.716 10.782 15321 Z= 0.372 Chirality : 0.042 0.177 1667 Planarity : 0.003 0.045 1998 Dihedral : 6.008 67.260 1528 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer Outliers : 2.46 % 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: -1.47 (0.22), residues: 1404 helix: -0.45 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -2.71 (0.37), residues: 272 *********************** 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 418 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 389 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 401 average time/residue: 0.2570 time to fit residues: 140.3831 Evaluate side-chains 357 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 340 time to evaluate : 1.199 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1097 time to fit residues: 5.1009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.0570 chunk 115 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- 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 ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN D 188 ASN ** E 50 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.7197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 11412 Z= 0.224 Angle : 0.747 15.730 15321 Z= 0.382 Chirality : 0.043 0.191 1667 Planarity : 0.003 0.049 1998 Dihedral : 6.010 68.987 1528 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 3.22 % 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: -1.02 (0.23), residues: 1404 helix: -0.14 (0.16), residues: 1124 sheet: None (None), residues: 0 loop : -2.46 (0.38), residues: 280 *********************** 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 401 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 363 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 15 residues processed: 378 average time/residue: 0.2640 time to fit residues: 135.7686 Evaluate side-chains 342 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 327 time to evaluate : 1.380 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1041 time to fit residues: 4.7203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN D 169 ASN D 188 ASN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN H 226 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.7549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 11412 Z= 0.200 Angle : 0.744 15.936 15321 Z= 0.377 Chirality : 0.042 0.213 1667 Planarity : 0.003 0.055 1998 Dihedral : 6.012 70.379 1528 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer Outliers : 2.96 % 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: -0.08 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -2.26 (0.40), residues: 270 *********************** 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 410 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 375 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 17 residues processed: 390 average time/residue: 0.2723 time to fit residues: 143.9855 Evaluate side-chains 345 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 328 time to evaluate : 1.401 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1438 time to fit residues: 6.4723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 49 ASN ** B 226 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** C 56 GLN E 50 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 23 ASN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.7847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 11412 Z= 0.208 Angle : 0.757 14.884 15321 Z= 0.384 Chirality : 0.042 0.230 1667 Planarity : 0.003 0.060 1998 Dihedral : 6.019 71.632 1528 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 2.03 % 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: -0.77 (0.23), residues: 1404 helix: 0.01 (0.16), residues: 1142 sheet: None (None), residues: 0 loop : -2.40 (0.40), residues: 262 *********************** 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 380 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 356 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 368 average time/residue: 0.2626 time to fit residues: 134.6167 Evaluate side-chains 349 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 337 time to evaluate : 1.437 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1345 time to fit residues: 4.7305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 85 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 122 optimal weight: 0.0770 chunk 129 optimal weight: 6.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 49 ASN ** B 226 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** D 169 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.8014 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= 0.217 Angle : 0.808 14.045 15321 Z= 0.405 Chirality : 0.044 0.259 1667 Planarity : 0.003 0.064 1998 Dihedral : 6.001 72.738 1528 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer Outliers : 1.86 % 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: -0.65 (0.23), residues: 1404 helix: 0.07 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -2.19 (0.40), residues: 270 *********************** 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 357 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 335 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 342 average time/residue: 0.2582 time to fit residues: 121.0779 Evaluate side-chains 333 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 320 time to evaluate : 1.354 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1184 time to fit residues: 4.6349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 129 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 HIS ** 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** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.8144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 11412 Z= 0.234 Angle : 0.836 13.496 15321 Z= 0.420 Chirality : 0.045 0.268 1667 Planarity : 0.004 0.066 1998 Dihedral : 6.036 73.244 1528 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer Outliers : 1.44 % 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: -0.53 (0.23), residues: 1404 helix: 0.10 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.83 (0.41), residues: 274 *********************** 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 354 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 337 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 344 average time/residue: 0.2548 time to fit residues: 120.9846 Evaluate side-chains 341 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 329 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1168 time to fit residues: 4.2678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.8315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 11412 Z= 0.297 Angle : 0.891 13.511 15321 Z= 0.454 Chirality : 0.046 0.240 1667 Planarity : 0.004 0.065 1998 Dihedral : 6.151 74.076 1528 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer Outliers : 1.10 % 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: -0.66 (0.23), residues: 1404 helix: 0.02 (0.16), residues: 1113 sheet: None (None), residues: 0 loop : -1.83 (0.39), residues: 291 ********************** 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 355 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 342 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 346 average time/residue: 0.2528 time to fit residues: 121.4683 Evaluate side-chains 335 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 327 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1134 time to fit residues: 3.2988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 HIS ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.153904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.132526 restraints weight = 25237.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.135768 restraints weight = 14576.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.137911 restraints weight = 9710.912| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.8494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 11412 Z= 0.233 Angle : 0.860 13.681 15321 Z= 0.429 Chirality : 0.045 0.343 1667 Planarity : 0.003 0.066 1998 Dihedral : 6.101 75.231 1528 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 0.76 % 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: -0.42 (0.23), residues: 1404 helix: 0.08 (0.16), residues: 1104 sheet: None (None), residues: 0 loop : -1.17 (0.39), residues: 300 =============================================================================== Job complete usr+sys time: 2801.02 seconds wall clock time: 51 minutes 49.87 seconds (3109.87 seconds total)