Starting phenix.real_space_refine on Sun Dec 10 08:11:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yox_33989/12_2023/7yox_33989.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yox_33989/12_2023/7yox_33989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yox_33989/12_2023/7yox_33989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yox_33989/12_2023/7yox_33989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yox_33989/12_2023/7yox_33989.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yox_33989/12_2023/7yox_33989.pdb" } resolution = 3.95 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= 0.014 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 102 5.16 5 C 8745 2.51 5 N 2355 2.21 5 O 2676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A ASP 300": "OD1" <-> "OD2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B ASP 227": "OD1" <-> "OD2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 327": "OD1" <-> "OD2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "D ASP 24": "OD1" <-> "OD2" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 161": "OE1" <-> "OE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "E ASP 4": "OD1" <-> "OD2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 35": "OD1" <-> "OD2" Residue "E TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E ASP 159": "OD1" <-> "OD2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 201": "OE1" <-> "OE2" Residue "E PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 140": "OD1" <-> "OD2" Residue "F TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 247": "OE1" <-> "OE2" Residue "F ASP 255": "OD1" <-> "OD2" Residue "F ASP 287": "OD1" <-> "OD2" Residue "F ASP 300": "OD1" <-> "OD2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "F ASP 349": "OD1" <-> "OD2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13878 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 15, 'TRANS': 291} Chain: "B" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2206 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "C" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 15, 'TRANS': 291} Chain: "D" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2206 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "E" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2206 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "F" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 15, 'TRANS': 291} Time building chain proxies: 7.97, per 1000 atoms: 0.57 Number of scatterers: 13878 At special positions: 0 Unit cell: (77.738, 138.109, 143.071, 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 102 16.00 O 2676 8.00 N 2355 7.00 C 8745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 172 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 172 " distance=2.54 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 172 " distance=2.03 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS F 245 " distance=2.03 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: 6.00 Conformation dependent library (CDL) restraints added in 2.8 seconds 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3342 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 17 sheets defined 33.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 91 through 106 removed outlier: 3.901A pdb=" N LYS A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 131 through 138 removed outlier: 3.639A pdb=" N THR A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.537A pdb=" N GLU A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 177 Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'B' and resid 2 through 21 Processing helix chain 'B' and resid 21 through 31 Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 61 through 84 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 186 through 190 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'C' and resid 65 through 73 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 91 through 106 Processing helix chain 'C' and resid 111 through 119 Processing helix chain 'C' and resid 125 through 131 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 140 through 148 removed outlier: 3.761A pdb=" N GLU C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 179 Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'D' and resid 2 through 31 removed outlier: 3.763A pdb=" N LYS D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN D 23 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 51 Processing helix chain 'D' and resid 51 through 61 removed outlier: 3.548A pdb=" N GLY D 55 " --> pdb=" O ASN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 84 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'E' and resid 3 through 26 removed outlier: 4.544A pdb=" N GLU E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR E 20 " --> pdb=" O TYR E 16 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN E 23 " --> pdb=" O GLU E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 51 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 61 through 83 Processing helix chain 'E' and resid 161 through 165 removed outlier: 3.811A pdb=" N THR E 165 " --> pdb=" O GLN E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 190 Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'E' and resid 270 through 276 Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 77 through 82 Processing helix chain 'F' and resid 90 through 108 removed outlier: 4.092A pdb=" N GLU F 94 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP F 108 " --> pdb=" O THR F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 119 Processing helix chain 'F' and resid 125 through 131 Processing helix chain 'F' and resid 131 through 138 removed outlier: 3.704A pdb=" N THR F 135 " --> pdb=" O GLY F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 148 Processing helix chain 'F' and resid 148 through 179 Processing helix chain 'F' and resid 254 through 257 Processing helix chain 'F' and resid 318 through 320 No H-bonds generated for 'chain 'F' and resid 318 through 320' Processing helix chain 'F' and resid 341 through 346 Processing helix chain 'F' and resid 365 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 124 removed outlier: 5.686A pdb=" N ILE A 121 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR A 199 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL A 123 " --> pdb=" O TYR A 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 228 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 218 through 228 current: chain 'A' and resid 248 through 252 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 248 through 252 current: chain 'A' and resid 310 through 316 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 310 through 316 current: chain 'A' and resid 352 through 364 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 43 removed outlier: 6.784A pdb=" N TYR B 38 " --> pdb=" O HIS B 97 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG B 99 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 40 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N SER B 101 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 42 " --> pdb=" O SER B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 137 through 140 removed outlier: 3.546A pdb=" N GLN B 200 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 12.901A pdb=" N SER B 219 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE B 261 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS B 221 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR B 241 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE B 268 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR B 239 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL B 130 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN B 205 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG B 132 " --> pdb=" O LYS B 203 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 142 through 143 Processing sheet with id=AA6, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA7, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.017A pdb=" N ILE C 121 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR C 199 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 123 " --> pdb=" O TYR C 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 205 removed outlier: 3.873A pdb=" N ARG C 222 " --> pdb=" O THR C 205 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 218 through 225 current: chain 'C' and resid 248 through 252 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 248 through 252 current: chain 'C' and resid 310 through 315 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 310 through 315 current: chain 'C' and resid 356 through 363 Processing sheet with id=AA9, first strand: chain 'C' and resid 338 through 339 Processing sheet with id=AB1, first strand: chain 'D' and resid 38 through 43 removed outlier: 5.483A pdb=" N TYR D 38 " --> pdb=" O HIS D 97 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG D 99 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL D 40 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER D 101 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL D 42 " --> pdb=" O SER D 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 123 through 133 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 123 through 133 current: chain 'D' and resid 196 through 205 removed outlier: 3.605A pdb=" N GLN D 200 " --> pdb=" O LEU D 224 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 219 through 225 current: chain 'D' and resid 259 through 264 Processing sheet with id=AB3, first strand: chain 'D' and resid 142 through 147 removed outlier: 3.605A pdb=" N PHE D 154 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS D 147 " --> pdb=" O HIS D 152 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS D 152 " --> pdb=" O CYS D 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 38 through 43 Processing sheet with id=AB5, first strand: chain 'E' and resid 137 through 139 removed outlier: 8.542A pdb=" N SER E 219 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LEU E 263 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS E 221 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA E 265 " --> pdb=" O LYS E 221 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE E 223 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR E 267 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLU E 225 " --> pdb=" O TYR E 267 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N GLN E 269 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE E 261 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG E 247 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU E 263 " --> pdb=" O MET E 245 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET E 245 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA E 265 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E 243 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL E 130 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLN E 205 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG E 132 " --> pdb=" O LYS E 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 142 through 146 removed outlier: 4.224A pdb=" N ARG E 143 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE E 156 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 120 through 124 Processing sheet with id=AB8, first strand: chain 'F' and resid 218 through 221 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 218 through 221 current: chain 'F' and resid 248 through 252 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 248 through 252 current: chain 'F' and resid 310 through 316 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 310 through 316 current: chain 'F' and resid 355 through 358 No H-bonds generated for sheet with id=AB8 434 hydrogen bonds defined for protein. 1254 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: 3.70 Time building geometry restraints manager: 6.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3992 1.33 - 1.45: 1993 1.45 - 1.57: 8001 1.57 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 14133 Sorted by residual: bond pdb=" CA GLN D 162 " pdb=" C GLN D 162 " ideal model delta sigma weight residual 1.526 1.493 0.033 1.28e-02 6.10e+03 6.61e+00 bond pdb=" CA ARG E 247 " pdb=" C ARG E 247 " ideal model delta sigma weight residual 1.521 1.492 0.029 1.19e-02 7.06e+03 6.10e+00 bond pdb=" C ASN D 266 " pdb=" O ASN D 266 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.17e-02 7.31e+03 5.79e+00 bond pdb=" C LEU F 145 " pdb=" O LEU F 145 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.33e+00 bond pdb=" C PHE E 13 " pdb=" O PHE E 13 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.13e+00 ... (remaining 14128 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.68: 345 105.68 - 112.76: 7192 112.76 - 119.84: 5071 119.84 - 126.91: 6383 126.91 - 133.99: 122 Bond angle restraints: 19113 Sorted by residual: angle pdb=" N GLN D 162 " pdb=" CA GLN D 162 " pdb=" C GLN D 162 " ideal model delta sigma weight residual 112.26 98.92 13.34 1.32e+00 5.74e-01 1.02e+02 angle pdb=" N CYS D 106 " pdb=" CA CYS D 106 " pdb=" C CYS D 106 " ideal model delta sigma weight residual 108.22 101.45 6.77 9.00e-01 1.23e+00 5.65e+01 angle pdb=" N GLY C 132 " pdb=" CA GLY C 132 " pdb=" C GLY C 132 " ideal model delta sigma weight residual 112.73 120.80 -8.07 1.20e+00 6.94e-01 4.52e+01 angle pdb=" N TYR B 20 " pdb=" CA TYR B 20 " pdb=" C TYR B 20 " ideal model delta sigma weight residual 111.36 118.63 -7.27 1.09e+00 8.42e-01 4.44e+01 angle pdb=" N ILE A 93 " pdb=" CA ILE A 93 " pdb=" C ILE A 93 " ideal model delta sigma weight residual 110.62 117.15 -6.53 1.02e+00 9.61e-01 4.10e+01 ... (remaining 19108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6568 17.90 - 35.81: 932 35.81 - 53.71: 846 53.71 - 71.61: 334 71.61 - 89.51: 41 Dihedral angle restraints: 8721 sinusoidal: 3573 harmonic: 5148 Sorted by residual: dihedral pdb=" CB CYS F 242 " pdb=" SG CYS F 242 " pdb=" SG CYS F 245 " pdb=" CB CYS F 245 " ideal model delta sinusoidal sigma weight residual 93.00 166.91 -73.91 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" C VAL B 155 " pdb=" N VAL B 155 " pdb=" CA VAL B 155 " pdb=" CB VAL B 155 " ideal model delta harmonic sigma weight residual -122.00 -137.57 15.57 0 2.50e+00 1.60e-01 3.88e+01 dihedral pdb=" C PHE C 72 " pdb=" N PHE C 72 " pdb=" CA PHE C 72 " pdb=" CB PHE C 72 " ideal model delta harmonic sigma weight residual -122.60 -137.66 15.06 0 2.50e+00 1.60e-01 3.63e+01 ... (remaining 8718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1745 0.112 - 0.224: 364 0.224 - 0.335: 54 0.335 - 0.447: 12 0.447 - 0.559: 3 Chirality restraints: 2178 Sorted by residual: chirality pdb=" CA PHE C 72 " pdb=" N PHE C 72 " pdb=" C PHE C 72 " pdb=" CB PHE C 72 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.81e+00 chirality pdb=" CA VAL B 155 " pdb=" N VAL B 155 " pdb=" C VAL B 155 " pdb=" CB VAL B 155 " both_signs ideal model delta sigma weight residual False 2.44 1.96 0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CA GLU F 202 " pdb=" N GLU F 202 " pdb=" C GLU F 202 " pdb=" CB GLU F 202 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.51e+00 ... (remaining 2175 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 38 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO B 39 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 249 " -0.047 5.00e-02 4.00e+02 7.15e-02 8.17e+00 pdb=" N PRO D 250 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 250 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 250 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 168 " 0.045 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO D 169 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 169 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 169 " 0.039 5.00e-02 4.00e+02 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 0.79 - 1.61: 22 1.61 - 2.43: 136 2.43 - 3.25: 14381 3.25 - 4.08: 42455 4.08 - 4.90: 68604 Warning: very small nonbonded interaction distances. Nonbonded interactions: 125598 Sorted by model distance: nonbonded pdb=" O ILE E 28 " pdb=" CB SER E 91 " model vdw 0.786 3.440 nonbonded pdb=" C ILE E 28 " pdb=" CB SER E 91 " model vdw 0.870 3.670 nonbonded pdb=" CA SER E 18 " pdb=" CE1 HIS E 21 " model vdw 0.903 3.690 nonbonded pdb=" O ILE E 28 " pdb=" OG SER E 91 " model vdw 0.918 2.440 nonbonded pdb=" O LEU B 78 " pdb=" OE1 GLN B 82 " model vdw 0.982 3.040 ... (remaining 125593 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 'A' selection = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' } 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: 1.130 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: 4.430 Check model and map are aligned: 0.210 Set scattering table: 0.150 Process input model: 40.590 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 0.033 14133 Z= 0.418 Angle : 1.308 13.338 19113 Z= 0.894 Chirality : 0.095 0.559 2178 Planarity : 0.007 0.074 2466 Dihedral : 27.063 89.513 5367 Min Nonbonded Distance : 0.786 Molprobity Statistics. All-atom Clashscore : 33.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.04 % Favored : 98.79 % Rotamer: Outliers : 46.70 % Allowed : 16.89 % Favored : 36.41 % Cbeta Deviations : 0.48 % 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: 2.84 (0.19), residues: 1737 helix: 3.80 (0.20), residues: 518 sheet: 1.37 (0.25), residues: 426 loop : 0.97 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP F 288 HIS 0.005 0.001 HIS C 195 PHE 0.031 0.003 PHE C 72 TYR 0.024 0.002 TYR C 86 ARG 0.006 0.001 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 744 poor density : 463 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 744 outliers final: 179 residues processed: 980 average time/residue: 0.3026 time to fit residues: 405.0985 Evaluate side-chains 460 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 281 time to evaluate : 1.750 Switching outliers to nearest non-outliers 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: 179 outliers final: 8 residues processed: 179 average time/residue: 0.2137 time to fit residues: 62.6374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.0970 chunk 69 optimal weight: 30.0000 chunk 134 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 360 ASN B 11 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN C 106 HIS C 136 ASN D 2 ASN D 59 ASN D 82 GLN D 152 HIS D 266 ASN ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 GLN E 272 ASN ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14133 Z= 0.316 Angle : 0.816 11.764 19113 Z= 0.427 Chirality : 0.049 0.319 2178 Planarity : 0.006 0.092 2466 Dihedral : 5.155 21.147 1896 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 30.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 6.97 % Allowed : 31.70 % Favored : 61.33 % 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: 1.49 (0.19), residues: 1737 helix: 1.78 (0.22), residues: 513 sheet: 0.85 (0.26), residues: 403 loop : 0.70 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 248 HIS 0.017 0.002 HIS E 21 PHE 0.042 0.003 PHE D 69 TYR 0.025 0.003 TYR F 201 ARG 0.012 0.001 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 275 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 54 residues processed: 360 average time/residue: 0.2639 time to fit residues: 140.4879 Evaluate side-chains 257 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 203 time to evaluate : 1.949 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 54 outliers final: 1 residues processed: 54 average time/residue: 0.1809 time to fit residues: 20.1903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 30.0000 chunk 129 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 124 optimal weight: 40.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 2 ASN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN D 97 HIS D 209 GLN ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 ASN ** F 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14133 Z= 0.273 Angle : 0.722 13.504 19113 Z= 0.376 Chirality : 0.048 0.270 2178 Planarity : 0.005 0.057 2466 Dihedral : 5.048 22.289 1896 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 28.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.58 % Allowed : 31.89 % Favored : 63.53 % 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: 1.05 (0.19), residues: 1737 helix: 1.34 (0.22), residues: 508 sheet: 0.59 (0.25), residues: 408 loop : 0.50 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP D 248 HIS 0.009 0.001 HIS E 21 PHE 0.043 0.003 PHE D 69 TYR 0.027 0.002 TYR E 267 ARG 0.015 0.001 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 234 time to evaluate : 1.712 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: 73 outliers final: 32 residues processed: 295 average time/residue: 0.2497 time to fit residues: 109.3974 Evaluate side-chains 230 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 198 time to evaluate : 1.790 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1356 time to fit residues: 10.1463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 104 optimal weight: 0.0970 chunk 156 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14133 Z= 0.231 Angle : 0.700 14.642 19113 Z= 0.356 Chirality : 0.047 0.328 2178 Planarity : 0.004 0.061 2466 Dihedral : 4.914 27.045 1896 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 27.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.64 % Allowed : 32.89 % Favored : 63.47 % 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: 0.92 (0.19), residues: 1737 helix: 1.26 (0.23), residues: 508 sheet: 0.47 (0.25), residues: 404 loop : 0.42 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 248 HIS 0.007 0.001 HIS E 21 PHE 0.067 0.003 PHE B 69 TYR 0.031 0.002 TYR B 16 ARG 0.011 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 228 time to evaluate : 1.784 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: 58 outliers final: 31 residues processed: 266 average time/residue: 0.2350 time to fit residues: 95.2002 Evaluate side-chains 233 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 202 time to evaluate : 1.848 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1580 time to fit residues: 10.8165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 141 optimal weight: 40.0000 chunk 114 optimal weight: 0.0570 chunk 0 optimal weight: 40.0000 chunk 84 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 41 optimal weight: 0.2980 overall best weight: 3.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 193 HIS ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.6638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14133 Z= 0.272 Angle : 0.693 13.137 19113 Z= 0.356 Chirality : 0.046 0.231 2178 Planarity : 0.005 0.061 2466 Dihedral : 4.979 23.691 1896 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 28.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.14 % Allowed : 34.34 % Favored : 62.52 % 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: 0.59 (0.20), residues: 1737 helix: 1.00 (0.22), residues: 508 sheet: 0.12 (0.25), residues: 416 loop : 0.31 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP D 248 HIS 0.008 0.001 HIS E 21 PHE 0.068 0.003 PHE B 69 TYR 0.025 0.002 TYR E 267 ARG 0.007 0.001 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 212 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 28 residues processed: 251 average time/residue: 0.2242 time to fit residues: 86.4732 Evaluate side-chains 224 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 196 time to evaluate : 1.783 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1407 time to fit residues: 9.5792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.2980 chunk 148 optimal weight: 40.0000 chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 0.0020 chunk 40 optimal weight: 0.4980 chunk 165 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.6826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14133 Z= 0.198 Angle : 0.672 13.035 19113 Z= 0.340 Chirality : 0.045 0.160 2178 Planarity : 0.004 0.065 2466 Dihedral : 4.813 22.806 1896 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.20 % Allowed : 34.65 % Favored : 63.15 % 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: 0.52 (0.19), residues: 1737 helix: 1.02 (0.23), residues: 502 sheet: 0.07 (0.26), residues: 398 loop : 0.23 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP D 248 HIS 0.008 0.001 HIS E 21 PHE 0.068 0.003 PHE B 69 TYR 0.018 0.002 TYR B 38 ARG 0.005 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 220 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 22 residues processed: 242 average time/residue: 0.2351 time to fit residues: 86.7795 Evaluate side-chains 220 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 198 time to evaluate : 1.840 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1396 time to fit residues: 8.0341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.7219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14133 Z= 0.304 Angle : 0.725 13.180 19113 Z= 0.375 Chirality : 0.047 0.226 2178 Planarity : 0.005 0.066 2466 Dihedral : 5.093 24.468 1896 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 30.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.26 % Allowed : 35.59 % Favored : 62.15 % 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: 0.29 (0.20), residues: 1737 helix: 0.76 (0.22), residues: 513 sheet: -0.25 (0.25), residues: 404 loop : 0.24 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP D 248 HIS 0.026 0.002 HIS C 195 PHE 0.072 0.004 PHE B 69 TYR 0.018 0.002 TYR B 163 ARG 0.008 0.001 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 1.852 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: 36 outliers final: 21 residues processed: 218 average time/residue: 0.2338 time to fit residues: 78.1242 Evaluate side-chains 201 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 180 time to evaluate : 1.602 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1700 time to fit residues: 8.2956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 HIS ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 GLN ** F 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.7426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14133 Z= 0.247 Angle : 0.721 15.201 19113 Z= 0.363 Chirality : 0.046 0.196 2178 Planarity : 0.004 0.062 2466 Dihedral : 5.027 23.785 1896 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 27.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.76 % Allowed : 36.79 % Favored : 61.46 % 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: 0.21 (0.20), residues: 1737 helix: 0.77 (0.22), residues: 508 sheet: -0.38 (0.26), residues: 391 loop : 0.17 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 248 HIS 0.012 0.001 HIS F 171 PHE 0.071 0.003 PHE B 69 TYR 0.024 0.002 TYR E 199 ARG 0.005 0.001 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 217 average time/residue: 0.2459 time to fit residues: 80.9618 Evaluate side-chains 203 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 183 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1785 time to fit residues: 8.2975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 120 optimal weight: 0.0570 chunk 47 optimal weight: 0.0470 chunk 138 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.7639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14133 Z= 0.206 Angle : 0.731 14.176 19113 Z= 0.364 Chirality : 0.047 0.287 2178 Planarity : 0.004 0.057 2466 Dihedral : 4.882 23.956 1896 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 25.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.56 % Allowed : 37.98 % Favored : 61.46 % 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: 0.20 (0.20), residues: 1737 helix: 0.70 (0.23), residues: 507 sheet: -0.31 (0.26), residues: 391 loop : 0.18 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 248 HIS 0.012 0.001 HIS F 171 PHE 0.066 0.003 PHE B 69 TYR 0.019 0.002 TYR E 199 ARG 0.005 0.001 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 203 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 209 average time/residue: 0.2453 time to fit residues: 77.8342 Evaluate side-chains 195 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 191 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1364 time to fit residues: 3.1692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 4.9990 chunk 99 optimal weight: 0.0270 chunk 77 optimal weight: 0.9980 chunk 112 optimal weight: 0.0980 chunk 170 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.7828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14133 Z= 0.191 Angle : 0.736 13.941 19113 Z= 0.362 Chirality : 0.047 0.298 2178 Planarity : 0.004 0.070 2466 Dihedral : 4.698 23.135 1896 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.44 % Allowed : 38.92 % Favored : 60.64 % 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: 0.19 (0.20), residues: 1737 helix: 0.69 (0.22), residues: 514 sheet: -0.22 (0.27), residues: 375 loop : 0.10 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 78 HIS 0.013 0.001 HIS F 171 PHE 0.062 0.003 PHE B 69 TYR 0.022 0.002 TYR E 199 ARG 0.007 0.001 ARG C 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 211 average time/residue: 0.2431 time to fit residues: 78.1017 Evaluate side-chains 196 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 1.738 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1482 time to fit residues: 3.3023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 135 optimal weight: 0.0010 chunk 56 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.099529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.076684 restraints weight = 58117.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.077849 restraints weight = 38545.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.078566 restraints weight = 29733.847| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.7961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14133 Z= 0.212 Angle : 0.735 13.612 19113 Z= 0.363 Chirality : 0.046 0.277 2178 Planarity : 0.004 0.063 2466 Dihedral : 4.738 22.186 1896 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.38 % Allowed : 38.92 % Favored : 60.70 % 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: 0.19 (0.20), residues: 1737 helix: 0.67 (0.23), residues: 507 sheet: -0.21 (0.27), residues: 374 loop : 0.10 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 78 HIS 0.013 0.001 HIS F 171 PHE 0.065 0.003 PHE B 69 TYR 0.035 0.002 TYR B 57 ARG 0.006 0.001 ARG C 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3430.57 seconds wall clock time: 68 minutes 14.03 seconds (4094.03 seconds total)