Starting phenix.real_space_refine on Fri Jul 19 23:52:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhy_36300/07_2024/8jhy_36300_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhy_36300/07_2024/8jhy_36300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhy_36300/07_2024/8jhy_36300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhy_36300/07_2024/8jhy_36300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhy_36300/07_2024/8jhy_36300_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhy_36300/07_2024/8jhy_36300_neut.cif" } resolution = 2.87 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= 0.024 sd= 0.106 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 69 5.16 5 C 5800 2.51 5 N 1542 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9073 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2370 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'CLR': 1, 'IX8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.07, per 1000 atoms: 0.67 Number of scatterers: 9073 At special positions: 0 Unit cell: (91.8, 122.4, 133.45, 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 69 16.00 O 1662 8.00 N 1542 7.00 C 5800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " 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: 3.72 Conformation dependent library (CDL) restraints added in 1.7 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 33.9% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'B' and resid 1 through 24 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.609A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 removed outlier: 3.545A pdb=" N ALA C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.998A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 removed outlier: 4.016A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 31 removed outlier: 3.643A pdb=" N ALA D 12 " --> pdb=" O GLU D 8 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 13 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU D 14 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 28 " --> pdb=" O ARG D 24 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 52 Processing helix chain 'D' and resid 207 through 216 removed outlier: 4.738A pdb=" N ILE D 212 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N HIS D 213 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU D 216 " --> pdb=" O HIS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 255 removed outlier: 3.604A pdb=" N ALA D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN D 255 " --> pdb=" O ASP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 260 removed outlier: 3.880A pdb=" N THR D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.536A pdb=" N GLU D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER D 281 " --> pdb=" O LYS D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 309 Processing helix chain 'D' and resid 329 through 351 removed outlier: 3.774A pdb=" N CYS D 351 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.517A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.896A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 55 Proline residue: A 31 - end of helix removed outlier: 3.706A pdb=" N PHE A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.704A pdb=" N LEU A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.876A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 74 through 79' Processing helix chain 'A' and resid 79 through 89 removed outlier: 4.082A pdb=" N LEU A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 4.429A pdb=" N LEU A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 107 " --> pdb=" O MET A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 120 removed outlier: 4.318A pdb=" N PHE A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 4.006A pdb=" N TYR A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.754A pdb=" N ASN A 137 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 160 removed outlier: 4.106A pdb=" N ILE A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 156 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 188 through 215 removed outlier: 4.261A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 4.113A pdb=" N PHE A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 239 removed outlier: 3.562A pdb=" N MET A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 261 removed outlier: 3.638A pdb=" N VAL A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.581A pdb=" N VAL A 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.507A pdb=" N PHE A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 285 through 294 Proline residue: A 291 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.758A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.956A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.074A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.622A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.255A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.551A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.504A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 185 through 190 removed outlier: 3.600A pdb=" N ALA D 220 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE D 221 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE D 267 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE D 223 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASN D 269 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL D 225 " --> pdb=" O ASN D 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.501A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.457A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB4, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.971A pdb=" N ILE A 182 " --> pdb=" O CYS A 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 169 through 170 345 hydrogen bonds defined for protein. 951 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: 2.58 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 1446 1.25 - 1.39: 2357 1.39 - 1.54: 5291 1.54 - 1.68: 80 1.68 - 1.83: 100 Bond restraints: 9274 Sorted by residual: bond pdb=" C9 IX8 A 401 " pdb=" N10 IX8 A 401 " ideal model delta sigma weight residual 1.386 1.265 0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" C27 IX8 A 401 " pdb=" C32 IX8 A 401 " ideal model delta sigma weight residual 1.396 1.277 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C4 IX8 A 401 " pdb=" O5 IX8 A 401 " ideal model delta sigma weight residual 1.221 1.105 0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" CA TYR A 87 " pdb=" C TYR A 87 " ideal model delta sigma weight residual 1.522 1.445 0.077 1.40e-02 5.10e+03 3.00e+01 bond pdb=" C GLU A 190 " pdb=" N ALA A 191 " ideal model delta sigma weight residual 1.335 1.270 0.065 1.30e-02 5.92e+03 2.48e+01 ... (remaining 9269 not shown) Histogram of bond angle deviations from ideal: 95.45 - 103.18: 64 103.18 - 110.92: 3225 110.92 - 118.65: 4035 118.65 - 126.39: 5074 126.39 - 134.12: 155 Bond angle restraints: 12553 Sorted by residual: angle pdb=" N VAL A 123 " pdb=" CA VAL A 123 " pdb=" C VAL A 123 " ideal model delta sigma weight residual 112.96 106.51 6.45 1.00e+00 1.00e+00 4.17e+01 angle pdb=" C6 IX8 A 401 " pdb=" C4 IX8 A 401 " pdb=" N3 IX8 A 401 " ideal model delta sigma weight residual 114.73 132.12 -17.39 3.00e+00 1.11e-01 3.36e+01 angle pdb=" CA HIS A 189 " pdb=" C HIS A 189 " pdb=" N GLU A 190 " ideal model delta sigma weight residual 117.82 110.18 7.64 1.42e+00 4.96e-01 2.89e+01 angle pdb=" C23 IX8 A 401 " pdb=" C22 IX8 A 401 " pdb=" C24 IX8 A 401 " ideal model delta sigma weight residual 110.88 95.45 15.43 3.00e+00 1.11e-01 2.65e+01 angle pdb=" O HIS A 189 " pdb=" C HIS A 189 " pdb=" N GLU A 190 " ideal model delta sigma weight residual 122.33 129.19 -6.86 1.34e+00 5.57e-01 2.62e+01 ... (remaining 12548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 4918 15.89 - 31.77: 477 31.77 - 47.66: 118 47.66 - 63.55: 22 63.55 - 79.43: 11 Dihedral angle restraints: 5546 sinusoidal: 2234 harmonic: 3312 Sorted by residual: dihedral pdb=" CA SER A 62 " pdb=" C SER A 62 " pdb=" N ARG A 63 " pdb=" CA ARG A 63 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA VAL A 239 " pdb=" C VAL A 239 " pdb=" N PHE A 240 " pdb=" CA PHE A 240 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ARG S 38 " pdb=" C ARG S 38 " pdb=" N GLN S 39 " pdb=" CA GLN S 39 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 5543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1195 0.071 - 0.142: 202 0.142 - 0.213: 7 0.213 - 0.284: 2 0.284 - 0.355: 2 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CB ILE S 100 " pdb=" CA ILE S 100 " pdb=" CG1 ILE S 100 " pdb=" CG2 ILE S 100 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C13 CLR A 402 " pdb=" C12 CLR A 402 " pdb=" C14 CLR A 402 " pdb=" C17 CLR A 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.61 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C10 CLR A 402 " pdb=" C1 CLR A 402 " pdb=" C5 CLR A 402 " pdb=" C9 CLR A 402 " both_signs ideal model delta sigma weight residual False -2.85 -2.59 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 1405 not shown) Planarity restraints: 1579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 IX8 A 401 " -0.015 2.00e-02 2.50e+03 3.13e-02 1.22e+01 pdb=" C4 IX8 A 401 " 0.060 2.00e-02 2.50e+03 pdb=" C6 IX8 A 401 " -0.030 2.00e-02 2.50e+03 pdb=" N3 IX8 A 401 " -0.002 2.00e-02 2.50e+03 pdb=" O5 IX8 A 401 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 86 " 0.014 2.00e-02 2.50e+03 2.67e-02 7.14e+00 pdb=" C ASN A 86 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN A 86 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR A 87 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.040 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO S 75 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.034 5.00e-02 4.00e+02 ... (remaining 1576 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 116 2.64 - 3.21: 7970 3.21 - 3.77: 12747 3.77 - 4.34: 18608 4.34 - 4.90: 31442 Nonbonded interactions: 70883 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.078 2.440 nonbonded pdb=" NH1 ARG S 67 " pdb=" O SER S 85 " model vdw 2.140 2.520 nonbonded pdb=" O ALA C 56 " pdb=" NH1 ARG C 62 " model vdw 2.172 2.520 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.203 2.440 nonbonded pdb=" OG SER S 30 " pdb=" OD1 ASP S 74 " model vdw 2.214 2.440 ... (remaining 70878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.910 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 0.007 0.121 9274 Z= 0.488 Angle : 0.964 17.386 12553 Z= 0.525 Chirality : 0.052 0.355 1408 Planarity : 0.005 0.061 1579 Dihedral : 13.896 79.432 3394 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.25 (0.23), residues: 1130 helix: -1.74 (0.26), residues: 355 sheet: 0.08 (0.29), residues: 296 loop : -2.27 (0.23), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 82 HIS 0.015 0.002 HIS A 189 PHE 0.030 0.002 PHE B 234 TYR 0.021 0.003 TYR B 105 ARG 0.008 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.992 Fit side-chains REVERT: D 310 LEU cc_start: 0.8185 (mm) cc_final: 0.7896 (mt) REVERT: A 220 MET cc_start: 0.7790 (mtt) cc_final: 0.7392 (mtt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 1.2424 time to fit residues: 203.7039 Evaluate side-chains 133 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN D 255 ASN S 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9274 Z= 0.173 Angle : 0.625 9.663 12553 Z= 0.327 Chirality : 0.044 0.182 1408 Planarity : 0.004 0.050 1579 Dihedral : 6.771 66.492 1320 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.81 % Allowed : 10.65 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.24), residues: 1130 helix: -0.89 (0.28), residues: 357 sheet: 0.40 (0.30), residues: 291 loop : -1.91 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 189 PHE 0.013 0.001 PHE D 354 TYR 0.016 0.002 TYR A 87 ARG 0.007 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 1.034 Fit side-chains REVERT: D 310 LEU cc_start: 0.8142 (mm) cc_final: 0.7822 (mt) outliers start: 8 outliers final: 1 residues processed: 145 average time/residue: 1.2354 time to fit residues: 191.9547 Evaluate side-chains 131 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 188 HIS D 241 ASN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9274 Z= 0.294 Angle : 0.689 10.126 12553 Z= 0.358 Chirality : 0.046 0.230 1408 Planarity : 0.005 0.050 1579 Dihedral : 6.655 65.158 1320 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.13 % Allowed : 14.10 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.33 (0.24), residues: 1130 helix: -0.77 (0.28), residues: 355 sheet: 0.47 (0.30), residues: 283 loop : -1.76 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.011 0.002 HIS A 189 PHE 0.021 0.002 PHE B 234 TYR 0.025 0.002 TYR B 105 ARG 0.004 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.035 Fit side-chains REVERT: B 312 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7476 (t0) REVERT: C 29 LYS cc_start: 0.8158 (mmtp) cc_final: 0.7901 (mmtp) REVERT: D 243 MET cc_start: 0.8030 (ttp) cc_final: 0.7740 (ttm) REVERT: D 310 LEU cc_start: 0.8155 (mm) cc_final: 0.7808 (mt) REVERT: A 219 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7691 (mp10) outliers start: 21 outliers final: 8 residues processed: 144 average time/residue: 1.2546 time to fit residues: 193.6013 Evaluate side-chains 137 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 0.0980 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN D 188 HIS D 241 ASN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9274 Z= 0.190 Angle : 0.602 10.477 12553 Z= 0.313 Chirality : 0.043 0.152 1408 Planarity : 0.004 0.046 1579 Dihedral : 6.437 67.673 1320 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.74 % Allowed : 15.72 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.00 (0.24), residues: 1130 helix: -0.36 (0.29), residues: 352 sheet: 0.69 (0.31), residues: 277 loop : -1.67 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 189 PHE 0.019 0.001 PHE D 354 TYR 0.013 0.001 TYR B 105 ARG 0.007 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.024 Fit side-chains REVERT: D 309 ASP cc_start: 0.6954 (m-30) cc_final: 0.6729 (m-30) REVERT: D 310 LEU cc_start: 0.8111 (mm) cc_final: 0.7771 (mt) REVERT: A 40 PHE cc_start: 0.7987 (m-80) cc_final: 0.7654 (m-80) REVERT: A 219 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7655 (mp10) outliers start: 27 outliers final: 8 residues processed: 145 average time/residue: 1.1614 time to fit residues: 180.2379 Evaluate side-chains 131 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN D 188 HIS D 241 ASN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9274 Z= 0.324 Angle : 0.699 11.741 12553 Z= 0.359 Chirality : 0.047 0.249 1408 Planarity : 0.005 0.048 1579 Dihedral : 6.393 65.089 1320 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.35 % Allowed : 17.34 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.11 (0.24), residues: 1130 helix: -0.48 (0.29), residues: 345 sheet: 0.63 (0.31), residues: 271 loop : -1.67 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.011 0.002 HIS A 189 PHE 0.021 0.002 PHE D 354 TYR 0.019 0.002 TYR B 105 ARG 0.007 0.001 ARG S 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 0.965 Fit side-chains REVERT: B 137 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7462 (tpp-160) REVERT: B 291 ASP cc_start: 0.7367 (p0) cc_final: 0.7146 (p0) REVERT: D 310 LEU cc_start: 0.8118 (mm) cc_final: 0.7785 (mt) REVERT: A 219 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: A 220 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7133 (mtt) outliers start: 33 outliers final: 15 residues processed: 147 average time/residue: 1.1503 time to fit residues: 181.4976 Evaluate side-chains 137 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN D 241 ASN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9274 Z= 0.204 Angle : 0.608 9.900 12553 Z= 0.315 Chirality : 0.044 0.241 1408 Planarity : 0.004 0.046 1579 Dihedral : 6.029 66.194 1320 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.35 % Allowed : 18.46 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.86 (0.25), residues: 1130 helix: -0.26 (0.29), residues: 354 sheet: 0.74 (0.31), residues: 277 loop : -1.55 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 189 PHE 0.019 0.001 PHE D 354 TYR 0.012 0.001 TYR S 190 ARG 0.008 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 1.001 Fit side-chains REVERT: B 137 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7444 (tpp-160) REVERT: D 310 LEU cc_start: 0.8125 (mm) cc_final: 0.7779 (mt) REVERT: A 40 PHE cc_start: 0.7967 (m-80) cc_final: 0.7563 (m-80) REVERT: A 219 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7631 (mp10) REVERT: A 220 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7092 (mtt) outliers start: 33 outliers final: 17 residues processed: 144 average time/residue: 1.1871 time to fit residues: 183.3529 Evaluate side-chains 140 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 0.0170 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 259 GLN B 340 ASN D 241 ASN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9274 Z= 0.184 Angle : 0.590 9.999 12553 Z= 0.304 Chirality : 0.044 0.258 1408 Planarity : 0.004 0.045 1579 Dihedral : 5.929 68.054 1320 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.25 % Allowed : 18.86 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.72 (0.25), residues: 1130 helix: -0.08 (0.30), residues: 354 sheet: 0.69 (0.31), residues: 280 loop : -1.45 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.009 0.001 HIS A 161 PHE 0.019 0.001 PHE S 32 TYR 0.012 0.001 TYR S 190 ARG 0.008 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: B 137 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7459 (tpp-160) REVERT: C 29 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7927 (mmtp) REVERT: D 310 LEU cc_start: 0.8091 (mm) cc_final: 0.7754 (mt) REVERT: S 67 ARG cc_start: 0.7272 (ttp80) cc_final: 0.6893 (ttp80) REVERT: A 40 PHE cc_start: 0.7926 (m-80) cc_final: 0.7612 (m-80) REVERT: A 219 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7619 (mp10) REVERT: A 220 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7054 (mtt) outliers start: 32 outliers final: 21 residues processed: 148 average time/residue: 1.1088 time to fit residues: 176.1379 Evaluate side-chains 145 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 84 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9274 Z= 0.151 Angle : 0.576 9.441 12553 Z= 0.295 Chirality : 0.043 0.276 1408 Planarity : 0.004 0.045 1579 Dihedral : 5.849 70.706 1320 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.94 % Allowed : 19.78 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.60 (0.25), residues: 1130 helix: 0.07 (0.30), residues: 355 sheet: 0.72 (0.31), residues: 280 loop : -1.39 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.010 0.001 HIS A 161 PHE 0.021 0.001 PHE S 32 TYR 0.013 0.001 TYR S 190 ARG 0.008 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: B 137 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7344 (tpp-160) REVERT: B 217 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6598 (tpp) REVERT: C 29 LYS cc_start: 0.8171 (mmtp) cc_final: 0.7903 (mmtp) REVERT: D 310 LEU cc_start: 0.8061 (mm) cc_final: 0.7720 (mt) REVERT: S 67 ARG cc_start: 0.7273 (ttp80) cc_final: 0.7044 (ttp80) REVERT: A 40 PHE cc_start: 0.7928 (m-80) cc_final: 0.7664 (m-80) outliers start: 29 outliers final: 21 residues processed: 148 average time/residue: 1.0579 time to fit residues: 168.5595 Evaluate side-chains 143 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9274 Z= 0.270 Angle : 0.654 9.518 12553 Z= 0.334 Chirality : 0.046 0.378 1408 Planarity : 0.004 0.046 1579 Dihedral : 6.026 70.690 1320 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.25 % Allowed : 20.28 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1130 helix: -0.04 (0.29), residues: 354 sheet: 0.64 (0.31), residues: 275 loop : -1.40 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.008 0.002 HIS A 161 PHE 0.030 0.002 PHE S 32 TYR 0.013 0.002 TYR B 105 ARG 0.008 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: B 137 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7469 (tpp-160) REVERT: B 217 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6667 (tpt) REVERT: B 312 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7474 (t0) REVERT: C 29 LYS cc_start: 0.8161 (mmtp) cc_final: 0.7911 (mmtp) REVERT: D 310 LEU cc_start: 0.8079 (mm) cc_final: 0.7756 (mt) REVERT: S 67 ARG cc_start: 0.7258 (ttp80) cc_final: 0.6995 (ttp80) REVERT: A 40 PHE cc_start: 0.7937 (m-80) cc_final: 0.7616 (m-80) outliers start: 32 outliers final: 23 residues processed: 142 average time/residue: 1.1034 time to fit residues: 168.3054 Evaluate side-chains 146 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 259 GLN B 340 ASN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9274 Z= 0.233 Angle : 0.651 11.156 12553 Z= 0.332 Chirality : 0.046 0.329 1408 Planarity : 0.004 0.045 1579 Dihedral : 6.042 72.005 1320 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.14 % Allowed : 20.69 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.25), residues: 1130 helix: 0.01 (0.29), residues: 355 sheet: 0.62 (0.31), residues: 275 loop : -1.34 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.009 0.001 HIS A 161 PHE 0.030 0.002 PHE S 32 TYR 0.011 0.002 TYR B 105 ARG 0.008 0.000 ARG D 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 117 time to evaluate : 1.038 Fit side-chains REVERT: B 137 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7453 (tpp-160) REVERT: B 217 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6678 (tpt) REVERT: B 312 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7448 (t0) REVERT: C 29 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7922 (mmtp) REVERT: D 310 LEU cc_start: 0.8083 (mm) cc_final: 0.7758 (mt) REVERT: S 67 ARG cc_start: 0.7253 (ttp80) cc_final: 0.7028 (ttp80) REVERT: A 40 PHE cc_start: 0.7922 (m-80) cc_final: 0.7620 (m-80) REVERT: A 220 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7060 (mtt) outliers start: 31 outliers final: 22 residues processed: 138 average time/residue: 1.1671 time to fit residues: 172.8417 Evaluate side-chains 142 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.5209 > 50: distance: 53 - 95: 32.135 distance: 73 - 152: 36.498 distance: 76 - 149: 31.567 distance: 85 - 139: 32.497 distance: 87 - 92: 33.858 distance: 88 - 136: 37.562 distance: 92 - 93: 52.281 distance: 93 - 94: 32.803 distance: 93 - 96: 41.967 distance: 94 - 95: 6.674 distance: 94 - 98: 69.780 distance: 96 - 97: 39.736 distance: 98 - 126: 58.046 distance: 99 - 102: 41.112 distance: 100 - 104: 39.801 distance: 106 - 108: 39.817 distance: 108 - 109: 57.011 distance: 109 - 110: 38.815 distance: 109 - 112: 55.611 distance: 110 - 111: 45.651 distance: 110 - 116: 32.474 distance: 112 - 113: 12.578 distance: 113 - 114: 50.259 distance: 113 - 115: 16.501 distance: 116 - 117: 7.107 distance: 117 - 118: 57.387 distance: 120 - 121: 41.184 distance: 120 - 122: 38.726 distance: 123 - 124: 46.433 distance: 124 - 125: 43.724 distance: 124 - 127: 42.934 distance: 125 - 130: 39.544 distance: 127 - 128: 47.227 distance: 127 - 129: 40.721 distance: 130 - 131: 14.077 distance: 130 - 209: 35.678 distance: 131 - 132: 62.785 distance: 131 - 134: 63.108 distance: 132 - 133: 56.794 distance: 132 - 136: 56.778 distance: 133 - 206: 32.592 distance: 134 - 135: 56.392 distance: 136 - 137: 19.943 distance: 137 - 138: 19.695 distance: 137 - 140: 43.865 distance: 138 - 139: 40.958 distance: 138 - 141: 40.461 distance: 141 - 196: 34.883 distance: 142 - 143: 39.690 distance: 143 - 144: 57.582 distance: 145 - 146: 26.467 distance: 146 - 147: 28.826 distance: 146 - 148: 27.584 distance: 149 - 150: 39.657 distance: 150 - 151: 56.176 distance: 150 - 153: 39.942 distance: 151 - 152: 40.989 distance: 151 - 163: 34.060 distance: 153 - 154: 31.482 distance: 154 - 155: 56.484 distance: 154 - 156: 31.634 distance: 155 - 157: 57.085 distance: 156 - 158: 49.602 distance: 156 - 159: 9.057 distance: 157 - 158: 40.068 distance: 158 - 160: 6.821 distance: 159 - 161: 57.359 distance: 160 - 162: 40.917 distance: 161 - 162: 34.407