Starting phenix.real_space_refine on Sat Apr 6 23:31:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhy_36300/04_2024/8jhy_36300_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhy_36300/04_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_36300/04_2024/8jhy_36300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhy_36300/04_2024/8jhy_36300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhy_36300/04_2024/8jhy_36300_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhy_36300/04_2024/8jhy_36300_neut_updated.pdb" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 5.30, per 1000 atoms: 0.58 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: 3.05 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... running ksdssp... Secondary structure from input PDB file: 31 helices and 12 sheets defined 29.5% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.816A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'C' and resid 7 through 22 Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.800A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 45 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 30 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) Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'D' and resid 271 through 280 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) Processing helix chain 'D' and resid 296 through 310 removed outlier: 4.053A pdb=" N LEU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 350 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'A' and resid 26 through 54 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 66 through 71 Processing helix chain 'A' and resid 75 through 78 No H-bonds generated for 'chain 'A' and resid 75 through 78' Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.911A pdb=" N CYS A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 112 through 119 removed outlier: 4.318A pdb=" N PHE A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 removed outlier: 4.006A pdb=" N TYR A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 138 Processing helix chain 'A' and resid 144 through 158 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) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 189 through 214 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 231 through 238 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 246 through 260 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) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 272 through 282 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) removed outlier: 4.135A pdb=" N SER A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 293 removed outlier: 4.885A pdb=" N ASP A 290 " --> pdb=" O SER A 287 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing sheet with id= A, 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: 3.636A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.198A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, 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= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.709A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.770A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, 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: 3.704A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, 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= H, first strand: chain 'D' and resid 319 through 323 removed outlier: 6.696A pdb=" N ILE D 264 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N HIS D 322 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU D 266 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA D 220 " --> pdb=" O LYS D 35 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 115 through 117 removed outlier: 3.501A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.654A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (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= L, first strand: chain 'S' and resid 155 through 160 312 hydrogen bonds defined for protein. 873 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: 2.91 Time building geometry restraints manager: 3.36 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: 120 2.64 - 3.21: 7976 3.21 - 3.77: 12777 3.77 - 4.34: 18671 4.34 - 4.90: 31471 Nonbonded interactions: 71015 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 71010 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: 0.840 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: 4.050 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 27.010 Find NCS groups from input model: 0.260 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:13.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.310 ------------------------------------------------------------------------------- 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= 0.475 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 : 1.101 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: 1.3038 time to fit residues: 213.7768 Evaluate side-chains 133 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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: 0.9990 chunk 84 optimal weight: 0.0570 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 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: 0.0070 chunk 101 optimal weight: 0.9980 overall best weight: 0.3074 ------------------------------------------------------------------------------- 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 266 HIS C 44 HIS D 241 ASN D 255 ASN S 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9274 Z= 0.148 Angle : 0.579 8.732 12553 Z= 0.303 Chirality : 0.043 0.186 1408 Planarity : 0.004 0.050 1579 Dihedral : 6.649 68.096 1320 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.71 % Allowed : 10.45 % Favored : 88.84 % 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: -1.44 (0.24), residues: 1130 helix: -0.83 (0.28), residues: 352 sheet: 0.42 (0.30), residues: 293 loop : -1.90 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.013 0.001 PHE D 354 TYR 0.018 0.001 TYR A 87 ARG 0.008 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 148 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 141 time to evaluate : 0.965 Fit side-chains REVERT: D 310 LEU cc_start: 0.8138 (mm) cc_final: 0.7812 (mt) outliers start: 7 outliers final: 2 residues processed: 144 average time/residue: 1.2786 time to fit residues: 196.2013 Evaluate side-chains 133 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain A residue 79 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.7396 moved from start: 0.1313 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= 0.276 Angle : 0.658 10.027 12553 Z= 0.340 Chirality : 0.046 0.231 1408 Planarity : 0.005 0.050 1579 Dihedral : 6.553 67.937 1320 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.03 % Allowed : 13.79 % Favored : 84.18 % 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: -1.27 (0.24), residues: 1130 helix: -0.61 (0.29), residues: 350 sheet: 0.46 (0.30), residues: 289 loop : -1.81 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.010 0.002 HIS A 189 PHE 0.021 0.002 PHE B 234 TYR 0.023 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 154 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.017 Fit side-chains REVERT: B 259 GLN cc_start: 0.5357 (OUTLIER) cc_final: 0.5111 (tp-100) REVERT: B 312 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7471 (t0) REVERT: D 243 MET cc_start: 0.8003 (ttp) cc_final: 0.7760 (ttm) REVERT: D 310 LEU cc_start: 0.8128 (mm) cc_final: 0.7795 (mt) REVERT: A 219 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7631 (mp10) outliers start: 20 outliers final: 7 residues processed: 143 average time/residue: 1.2743 time to fit residues: 194.2592 Evaluate side-chains 135 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 105 SER 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: 1.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 96 optimal weight: 0.0020 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9274 Z= 0.154 Angle : 0.559 8.707 12553 Z= 0.290 Chirality : 0.043 0.242 1408 Planarity : 0.004 0.047 1579 Dihedral : 6.202 70.079 1320 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.03 % Allowed : 15.42 % Favored : 82.56 % 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: -0.91 (0.25), residues: 1130 helix: -0.23 (0.30), residues: 344 sheet: 0.59 (0.30), residues: 289 loop : -1.60 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS D 244 PHE 0.016 0.001 PHE D 354 TYR 0.016 0.001 TYR A 269 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 148 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 1.056 Fit side-chains REVERT: C 29 LYS cc_start: 0.8128 (mmtp) cc_final: 0.7894 (mmtp) REVERT: D 310 LEU cc_start: 0.8080 (mm) cc_final: 0.7741 (mt) outliers start: 20 outliers final: 10 residues processed: 138 average time/residue: 1.2229 time to fit residues: 180.4932 Evaluate side-chains 130 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 238 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 0.0980 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9274 Z= 0.372 Angle : 0.724 13.201 12553 Z= 0.368 Chirality : 0.048 0.231 1408 Planarity : 0.005 0.049 1579 Dihedral : 6.326 65.926 1320 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.35 % Allowed : 16.13 % Favored : 80.53 % 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: -1.15 (0.24), residues: 1130 helix: -0.51 (0.29), residues: 351 sheet: 0.53 (0.30), residues: 282 loop : -1.70 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.012 0.002 HIS A 189 PHE 0.022 0.002 PHE B 234 TYR 0.022 0.002 TYR B 105 ARG 0.007 0.001 ARG D 32 *********************** 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 160 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 1.122 Fit side-chains REVERT: D 208 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7832 (ttp80) REVERT: D 276 GLU cc_start: 0.6774 (mp0) cc_final: 0.6538 (tp30) REVERT: D 310 LEU cc_start: 0.8121 (mm) cc_final: 0.7787 (mt) REVERT: A 40 PHE cc_start: 0.7968 (m-80) cc_final: 0.7521 (m-80) REVERT: A 219 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7673 (mp10) outliers start: 33 outliers final: 19 residues processed: 146 average time/residue: 1.2847 time to fit residues: 200.2575 Evaluate side-chains 143 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 B residue 259 GLN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 105 SER 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 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: 1.9990 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9274 Z= 0.180 Angle : 0.586 9.576 12553 Z= 0.302 Chirality : 0.043 0.228 1408 Planarity : 0.004 0.046 1579 Dihedral : 6.043 67.326 1320 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.43 % Allowed : 18.46 % Favored : 79.11 % 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: -0.21 (0.29), residues: 350 sheet: 0.62 (0.30), residues: 289 loop : -1.56 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 189 PHE 0.018 0.001 PHE D 354 TYR 0.016 0.001 TYR A 269 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 152 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.001 Fit side-chains REVERT: B 258 ASP cc_start: 0.4394 (OUTLIER) cc_final: 0.4011 (p0) REVERT: D 208 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7823 (ttp80) REVERT: D 276 GLU cc_start: 0.6809 (mp0) cc_final: 0.6584 (tp30) REVERT: D 310 LEU cc_start: 0.8102 (mm) cc_final: 0.7755 (mt) REVERT: A 40 PHE cc_start: 0.7939 (m-80) cc_final: 0.7710 (m-80) outliers start: 24 outliers final: 16 residues processed: 143 average time/residue: 1.1787 time to fit residues: 180.7344 Evaluate side-chains 140 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 238 ILE 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: 5.9990 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 241 ASN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9274 Z= 0.273 Angle : 0.640 10.215 12553 Z= 0.328 Chirality : 0.045 0.231 1408 Planarity : 0.004 0.047 1579 Dihedral : 6.096 65.700 1320 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.25 % Allowed : 18.36 % Favored : 78.40 % 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: -0.83 (0.25), residues: 1130 helix: -0.18 (0.29), residues: 345 sheet: 0.65 (0.30), residues: 281 loop : -1.50 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS A 189 PHE 0.019 0.002 PHE D 354 TYR 0.016 0.002 TYR A 269 ARG 0.007 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 159 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 1.019 Fit side-chains REVERT: D 208 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7833 (ttp80) REVERT: D 310 LEU cc_start: 0.8064 (mm) cc_final: 0.7728 (mt) REVERT: A 40 PHE cc_start: 0.7944 (m-80) cc_final: 0.7555 (m-80) REVERT: A 219 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7628 (mp10) outliers start: 32 outliers final: 21 residues processed: 146 average time/residue: 1.1742 time to fit residues: 183.8282 Evaluate side-chains 147 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 93 MET 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 224 VAL 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 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: 4.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 0.0470 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- 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 241 ASN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1902 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= 0.191 Angle : 0.589 8.844 12553 Z= 0.302 Chirality : 0.043 0.226 1408 Planarity : 0.004 0.046 1579 Dihedral : 5.965 66.254 1320 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.54 % Allowed : 18.76 % Favored : 78.70 % 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: -0.68 (0.25), residues: 1130 helix: 0.03 (0.30), residues: 343 sheet: 0.70 (0.31), residues: 282 loop : -1.45 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 189 PHE 0.017 0.001 PHE D 354 TYR 0.016 0.002 TYR A 269 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 149 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.023 Fit side-chains REVERT: D 208 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7813 (ttp80) REVERT: D 310 LEU cc_start: 0.8041 (mm) cc_final: 0.7708 (mt) REVERT: A 40 PHE cc_start: 0.7918 (m-80) cc_final: 0.7584 (m-80) outliers start: 25 outliers final: 21 residues processed: 141 average time/residue: 1.1864 time to fit residues: 179.3652 Evaluate side-chains 142 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 93 MET 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 224 VAL 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 238 ILE Chi-restraints excluded: chain A residue 241 VAL 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: 4.9990 chunk 103 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.0470 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2068 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= 0.153 Angle : 0.560 10.276 12553 Z= 0.285 Chirality : 0.042 0.224 1408 Planarity : 0.004 0.045 1579 Dihedral : 5.816 67.759 1320 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.54 % Allowed : 18.97 % Favored : 78.50 % 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: -0.52 (0.25), residues: 1130 helix: 0.24 (0.30), residues: 344 sheet: 0.72 (0.31), residues: 282 loop : -1.37 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS D 244 PHE 0.015 0.001 PHE D 354 TYR 0.017 0.001 TYR A 269 ARG 0.009 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 154 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 0.971 Fit side-chains REVERT: D 208 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7783 (ttp80) REVERT: D 310 LEU cc_start: 0.8045 (mm) cc_final: 0.7711 (mt) REVERT: A 40 PHE cc_start: 0.7886 (m-80) cc_final: 0.7584 (m-80) outliers start: 25 outliers final: 17 residues processed: 147 average time/residue: 1.1709 time to fit residues: 184.6142 Evaluate side-chains 140 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 238 ILE 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: 0.7980 chunk 50 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2162 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= 0.173 Angle : 0.620 14.093 12553 Z= 0.315 Chirality : 0.043 0.223 1408 Planarity : 0.004 0.045 1579 Dihedral : 6.001 69.163 1320 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.33 % Allowed : 19.98 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.43 (0.25), residues: 1130 helix: 0.34 (0.30), residues: 343 sheet: 0.71 (0.31), residues: 290 loop : -1.32 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 184 PHE 0.015 0.001 PHE D 354 TYR 0.025 0.001 TYR A 269 ARG 0.009 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 145 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 0.920 Fit side-chains REVERT: C 29 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7877 (mmtp) REVERT: D 208 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7795 (ttp80) REVERT: D 310 LEU cc_start: 0.8037 (mm) cc_final: 0.7702 (mt) REVERT: A 40 PHE cc_start: 0.7876 (m-80) cc_final: 0.7596 (m-80) outliers start: 23 outliers final: 19 residues processed: 141 average time/residue: 1.2212 time to fit residues: 184.3188 Evaluate side-chains 138 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 97 VAL 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 98 ILE Chi-restraints excluded: chain A residue 238 ILE 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 27 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.136047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.113058 restraints weight = 14688.942| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.73 r_work: 0.3477 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9274 Z= 0.229 Angle : 0.656 11.767 12553 Z= 0.333 Chirality : 0.045 0.289 1408 Planarity : 0.004 0.045 1579 Dihedral : 6.126 69.659 1320 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.64 % Allowed : 19.88 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.49 (0.25), residues: 1130 helix: 0.30 (0.30), residues: 345 sheet: 0.68 (0.31), residues: 291 loop : -1.39 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 189 PHE 0.030 0.002 PHE S 32 TYR 0.020 0.002 TYR A 269 ARG 0.008 0.000 ARG D 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3714.81 seconds wall clock time: 67 minutes 11.54 seconds (4031.54 seconds total)