Starting phenix.real_space_refine on Thu Mar 14 16:02:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoo_33985/03_2024/7yoo_33985_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoo_33985/03_2024/7yoo_33985.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoo_33985/03_2024/7yoo_33985_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoo_33985/03_2024/7yoo_33985_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoo_33985/03_2024/7yoo_33985_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoo_33985/03_2024/7yoo_33985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoo_33985/03_2024/7yoo_33985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoo_33985/03_2024/7yoo_33985_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoo_33985/03_2024/7yoo_33985_updated.pdb" } resolution = 3.11 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= 0.021 sd= 0.083 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 61 5.16 5 C 5856 2.51 5 N 1559 2.21 5 O 1712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9188 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1743 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "L" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 255 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain breaks: 1 Chain: "R" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2402 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain: "S" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1794 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Time building chain proxies: 5.30, per 1000 atoms: 0.58 Number of scatterers: 9188 At special positions: 0 Unit cell: (122.018, 138.006, 108.554, 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 61 16.00 O 1712 8.00 N 1559 7.00 C 5856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 123 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 3.02 Conformation dependent library (CDL) restraints added in 1.8 seconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 15 sheets defined 33.0% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.582A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.650A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.025A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.747A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.624A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.704A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.557A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 348 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.531A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.217A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 23 removed outlier: 3.515A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.744A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'L' and resid 17 through 31 Processing helix chain 'R' and resid 43 through 45 No H-bonds generated for 'chain 'R' and resid 43 through 45' Processing helix chain 'R' and resid 47 through 77 removed outlier: 3.614A pdb=" N VAL R 52 " --> pdb=" O GLU R 48 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU R 70 " --> pdb=" O ILE R 66 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL R 71 " --> pdb=" O GLY R 67 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE R 72 " --> pdb=" O ASN R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 112 removed outlier: 3.530A pdb=" N PHE R 88 " --> pdb=" O VAL R 84 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE R 89 " --> pdb=" O THR R 85 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU R 104 " --> pdb=" O ASN R 100 " (cutoff:3.500A) Proline residue: R 105 - end of helix Processing helix chain 'R' and resid 120 through 152 removed outlier: 4.032A pdb=" N HIS R 124 " --> pdb=" O PRO R 120 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU R 125 " --> pdb=" O VAL R 121 " (cutoff:3.500A) Proline residue: R 127 - end of helix removed outlier: 3.960A pdb=" N VAL R 134 " --> pdb=" O GLN R 130 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR R 142 " --> pdb=" O THR R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 179 removed outlier: 3.519A pdb=" N TRP R 173 " --> pdb=" O ILE R 169 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU R 178 " --> pdb=" O GLY R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 185 Processing helix chain 'R' and resid 214 through 227 removed outlier: 3.693A pdb=" N TYR R 219 " --> pdb=" O TYR R 215 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER R 220 " --> pdb=" O GLY R 216 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU R 221 " --> pdb=" O THR R 217 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU R 225 " --> pdb=" O LEU R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 247 Processing helix chain 'R' and resid 256 through 280 removed outlier: 3.698A pdb=" N GLN R 264 " --> pdb=" O HIS R 260 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS R 265 " --> pdb=" O GLN R 261 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR R 266 " --> pdb=" O ARG R 262 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR R 267 " --> pdb=" O ARG R 263 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS R 268 " --> pdb=" O GLN R 264 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET R 269 " --> pdb=" O LYS R 265 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL R 273 " --> pdb=" O MET R 269 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL R 274 " --> pdb=" O LEU R 270 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE R 277 " --> pdb=" O VAL R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 293 Processing helix chain 'R' and resid 303 through 318 removed outlier: 4.336A pdb=" N SER R 317 " --> pdb=" O ILE R 313 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N THR R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 324 No H-bonds generated for 'chain 'R' and resid 321 through 324' Processing helix chain 'R' and resid 330 through 340 removed outlier: 4.005A pdb=" N LYS R 334 " --> pdb=" O SER R 330 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA R 335 " --> pdb=" O ASN R 331 " (cutoff:3.500A) 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 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 263 through 269 removed outlier: 3.960A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.032A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.868A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.690A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.812A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.655A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.804A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.531A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 188 through 195 removed outlier: 4.061A pdb=" N SER R 190 " --> pdb=" O ALA R 202 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE R 198 " --> pdb=" O ILE R 194 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 11 through 13 removed outlier: 6.323A pdb=" N THR S 118 " --> pdb=" O VAL S 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S' and resid 17 through 19 removed outlier: 3.641A pdb=" N PHE S 80 " --> pdb=" O SER S 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 115 through 117 removed outlier: 3.538A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 155 through 159 removed outlier: 3.619A pdb=" N ILE S 157 " --> pdb=" O LEU S 214 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'S' and resid 226 through 231 removed outlier: 3.650A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 987 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: 2.56 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1484 1.31 - 1.44: 2578 1.44 - 1.57: 5229 1.57 - 1.70: 0 1.70 - 1.83: 88 Bond restraints: 9379 Sorted by residual: bond pdb=" C LEU R 104 " pdb=" N PRO R 105 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.20e-02 6.94e+03 1.36e+00 bond pdb=" CA GLY A 183 " pdb=" C GLY A 183 " ideal model delta sigma weight residual 1.523 1.513 0.010 1.19e-02 7.06e+03 6.46e-01 bond pdb=" C TYR S 235 " pdb=" N PRO S 236 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.56e-01 bond pdb=" C ILE R 195 " pdb=" N PRO R 196 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.53e-01 bond pdb=" CB ARG A 242 " pdb=" CG ARG A 242 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.33e-01 ... (remaining 9374 not shown) Histogram of bond angle deviations from ideal: 99.85 - 106.68: 203 106.68 - 113.52: 5169 113.52 - 120.35: 3326 120.35 - 127.18: 3911 127.18 - 134.01: 93 Bond angle restraints: 12702 Sorted by residual: angle pdb=" CE2 TYC L 36 " pdb=" CZ TYC L 36 " pdb=" OH TYC L 36 " ideal model delta sigma weight residual 129.45 120.08 9.37 3.00e+00 1.11e-01 9.75e+00 angle pdb=" CE1 TYC L 36 " pdb=" CZ TYC L 36 " pdb=" OH TYC L 36 " ideal model delta sigma weight residual 110.51 119.86 -9.35 3.00e+00 1.11e-01 9.70e+00 angle pdb=" CA GLY B 216 " pdb=" C GLY B 216 " pdb=" N MET B 217 " ideal model delta sigma weight residual 118.67 115.93 2.74 9.80e-01 1.04e+00 7.82e+00 angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 126.69 -5.15 1.91e+00 2.74e-01 7.26e+00 angle pdb=" N GLY B 216 " pdb=" CA GLY B 216 " pdb=" C GLY B 216 " ideal model delta sigma weight residual 116.01 111.60 4.41 1.64e+00 3.72e-01 7.24e+00 ... (remaining 12697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5075 17.75 - 35.50: 409 35.50 - 53.26: 90 53.26 - 71.01: 8 71.01 - 88.76: 3 Dihedral angle restraints: 5585 sinusoidal: 2187 harmonic: 3398 Sorted by residual: dihedral pdb=" CG ARG B 52 " pdb=" CD ARG B 52 " pdb=" NE ARG B 52 " pdb=" CZ ARG B 52 " ideal model delta sinusoidal sigma weight residual -180.00 -135.10 -44.90 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG S 98 " pdb=" CD ARG S 98 " pdb=" NE ARG S 98 " pdb=" CZ ARG S 98 " ideal model delta sinusoidal sigma weight residual 180.00 139.00 41.00 2 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" CB LYS R 117 " pdb=" CG LYS R 117 " pdb=" CD LYS R 117 " pdb=" CE LYS R 117 " ideal model delta sinusoidal sigma weight residual -60.00 -112.40 52.40 3 1.50e+01 4.44e-03 9.11e+00 ... (remaining 5582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 904 0.029 - 0.059: 372 0.059 - 0.088: 93 0.088 - 0.118: 66 0.118 - 0.147: 11 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CA ILE R 195 " pdb=" N ILE R 195 " pdb=" C ILE R 195 " pdb=" CB ILE R 195 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 1443 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 287 " -0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO A 288 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 193 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.45e+00 pdb=" CG ASP A 193 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP A 193 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 193 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 195 " -0.024 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO R 196 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO R 196 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 196 " -0.021 5.00e-02 4.00e+02 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 179 2.70 - 3.25: 8661 3.25 - 3.80: 13296 3.80 - 4.35: 17740 4.35 - 4.90: 30777 Nonbonded interactions: 70653 Sorted by model distance: nonbonded pdb=" O ASP B 333 " pdb=" OD1 ASP B 333 " model vdw 2.153 3.040 nonbonded pdb=" O GLY A 40 " pdb=" OG SER A 44 " model vdw 2.283 2.440 nonbonded pdb=" NH2 ARG S 67 " pdb=" OD2 ASP S 90 " model vdw 2.286 2.520 nonbonded pdb=" OG SER S 17 " pdb=" O MET S 83 " model vdw 2.319 2.440 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.334 2.440 ... (remaining 70648 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: 3.090 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: 13.560 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.710 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.002 0.022 9379 Z= 0.136 Angle : 0.448 9.366 12702 Z= 0.231 Chirality : 0.039 0.147 1446 Planarity : 0.003 0.080 1598 Dihedral : 13.299 88.762 3381 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1148 helix: -0.06 (0.27), residues: 370 sheet: 0.37 (0.34), residues: 251 loop : -0.23 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S 47 HIS 0.004 0.001 HIS B 62 PHE 0.008 0.001 PHE B 199 TYR 0.009 0.001 TYR S 190 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.038 Fit side-chains REVERT: A 246 SER cc_start: 0.7112 (p) cc_final: 0.6875 (p) REVERT: A 305 CYS cc_start: 0.7607 (m) cc_final: 0.7299 (m) REVERT: R 315 MET cc_start: 0.7175 (mmt) cc_final: 0.6875 (mmt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2646 time to fit residues: 52.5842 Evaluate side-chains 128 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.0970 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 ASN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9379 Z= 0.169 Angle : 0.485 5.612 12702 Z= 0.258 Chirality : 0.041 0.157 1446 Planarity : 0.003 0.056 1598 Dihedral : 3.750 19.304 1269 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.19 % Allowed : 7.45 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1148 helix: 0.82 (0.27), residues: 380 sheet: 0.46 (0.32), residues: 279 loop : -0.13 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE A 199 TYR 0.010 0.001 TYR S 235 ARG 0.005 0.000 ARG R 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.069 Fit side-chains REVERT: A 305 CYS cc_start: 0.7418 (m) cc_final: 0.7027 (m) REVERT: B 13 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8208 (tm-30) REVERT: B 18 ILE cc_start: 0.7534 (mm) cc_final: 0.7218 (mt) REVERT: B 258 ASP cc_start: 0.6552 (t0) cc_final: 0.5877 (t70) REVERT: R 69 SER cc_start: 0.8599 (p) cc_final: 0.8397 (m) outliers start: 12 outliers final: 10 residues processed: 148 average time/residue: 0.2543 time to fit residues: 49.4114 Evaluate side-chains 134 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 186 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.0770 chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN ** R 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9379 Z= 0.173 Angle : 0.460 5.166 12702 Z= 0.244 Chirality : 0.040 0.156 1446 Planarity : 0.003 0.048 1598 Dihedral : 3.695 19.683 1269 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.69 % Allowed : 9.43 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1148 helix: 1.17 (0.28), residues: 381 sheet: 0.40 (0.32), residues: 274 loop : -0.14 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE A 199 TYR 0.011 0.001 TYR B 59 ARG 0.006 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 0.960 Fit side-chains REVERT: A 305 CYS cc_start: 0.7480 (m) cc_final: 0.7060 (m) REVERT: B 129 ARG cc_start: 0.7314 (mtp180) cc_final: 0.6980 (mmm160) REVERT: B 258 ASP cc_start: 0.6677 (t0) cc_final: 0.6064 (t70) REVERT: B 335 PHE cc_start: 0.8620 (m-80) cc_final: 0.8409 (m-80) outliers start: 17 outliers final: 15 residues processed: 137 average time/residue: 0.2698 time to fit residues: 48.2910 Evaluate side-chains 141 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 183 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 0.0270 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9379 Z= 0.235 Angle : 0.495 6.490 12702 Z= 0.261 Chirality : 0.041 0.159 1446 Planarity : 0.003 0.042 1598 Dihedral : 3.857 22.558 1269 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.89 % Allowed : 12.21 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1148 helix: 1.25 (0.27), residues: 381 sheet: 0.27 (0.31), residues: 283 loop : -0.20 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.005 0.001 HIS S 35 PHE 0.011 0.001 PHE A 199 TYR 0.015 0.001 TYR B 59 ARG 0.006 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 0.952 Fit side-chains REVERT: A 305 CYS cc_start: 0.7478 (m) cc_final: 0.7051 (m) REVERT: B 61 MET cc_start: 0.8241 (ptm) cc_final: 0.8018 (ptm) REVERT: B 258 ASP cc_start: 0.6701 (t0) cc_final: 0.6148 (t70) outliers start: 19 outliers final: 17 residues processed: 144 average time/residue: 0.2765 time to fit residues: 51.4682 Evaluate side-chains 143 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 269 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 168 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.0980 chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN R 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9379 Z= 0.178 Angle : 0.457 5.254 12702 Z= 0.242 Chirality : 0.040 0.160 1446 Planarity : 0.003 0.039 1598 Dihedral : 3.754 23.712 1269 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.38 % Allowed : 13.80 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1148 helix: 1.35 (0.27), residues: 384 sheet: 0.33 (0.31), residues: 268 loop : -0.27 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS S 35 PHE 0.010 0.001 PHE B 199 TYR 0.014 0.001 TYR B 59 ARG 0.007 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.948 Fit side-chains REVERT: A 305 CYS cc_start: 0.7448 (m) cc_final: 0.7018 (m) REVERT: B 258 ASP cc_start: 0.6674 (t0) cc_final: 0.6142 (t70) outliers start: 24 outliers final: 18 residues processed: 144 average time/residue: 0.2617 time to fit residues: 49.3250 Evaluate side-chains 147 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 168 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.0030 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9379 Z= 0.198 Angle : 0.472 5.679 12702 Z= 0.249 Chirality : 0.041 0.160 1446 Planarity : 0.003 0.038 1598 Dihedral : 3.804 25.478 1269 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.58 % Allowed : 14.00 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1148 helix: 1.35 (0.27), residues: 385 sheet: 0.29 (0.31), residues: 280 loop : -0.24 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS S 35 PHE 0.010 0.001 PHE B 241 TYR 0.014 0.001 TYR B 59 ARG 0.006 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.027 Fit side-chains REVERT: A 305 CYS cc_start: 0.7450 (m) cc_final: 0.7025 (m) REVERT: B 258 ASP cc_start: 0.6650 (t0) cc_final: 0.6140 (t70) REVERT: R 214 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7960 (pt) REVERT: R 291 VAL cc_start: 0.8242 (t) cc_final: 0.8024 (p) outliers start: 26 outliers final: 20 residues processed: 146 average time/residue: 0.2706 time to fit residues: 51.4930 Evaluate side-chains 151 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 168 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 92 optimal weight: 0.0470 chunk 61 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9379 Z= 0.180 Angle : 0.467 7.001 12702 Z= 0.247 Chirality : 0.040 0.161 1446 Planarity : 0.003 0.038 1598 Dihedral : 3.778 26.174 1269 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.38 % Allowed : 14.60 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1148 helix: 1.42 (0.27), residues: 385 sheet: 0.30 (0.31), residues: 268 loop : -0.27 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS S 35 PHE 0.010 0.001 PHE B 199 TYR 0.012 0.001 TYR B 59 ARG 0.006 0.000 ARG R 241 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 0.857 Fit side-chains REVERT: A 305 CYS cc_start: 0.7443 (m) cc_final: 0.7006 (m) REVERT: B 258 ASP cc_start: 0.6639 (t0) cc_final: 0.6145 (t70) REVERT: R 214 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7942 (pt) REVERT: R 291 VAL cc_start: 0.8248 (t) cc_final: 0.8038 (p) outliers start: 24 outliers final: 17 residues processed: 148 average time/residue: 0.2756 time to fit residues: 53.4615 Evaluate side-chains 150 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 168 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 0.0370 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9379 Z= 0.171 Angle : 0.463 6.845 12702 Z= 0.246 Chirality : 0.040 0.162 1446 Planarity : 0.003 0.038 1598 Dihedral : 3.728 26.729 1269 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.18 % Allowed : 15.39 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1148 helix: 1.48 (0.27), residues: 385 sheet: 0.33 (0.31), residues: 268 loop : -0.26 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE B 199 TYR 0.012 0.001 TYR B 59 ARG 0.006 0.000 ARG R 241 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.070 Fit side-chains REVERT: A 305 CYS cc_start: 0.7390 (m) cc_final: 0.7050 (m) REVERT: B 258 ASP cc_start: 0.6639 (t0) cc_final: 0.6154 (t70) REVERT: R 214 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7920 (pt) REVERT: R 291 VAL cc_start: 0.8252 (t) cc_final: 0.8039 (p) outliers start: 22 outliers final: 19 residues processed: 147 average time/residue: 0.2722 time to fit residues: 52.2629 Evaluate side-chains 154 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 231 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 61 optimal weight: 0.0000 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9379 Z= 0.183 Angle : 0.479 6.815 12702 Z= 0.253 Chirality : 0.040 0.163 1446 Planarity : 0.003 0.040 1598 Dihedral : 3.760 27.339 1269 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.28 % Allowed : 15.69 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1148 helix: 1.50 (0.27), residues: 385 sheet: 0.30 (0.31), residues: 268 loop : -0.28 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS R 258 PHE 0.010 0.001 PHE B 199 TYR 0.013 0.001 TYR B 59 ARG 0.007 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.061 Fit side-chains REVERT: B 258 ASP cc_start: 0.6636 (t0) cc_final: 0.6156 (t70) REVERT: R 214 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7933 (pt) REVERT: R 291 VAL cc_start: 0.8255 (t) cc_final: 0.8044 (p) outliers start: 23 outliers final: 20 residues processed: 146 average time/residue: 0.2800 time to fit residues: 52.9527 Evaluate side-chains 152 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 188 GLU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 231 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 113 optimal weight: 0.3980 chunk 104 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.0670 chunk 55 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9379 Z= 0.173 Angle : 0.475 6.675 12702 Z= 0.251 Chirality : 0.040 0.162 1446 Planarity : 0.003 0.040 1598 Dihedral : 3.744 27.770 1269 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.28 % Allowed : 15.69 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1148 helix: 1.53 (0.27), residues: 385 sheet: 0.34 (0.31), residues: 268 loop : -0.26 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS R 258 PHE 0.009 0.001 PHE B 199 TYR 0.012 0.001 TYR B 59 ARG 0.007 0.000 ARG R 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.028 Fit side-chains REVERT: A 51 LYS cc_start: 0.7823 (pttp) cc_final: 0.7432 (ptmm) REVERT: B 258 ASP cc_start: 0.6629 (t0) cc_final: 0.6138 (t70) REVERT: R 214 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7943 (pt) REVERT: R 291 VAL cc_start: 0.8258 (t) cc_final: 0.8050 (p) outliers start: 23 outliers final: 18 residues processed: 146 average time/residue: 0.2699 time to fit residues: 51.2019 Evaluate side-chains 149 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 231 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.0050 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 93 optimal weight: 0.0980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 0.0040 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 overall best weight: 0.3006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.121434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.092744 restraints weight = 15959.740| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.75 r_work: 0.3113 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9379 Z= 0.134 Angle : 0.453 6.178 12702 Z= 0.241 Chirality : 0.040 0.164 1446 Planarity : 0.003 0.040 1598 Dihedral : 3.635 27.525 1269 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.59 % Allowed : 16.19 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1148 helix: 1.61 (0.28), residues: 385 sheet: 0.41 (0.32), residues: 267 loop : -0.22 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS R 258 PHE 0.009 0.001 PHE B 199 TYR 0.011 0.001 TYR S 190 ARG 0.007 0.000 ARG R 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2388.50 seconds wall clock time: 43 minutes 29.11 seconds (2609.11 seconds total)