Starting phenix.real_space_refine on Fri Nov 15 14:55:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg1_40450/11_2024/8sg1_40450.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg1_40450/11_2024/8sg1_40450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg1_40450/11_2024/8sg1_40450.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg1_40450/11_2024/8sg1_40450.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg1_40450/11_2024/8sg1_40450.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg1_40450/11_2024/8sg1_40450.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 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 66 5.16 5 C 5669 2.51 5 N 1490 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8846 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2172 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} 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: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 3 Chain: "L" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 77 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "E" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'CLR': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.40, per 1000 atoms: 0.61 Number of scatterers: 8846 At special positions: 0 Unit cell: (94.976, 119.568, 125.504, 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 66 16.00 O 1621 8.00 N 1490 7.00 C 5669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 189 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 36.2% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'R' and resid 36 through 65 removed outlier: 3.929A pdb=" N ILE R 41 " --> pdb=" O ARG R 37 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 92 removed outlier: 3.830A pdb=" N TRP R 77 " --> pdb=" O VAL R 73 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE R 88 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 101 Processing helix chain 'R' and resid 108 through 112 Processing helix chain 'R' and resid 114 through 126 Processing helix chain 'R' and resid 127 through 143 removed outlier: 3.802A pdb=" N SER R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 150 removed outlier: 3.641A pdb=" N ASN R 149 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 172 removed outlier: 3.648A pdb=" N ALA R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 177 removed outlier: 3.921A pdb=" N VAL R 176 " --> pdb=" O SER R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 251 removed outlier: 5.043A pdb=" N VAL R 231 " --> pdb=" O CYS R 227 " (cutoff:3.500A) Proline residue: R 232 - end of helix Processing helix chain 'R' and resid 256 through 283 removed outlier: 3.617A pdb=" N ILE R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 284 through 286 No H-bonds generated for 'chain 'R' and resid 284 through 286' Processing helix chain 'R' and resid 291 through 307 removed outlier: 3.758A pdb=" N LEU R 296 " --> pdb=" O SER R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix removed outlier: 3.889A pdb=" N ALA R 307 " --> pdb=" O ALA R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 312 removed outlier: 3.692A pdb=" N MET R 311 " --> pdb=" O ALA R 307 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN R 312 " --> pdb=" O ASN R 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 307 through 312' Processing helix chain 'R' and resid 312 through 317 removed outlier: 3.522A pdb=" N VAL R 317 " --> pdb=" O PRO R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 327 removed outlier: 4.031A pdb=" N PHE R 326 " --> pdb=" O ASP R 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.566A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 21 removed outlier: 4.235A pdb=" N MET G 21 " --> pdb=" O GLN G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'A' and resid 6 through 30 removed outlier: 3.853A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.197A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.689A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.576A pdb=" N GLY A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 221 through 225 removed outlier: 4.121A pdb=" N VAL E 225 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 183 Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.403A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.678A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.910A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.645A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.611A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.580A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.637A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.286A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.419A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 141 through 142 removed outlier: 3.714A pdb=" N VAL E 156 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 195 through 196 removed outlier: 6.674A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY E 226 " --> pdb=" O LEU E 246 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1143 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: 2.51 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1412 1.31 - 1.44: 2497 1.44 - 1.56: 5028 1.56 - 1.69: 2 1.69 - 1.81: 95 Bond restraints: 9034 Sorted by residual: bond pdb=" C CYS R 272 " pdb=" O CYS R 272 " ideal model delta sigma weight residual 1.236 1.325 -0.089 1.15e-02 7.56e+03 5.93e+01 bond pdb=" C THR R 268 " pdb=" O THR R 268 " ideal model delta sigma weight residual 1.236 1.304 -0.068 1.15e-02 7.56e+03 3.45e+01 bond pdb=" C TRP R 273 " pdb=" O TRP R 273 " ideal model delta sigma weight residual 1.237 1.189 0.047 1.19e-02 7.06e+03 1.58e+01 bond pdb=" C PHE R 270 " pdb=" O PHE R 270 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.16e-02 7.43e+03 1.47e+01 bond pdb=" C ILE R 266 " pdb=" O ILE R 266 " ideal model delta sigma weight residual 1.237 1.277 -0.041 1.12e-02 7.97e+03 1.33e+01 ... (remaining 9029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 12136 3.97 - 7.94: 85 7.94 - 11.91: 9 11.91 - 15.88: 0 15.88 - 19.85: 1 Bond angle restraints: 12231 Sorted by residual: angle pdb=" CA PRO R 275 " pdb=" N PRO R 275 " pdb=" CD PRO R 275 " ideal model delta sigma weight residual 112.00 92.15 19.85 1.40e+00 5.10e-01 2.01e+02 angle pdb=" N MET R 111 " pdb=" CA MET R 111 " pdb=" C MET R 111 " ideal model delta sigma weight residual 112.88 103.50 9.38 1.29e+00 6.01e-01 5.29e+01 angle pdb=" N VAL R 73 " pdb=" CA VAL R 73 " pdb=" C VAL R 73 " ideal model delta sigma weight residual 113.42 105.36 8.06 1.17e+00 7.31e-01 4.75e+01 angle pdb=" N CYS R 112 " pdb=" CA CYS R 112 " pdb=" C CYS R 112 " ideal model delta sigma weight residual 114.56 106.02 8.54 1.27e+00 6.20e-01 4.52e+01 angle pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " pdb=" CG TYR E 236 " ideal model delta sigma weight residual 113.90 103.37 10.53 1.80e+00 3.09e-01 3.42e+01 ... (remaining 12226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 4877 17.47 - 34.94: 408 34.94 - 52.41: 91 52.41 - 69.88: 14 69.88 - 87.34: 7 Dihedral angle restraints: 5397 sinusoidal: 2131 harmonic: 3266 Sorted by residual: dihedral pdb=" C TYR E 236 " pdb=" N TYR E 236 " pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " ideal model delta harmonic sigma weight residual -122.60 -145.35 22.75 0 2.50e+00 1.60e-01 8.28e+01 dihedral pdb=" N TYR E 236 " pdb=" C TYR E 236 " pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " ideal model delta harmonic sigma weight residual 122.80 144.39 -21.59 0 2.50e+00 1.60e-01 7.46e+01 dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 138.69 -45.69 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 5394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 1375 0.184 - 0.368: 19 0.368 - 0.552: 0 0.552 - 0.737: 0 0.737 - 0.921: 1 Chirality restraints: 1395 Sorted by residual: chirality pdb=" CA TYR E 236 " pdb=" N TYR E 236 " pdb=" C TYR E 236 " pdb=" CB TYR E 236 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CA MET R 101 " pdb=" N MET R 101 " pdb=" C MET R 101 " pdb=" CB MET R 101 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA MET R 111 " pdb=" N MET R 111 " pdb=" C MET R 111 " pdb=" CB MET R 111 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 1392 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS R 274 " -0.127 5.00e-02 4.00e+02 1.73e-01 4.78e+01 pdb=" N PRO R 275 " 0.298 5.00e-02 4.00e+02 pdb=" CA PRO R 275 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO R 275 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 271 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C LEU R 271 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU R 271 " 0.027 2.00e-02 2.50e+03 pdb=" N CYS R 272 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 275 " 0.021 2.00e-02 2.50e+03 4.21e-02 1.78e+01 pdb=" C PRO R 275 " -0.073 2.00e-02 2.50e+03 pdb=" O PRO R 275 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR R 276 " 0.025 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1528 2.77 - 3.30: 7933 3.30 - 3.83: 14018 3.83 - 4.37: 17055 4.37 - 4.90: 30530 Nonbonded interactions: 71064 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.235 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.246 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR E 151 " pdb=" OE1 GLU E 154 " model vdw 2.263 3.040 nonbonded pdb=" O THR E 145 " pdb=" OG1 THR E 244 " model vdw 2.265 3.040 ... (remaining 71059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.050 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 : 0.005 0.089 9034 Z= 0.342 Angle : 0.890 19.854 12231 Z= 0.605 Chirality : 0.063 0.921 1395 Planarity : 0.007 0.173 1532 Dihedral : 13.730 87.345 3276 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.78 % Allowed : 17.49 % Favored : 80.73 % Cbeta Deviations : 0.19 % 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: 0.06 (0.25), residues: 1105 helix: 0.90 (0.30), residues: 351 sheet: 0.41 (0.31), residues: 281 loop : -0.79 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 273 HIS 0.013 0.001 HIS B 225 PHE 0.029 0.001 PHE L 154 TYR 0.061 0.002 TYR E 236 ARG 0.009 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 275 PRO cc_start: 0.6854 (OUTLIER) cc_final: 0.6601 (Cg_exo) REVERT: B 197 ARG cc_start: 0.7576 (mmt90) cc_final: 0.7074 (mpt180) REVERT: E 235 GLU cc_start: 0.7585 (mt-10) cc_final: 0.6745 (mm-30) outliers start: 17 outliers final: 15 residues processed: 128 average time/residue: 1.2313 time to fit residues: 169.1749 Evaluate side-chains 121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 275 PRO Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 74 ASN R 150 HIS B 175 GLN B 266 HIS B 340 ASN G 59 ASN A 331 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9034 Z= 0.164 Angle : 0.543 7.389 12231 Z= 0.286 Chirality : 0.042 0.208 1395 Planarity : 0.004 0.052 1532 Dihedral : 5.968 58.917 1324 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.09 % Allowed : 17.17 % Favored : 80.73 % 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: 0.45 (0.25), residues: 1105 helix: 1.51 (0.29), residues: 362 sheet: 0.52 (0.30), residues: 280 loop : -0.79 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 PHE 0.019 0.001 PHE R 259 TYR 0.018 0.001 TYR E 191 ARG 0.003 0.000 ARG R 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 111 MET cc_start: 0.6829 (tpp) cc_final: 0.6554 (tpp) REVERT: B 215 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7515 (mm-30) REVERT: B 219 ARG cc_start: 0.7158 (ttm-80) cc_final: 0.6805 (mtt-85) REVERT: E 173 THR cc_start: 0.7946 (OUTLIER) cc_final: 0.7632 (t) REVERT: E 235 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6632 (mm-30) REVERT: E 236 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.5287 (t80) outliers start: 20 outliers final: 7 residues processed: 115 average time/residue: 1.1963 time to fit residues: 147.3535 Evaluate side-chains 104 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 82 optimal weight: 0.0670 chunk 67 optimal weight: 0.0980 chunk 27 optimal weight: 20.0000 chunk 99 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.4324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9034 Z= 0.223 Angle : 0.549 7.365 12231 Z= 0.288 Chirality : 0.043 0.246 1395 Planarity : 0.004 0.052 1532 Dihedral : 5.650 54.554 1308 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.14 % Allowed : 17.17 % Favored : 79.69 % 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: 0.56 (0.25), residues: 1105 helix: 1.80 (0.29), residues: 361 sheet: 0.41 (0.30), residues: 283 loop : -0.79 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.005 0.001 HIS E 233 PHE 0.021 0.001 PHE R 169 TYR 0.019 0.001 TYR E 236 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: R 271 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6795 (mp) REVERT: B 214 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7320 (mtm180) REVERT: B 215 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7691 (mm-30) REVERT: B 217 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7627 (pmm) REVERT: B 219 ARG cc_start: 0.7212 (ttm-80) cc_final: 0.6858 (mtt-85) REVERT: G 28 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.7005 (pp) REVERT: A 53 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6372 (mtp) REVERT: E 203 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6990 (mtp180) REVERT: E 235 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6764 (mm-30) REVERT: E 246 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6771 (mp) outliers start: 30 outliers final: 11 residues processed: 127 average time/residue: 1.1601 time to fit residues: 158.1132 Evaluate side-chains 117 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 250 ASN B 35 ASN B 175 GLN A 304 GLN A 322 HIS A 331 ASN E 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9034 Z= 0.390 Angle : 0.643 8.096 12231 Z= 0.336 Chirality : 0.047 0.276 1395 Planarity : 0.005 0.056 1532 Dihedral : 6.262 57.491 1308 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.87 % Allowed : 17.28 % Favored : 78.85 % 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: 0.35 (0.25), residues: 1105 helix: 1.64 (0.29), residues: 361 sheet: 0.29 (0.30), residues: 282 loop : -0.91 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 47 HIS 0.006 0.001 HIS E 35 PHE 0.027 0.002 PHE R 169 TYR 0.025 0.002 TYR E 236 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: R 271 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6759 (mp) REVERT: B 214 ARG cc_start: 0.7690 (mtt-85) cc_final: 0.7278 (mtm180) REVERT: B 215 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7592 (mm-30) REVERT: B 219 ARG cc_start: 0.7278 (ttm-80) cc_final: 0.6817 (mtt-85) REVERT: G 28 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6848 (pp) REVERT: A 53 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6049 (mtp) REVERT: E 38 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7776 (ttp-170) REVERT: E 62 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7091 (p0) REVERT: E 203 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7069 (mtp180) REVERT: E 235 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7073 (mt-10) REVERT: E 246 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6828 (mp) outliers start: 37 outliers final: 17 residues processed: 133 average time/residue: 1.1128 time to fit residues: 159.0740 Evaluate side-chains 129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 0.4980 chunk 94 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 250 ASN B 175 GLN A 304 GLN A 331 ASN E 82 GLN E 232 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9034 Z= 0.151 Angle : 0.514 7.542 12231 Z= 0.267 Chirality : 0.042 0.200 1395 Planarity : 0.004 0.051 1532 Dihedral : 5.608 56.778 1307 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.04 % Allowed : 18.32 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.25), residues: 1105 helix: 1.81 (0.29), residues: 367 sheet: 0.35 (0.30), residues: 282 loop : -0.86 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE E 68 TYR 0.015 0.001 TYR E 236 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: R 271 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6792 (mp) REVERT: B 214 ARG cc_start: 0.7619 (mtt-85) cc_final: 0.7212 (mtm180) REVERT: B 215 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 219 ARG cc_start: 0.7191 (ttm-80) cc_final: 0.6846 (mtt-85) REVERT: G 28 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6990 (pp) REVERT: G 47 GLU cc_start: 0.8084 (pt0) cc_final: 0.7752 (pt0) REVERT: A 247 MET cc_start: 0.7781 (mtp) cc_final: 0.7490 (mtp) REVERT: E 203 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7259 (mtp180) REVERT: E 231 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.6906 (tpt) REVERT: E 235 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6889 (mt-10) outliers start: 29 outliers final: 11 residues processed: 127 average time/residue: 1.2077 time to fit residues: 164.5525 Evaluate side-chains 119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 231 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 88 ASN B 175 GLN A 304 GLN E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9034 Z= 0.358 Angle : 0.624 10.557 12231 Z= 0.322 Chirality : 0.046 0.250 1395 Planarity : 0.004 0.055 1532 Dihedral : 5.977 58.086 1307 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.56 % Allowed : 18.22 % Favored : 78.22 % 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: 0.41 (0.25), residues: 1105 helix: 1.73 (0.28), residues: 365 sheet: 0.31 (0.29), residues: 282 loop : -0.94 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.017 0.002 PHE E 68 TYR 0.026 0.002 TYR E 236 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: R 271 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6728 (mp) REVERT: B 214 ARG cc_start: 0.7636 (mtt-85) cc_final: 0.7226 (mtm180) REVERT: B 215 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7497 (mm-30) REVERT: G 28 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6918 (pp) REVERT: E 62 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7097 (p0) REVERT: E 203 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7219 (mtp180) REVERT: E 231 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7168 (tpt) REVERT: E 235 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7058 (mt-10) REVERT: E 246 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6880 (mp) outliers start: 34 outliers final: 18 residues processed: 134 average time/residue: 1.1269 time to fit residues: 162.2724 Evaluate side-chains 129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.4980 chunk 60 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9034 Z= 0.157 Angle : 0.522 10.817 12231 Z= 0.268 Chirality : 0.042 0.196 1395 Planarity : 0.004 0.050 1532 Dihedral : 5.485 59.768 1307 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.72 % Allowed : 20.10 % Favored : 77.17 % 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: 1105 helix: 1.90 (0.29), residues: 366 sheet: 0.43 (0.30), residues: 280 loop : -0.85 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 PHE 0.028 0.001 PHE R 169 TYR 0.015 0.001 TYR E 191 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: R 271 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6822 (mp) REVERT: B 214 ARG cc_start: 0.7680 (mtt-85) cc_final: 0.7174 (mmm-85) REVERT: B 215 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7436 (mm-30) REVERT: B 217 MET cc_start: 0.8222 (pmt) cc_final: 0.7498 (ppp) REVERT: G 28 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.6995 (pp) REVERT: G 47 GLU cc_start: 0.8084 (pt0) cc_final: 0.7752 (pt0) REVERT: A 247 MET cc_start: 0.7750 (mtp) cc_final: 0.7446 (mtp) REVERT: E 62 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7146 (p0) REVERT: E 203 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7335 (mtp180) REVERT: E 231 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.6859 (tpt) REVERT: E 235 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6905 (mt-10) REVERT: E 246 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6843 (mp) outliers start: 26 outliers final: 13 residues processed: 122 average time/residue: 1.1971 time to fit residues: 156.6057 Evaluate side-chains 120 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9034 Z= 0.166 Angle : 0.530 10.904 12231 Z= 0.271 Chirality : 0.042 0.188 1395 Planarity : 0.004 0.054 1532 Dihedral : 5.375 58.593 1307 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.51 % Allowed : 20.52 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1105 helix: 1.97 (0.29), residues: 365 sheet: 0.44 (0.30), residues: 282 loop : -0.85 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 PHE 0.027 0.001 PHE R 169 TYR 0.017 0.001 TYR E 236 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.863 Fit side-chains REVERT: R 271 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6796 (mp) REVERT: B 214 ARG cc_start: 0.7670 (mtt-85) cc_final: 0.7162 (mmm-85) REVERT: B 215 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7584 (mm-30) REVERT: B 217 MET cc_start: 0.8236 (pmt) cc_final: 0.7751 (pmm) REVERT: G 28 ILE cc_start: 0.7248 (OUTLIER) cc_final: 0.7012 (pp) REVERT: G 47 GLU cc_start: 0.8075 (pt0) cc_final: 0.7729 (pt0) REVERT: E 11 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7464 (mp) REVERT: E 62 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7076 (p0) REVERT: E 235 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6892 (mt-10) outliers start: 24 outliers final: 12 residues processed: 121 average time/residue: 1.2159 time to fit residues: 157.7010 Evaluate side-chains 116 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 232 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9034 Z= 0.262 Angle : 0.581 12.102 12231 Z= 0.296 Chirality : 0.044 0.224 1395 Planarity : 0.004 0.053 1532 Dihedral : 5.492 58.395 1305 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.51 % Allowed : 20.52 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1105 helix: 1.90 (0.29), residues: 366 sheet: 0.38 (0.29), residues: 282 loop : -0.85 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 77 HIS 0.005 0.001 HIS E 233 PHE 0.022 0.001 PHE R 169 TYR 0.023 0.002 TYR E 236 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 1.153 Fit side-chains REVERT: R 271 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6777 (mp) REVERT: B 214 ARG cc_start: 0.7688 (mtt-85) cc_final: 0.7149 (mmm-85) REVERT: B 215 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 217 MET cc_start: 0.8175 (pmt) cc_final: 0.7703 (pmm) REVERT: G 28 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6981 (pp) REVERT: E 62 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7064 (p0) REVERT: E 235 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6948 (mt-10) outliers start: 24 outliers final: 18 residues processed: 121 average time/residue: 1.1584 time to fit residues: 150.6442 Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 232 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 99 optimal weight: 9.9990 chunk 86 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9034 Z= 0.171 Angle : 0.544 12.619 12231 Z= 0.277 Chirality : 0.042 0.200 1395 Planarity : 0.004 0.051 1532 Dihedral : 5.345 57.835 1305 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.41 % Allowed : 20.73 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1105 helix: 1.97 (0.29), residues: 366 sheet: 0.47 (0.30), residues: 281 loop : -0.82 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 PHE 0.023 0.001 PHE R 169 TYR 0.016 0.001 TYR E 236 ARG 0.003 0.000 ARG B 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 1.052 Fit side-chains REVERT: B 214 ARG cc_start: 0.7577 (mtt-85) cc_final: 0.7109 (mmm-85) REVERT: B 215 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B 217 MET cc_start: 0.8189 (pmt) cc_final: 0.7705 (pmm) REVERT: G 28 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.7011 (pp) REVERT: E 11 LEU cc_start: 0.7983 (tt) cc_final: 0.7496 (mp) REVERT: E 62 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7055 (p0) REVERT: E 235 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6916 (mt-10) outliers start: 23 outliers final: 17 residues processed: 118 average time/residue: 1.2449 time to fit residues: 157.6788 Evaluate side-chains 119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 232 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.0670 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.153923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106676 restraints weight = 10459.175| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.34 r_work: 0.3061 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9034 Z= 0.151 Angle : 0.531 13.674 12231 Z= 0.268 Chirality : 0.042 0.185 1395 Planarity : 0.004 0.052 1532 Dihedral : 5.209 57.511 1305 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.99 % Allowed : 21.05 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1105 helix: 2.00 (0.29), residues: 367 sheet: 0.50 (0.30), residues: 281 loop : -0.80 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 PHE 0.023 0.001 PHE R 169 TYR 0.017 0.001 TYR E 236 ARG 0.002 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3297.59 seconds wall clock time: 60 minutes 25.24 seconds (3625.24 seconds total)