Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:22:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwg_14187/11_2022/7qwg_14187.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwg_14187/11_2022/7qwg_14187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwg_14187/11_2022/7qwg_14187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwg_14187/11_2022/7qwg_14187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwg_14187/11_2022/7qwg_14187.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwg_14187/11_2022/7qwg_14187.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "C TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C ARG 247": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3258 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "C" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Time building chain proxies: 2.29, per 1000 atoms: 0.70 Number of scatterers: 3258 At special positions: 0 Unit cell: (98.9, 98.9, 34.5, 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 21 16.00 O 636 8.00 N 519 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.04 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: 1.14 Conformation dependent library (CDL) restraints added in 457.9 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 55.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 139 removed outlier: 9.102A pdb=" N SER A 134 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N VAL B 137 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N ASP A 136 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N LYS B 139 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLN A 138 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N SER B 134 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N VAL C 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N ASP B 136 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N LYS C 139 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLN B 138 " --> pdb=" O LYS C 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 153 Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 160 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 185 through 187 removed outlier: 6.202A pdb=" N THR A 185 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR B 185 " --> pdb=" O ILE C 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA9, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=AB1, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.433A pdb=" N VAL A 202 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL B 202 " --> pdb=" O ILE C 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AB3, first strand: chain 'A' and resid 214 through 218 Processing sheet with id=AB4, first strand: chain 'A' and resid 225 through 230 removed outlier: 9.034A pdb=" N LEU A 226 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N GLN B 229 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N MET A 228 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR B 231 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 230 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR B 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR A 233 " --> pdb=" O THR B 234 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N TYR B 236 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR A 235 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N GLY B 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N PHE A 237 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N SER B 240 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS A 239 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N GLN B 242 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU A 241 " --> pdb=" O GLN B 242 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N SER B 244 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE A 243 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N GLU B 246 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN A 245 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR B 248 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG A 247 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N TYR B 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N GLN A 249 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP B 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N VAL A 251 " --> pdb=" O ASP B 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 225 through 230 removed outlier: 9.034A pdb=" N LEU A 226 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N GLN B 229 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N MET A 228 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR B 231 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 230 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR B 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N MET C 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N MET B 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL C 230 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N GLN B 229 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 9.906A pdb=" N VAL C 232 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N THR B 231 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N THR C 234 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR B 233 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N TYR C 236 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR B 235 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N GLY C 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE B 237 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N SER C 240 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HIS B 239 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLN C 242 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU B 241 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N SER C 244 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 243 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLU C 246 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN B 245 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR C 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG B 247 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N TYR C 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N GLN B 249 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASP C 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N VAL B 251 " --> pdb=" O ASP C 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 55 hydrogen bonds defined for protein. 165 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: 0.75 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 850 1.33 - 1.45: 594 1.45 - 1.57: 1830 1.57 - 1.69: 2 1.69 - 1.81: 36 Bond restraints: 3312 Sorted by residual: bond pdb=" CA VAL B 199 " pdb=" CB VAL B 199 " ideal model delta sigma weight residual 1.537 1.587 -0.049 1.29e-02 6.01e+03 1.47e+01 bond pdb=" N SER A 130 " pdb=" CA SER A 130 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.23e-02 6.61e+03 8.08e+00 bond pdb=" CZ ARG C 247 " pdb=" NH2 ARG C 247 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.81e+00 bond pdb=" CZ ARG B 247 " pdb=" NH2 ARG B 247 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.30e+00 bond pdb=" N LYS A 129 " pdb=" CA LYS A 129 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 7.01e+00 ... (remaining 3307 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.87: 110 105.87 - 112.86: 1417 112.86 - 119.85: 1357 119.85 - 126.84: 1581 126.84 - 133.83: 38 Bond angle restraints: 4503 Sorted by residual: angle pdb=" N LYS C 129 " pdb=" CA LYS C 129 " pdb=" C LYS C 129 " ideal model delta sigma weight residual 112.97 125.45 -12.48 1.06e+00 8.90e-01 1.39e+02 angle pdb=" N LYS A 129 " pdb=" CA LYS A 129 " pdb=" C LYS A 129 " ideal model delta sigma weight residual 112.93 125.98 -13.05 1.12e+00 7.97e-01 1.36e+02 angle pdb=" N LYS B 129 " pdb=" CA LYS B 129 " pdb=" C LYS B 129 " ideal model delta sigma weight residual 113.02 126.71 -13.69 1.20e+00 6.94e-01 1.30e+02 angle pdb=" CA VAL A 202 " pdb=" CB VAL A 202 " pdb=" CG1 VAL A 202 " ideal model delta sigma weight residual 110.40 128.62 -18.22 1.70e+00 3.46e-01 1.15e+02 angle pdb=" N ASN A 182 " pdb=" CA ASN A 182 " pdb=" C ASN A 182 " ideal model delta sigma weight residual 111.07 122.20 -11.13 1.07e+00 8.73e-01 1.08e+02 ... (remaining 4498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 1767 16.06 - 32.12: 172 32.12 - 48.18: 38 48.18 - 64.24: 11 64.24 - 80.30: 7 Dihedral angle restraints: 1995 sinusoidal: 777 harmonic: 1218 Sorted by residual: dihedral pdb=" C LYS C 129 " pdb=" N LYS C 129 " pdb=" CA LYS C 129 " pdb=" CB LYS C 129 " ideal model delta harmonic sigma weight residual -122.60 -142.38 19.78 0 2.50e+00 1.60e-01 6.26e+01 dihedral pdb=" CA GLU B 246 " pdb=" C GLU B 246 " pdb=" N ARG B 247 " pdb=" CA ARG B 247 " ideal model delta harmonic sigma weight residual 180.00 144.46 35.54 0 5.00e+00 4.00e-02 5.05e+01 dihedral pdb=" N LYS C 129 " pdb=" C LYS C 129 " pdb=" CA LYS C 129 " pdb=" CB LYS C 129 " ideal model delta harmonic sigma weight residual 122.80 140.27 -17.47 0 2.50e+00 1.60e-01 4.88e+01 ... (remaining 1992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 467 0.194 - 0.388: 67 0.388 - 0.582: 5 0.582 - 0.776: 2 0.776 - 0.970: 2 Chirality restraints: 543 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -1.66 -0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CA LYS C 129 " pdb=" N LYS C 129 " pdb=" C LYS C 129 " pdb=" CB LYS C 129 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CB VAL C 202 " pdb=" CA VAL C 202 " pdb=" CG1 VAL C 202 " pdb=" CG2 VAL C 202 " both_signs ideal model delta sigma weight residual False -2.63 -1.97 -0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 540 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 143 " 0.148 2.00e-02 2.50e+03 7.53e-02 1.13e+02 pdb=" CG TYR C 143 " -0.090 2.00e-02 2.50e+03 pdb=" CD1 TYR C 143 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 TYR C 143 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR C 143 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR C 143 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR C 143 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 143 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 248 " 0.135 2.00e-02 2.50e+03 7.28e-02 1.06e+02 pdb=" CG TYR C 248 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR C 248 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR C 248 " -0.060 2.00e-02 2.50e+03 pdb=" CE1 TYR C 248 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR C 248 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYR C 248 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 248 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 143 " 0.125 2.00e-02 2.50e+03 6.60e-02 8.70e+01 pdb=" CG TYR B 143 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR B 143 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR B 143 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR B 143 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR B 143 " -0.033 2.00e-02 2.50e+03 pdb=" CZ TYR B 143 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 143 " 0.090 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 1703 3.00 - 3.47: 2895 3.47 - 3.95: 5237 3.95 - 4.42: 5659 4.42 - 4.90: 10437 Nonbonded interactions: 25931 Sorted by model distance: nonbonded pdb=" OE1 GLU A 241 " pdb=" OG SER B 120 " model vdw 2.525 2.440 nonbonded pdb=" OE1 GLU B 241 " pdb=" OG SER C 120 " model vdw 2.528 2.440 nonbonded pdb=" OD2 ASP A 212 " pdb=" OG1 THR A 215 " model vdw 2.547 2.440 nonbonded pdb=" N ASN B 223 " pdb=" O ASN B 223 " model vdw 2.556 2.496 nonbonded pdb=" OD2 ASP C 212 " pdb=" OG1 THR C 215 " model vdw 2.567 2.440 ... (remaining 25926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2082 2.51 5 N 519 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.590 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: 6.620 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 14.040 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.012 0.051 3312 Z= 0.814 Angle : 2.341 18.216 4503 Z= 1.561 Chirality : 0.147 0.970 543 Planarity : 0.014 0.075 558 Dihedral : 14.889 80.297 1206 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer Outliers : 0.26 % Cbeta Deviations : 2.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -3.26 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.24), residues: 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.410 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.1799 time to fit residues: 20.9815 Evaluate side-chains 78 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0325 time to fit residues: 0.6084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN C 155 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3312 Z= 0.192 Angle : 0.686 4.936 4503 Z= 0.384 Chirality : 0.054 0.143 543 Planarity : 0.003 0.014 558 Dihedral : 8.297 30.291 447 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.10 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.25), residues: 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.389 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 84 average time/residue: 0.1619 time to fit residues: 16.2481 Evaluate side-chains 77 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0343 time to fit residues: 0.8374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 3312 Z= 0.355 Angle : 0.719 8.048 4503 Z= 0.401 Chirality : 0.055 0.158 543 Planarity : 0.003 0.012 558 Dihedral : 8.145 28.501 447 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer Outliers : 3.44 % 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: -3.19 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.25), residues: 399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.385 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 90 average time/residue: 0.1824 time to fit residues: 19.7510 Evaluate side-chains 81 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0370 time to fit residues: 0.9704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 0.0020 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 229 GLN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 3312 Z= 0.349 Angle : 0.674 5.171 4503 Z= 0.379 Chirality : 0.053 0.148 543 Planarity : 0.003 0.014 558 Dihedral : 7.963 26.966 447 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer Outliers : 3.97 % 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: -3.41 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.25), residues: 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.375 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 78 average time/residue: 0.1771 time to fit residues: 16.3200 Evaluate side-chains 79 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0757 time to fit residues: 1.6274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 3312 Z= 0.364 Angle : 0.687 6.672 4503 Z= 0.384 Chirality : 0.053 0.148 543 Planarity : 0.003 0.021 558 Dihedral : 7.931 28.151 447 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer Outliers : 1.06 % 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: -3.51 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.25), residues: 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.391 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 0.1851 time to fit residues: 16.7898 Evaluate side-chains 78 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0380 time to fit residues: 0.7211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 7.9990 chunk 37 optimal weight: 0.0570 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 3312 Z= 0.349 Angle : 0.686 6.665 4503 Z= 0.383 Chirality : 0.053 0.147 543 Planarity : 0.002 0.011 558 Dihedral : 7.838 29.713 447 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer Outliers : 2.38 % 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: -3.60 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.25), residues: 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.303 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 80 average time/residue: 0.1870 time to fit residues: 17.5469 Evaluate side-chains 82 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0389 time to fit residues: 1.0294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 3312 Z= 0.297 Angle : 0.665 8.649 4503 Z= 0.370 Chirality : 0.053 0.148 543 Planarity : 0.003 0.028 558 Dihedral : 7.639 29.938 447 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer Outliers : 0.79 % 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: -3.61 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.25), residues: 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.377 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 77 average time/residue: 0.1862 time to fit residues: 16.8914 Evaluate side-chains 75 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0419 time to fit residues: 0.6609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 3312 Z= 0.429 Angle : 0.735 8.858 4503 Z= 0.409 Chirality : 0.054 0.145 543 Planarity : 0.003 0.031 558 Dihedral : 7.973 30.457 447 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.76 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.25), residues: 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.401 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 0.1781 time to fit residues: 16.0025 Evaluate side-chains 76 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0366 time to fit residues: 0.6941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 3312 Z= 0.214 Angle : 0.645 8.694 4503 Z= 0.358 Chirality : 0.052 0.149 543 Planarity : 0.002 0.029 558 Dihedral : 7.381 29.621 447 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer Outliers : 0.26 % 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: -3.64 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.26), residues: 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.401 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 0.1725 time to fit residues: 17.4273 Evaluate side-chains 84 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.406 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0355 time to fit residues: 0.6063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 31 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: A 229 GLN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 3312 Z= 0.342 Angle : 0.676 6.795 4503 Z= 0.378 Chirality : 0.052 0.147 543 Planarity : 0.003 0.028 558 Dihedral : 7.594 29.690 447 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer Outliers : 0.79 % 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: -3.71 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.26), residues: 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.405 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.1761 time to fit residues: 16.4619 Evaluate side-chains 77 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0583 time to fit residues: 0.7428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.120060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.102492 restraints weight = 4357.055| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.22 r_work: 0.3621 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work: 0.3601 rms_B_bonded: 2.00 restraints_weight: 0.1250 r_work: 0.3590 rms_B_bonded: 2.06 restraints_weight: 0.0625 r_work: 0.3578 rms_B_bonded: 2.16 restraints_weight: 0.0312 r_work: 0.3566 rms_B_bonded: 2.29 restraints_weight: 0.0156 r_work: 0.3553 rms_B_bonded: 2.45 restraints_weight: 0.0078 r_work: 0.3539 rms_B_bonded: 2.63 restraints_weight: 0.0039 r_work: 0.3523 rms_B_bonded: 2.86 restraints_weight: 0.0020 r_work: 0.3506 rms_B_bonded: 3.12 restraints_weight: 0.0010 r_work: 0.3488 rms_B_bonded: 3.42 restraints_weight: 0.0005 r_work: 0.3468 rms_B_bonded: 3.76 restraints_weight: 0.0002 r_work: 0.3446 rms_B_bonded: 4.16 restraints_weight: 0.0001 r_work: 0.3423 rms_B_bonded: 4.61 restraints_weight: 0.0001 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 3312 Z= 0.342 Angle : 0.687 6.696 4503 Z= 0.385 Chirality : 0.053 0.148 543 Planarity : 0.003 0.026 558 Dihedral : 7.665 30.286 447 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.71 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.26), residues: 399 =============================================================================== Job complete usr+sys time: 1159.65 seconds wall clock time: 21 minutes 41.59 seconds (1301.59 seconds total)