Starting phenix.real_space_refine on Sun Mar 10 16:11:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwg_14187/03_2024/7qwg_14187.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwg_14187/03_2024/7qwg_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_14187/03_2024/7qwg_14187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwg_14187/03_2024/7qwg_14187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwg_14187/03_2024/7qwg_14187.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwg_14187/03_2024/7qwg_14187.pdb" } resolution = 3.38 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= 0.000 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 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. 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-5265/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: 2.27, 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: 1.26 Conformation dependent library (CDL) restraints added in 630.1 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: 0.38 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: 0.78 Time building geometry restraints manager: 1.39 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 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: 1.350 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: 6.690 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.250 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 : 0.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 0.26 % Allowed : 4.76 % Favored : 94.97 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.005 HIS A 222 PHE 0.051 0.013 PHE C 237 TYR 0.148 0.023 TYR C 143 ARG 0.005 0.001 ARG C 247 *********************** 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 : 0.384 Fit side-chains REVERT: A 140 ARG cc_start: 0.8099 (mtp85) cc_final: 0.7764 (mtp-110) REVERT: A 186 ILE cc_start: 0.8656 (mp) cc_final: 0.8405 (mt) REVERT: B 186 ILE cc_start: 0.8791 (mp) cc_final: 0.8532 (mt) REVERT: B 210 MET cc_start: 0.8244 (mtm) cc_final: 0.8038 (mtt) REVERT: C 122 ASP cc_start: 0.8460 (t0) cc_final: 0.8228 (t70) REVERT: C 140 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7384 (mmt180) REVERT: C 186 ILE cc_start: 0.8726 (mp) cc_final: 0.8520 (mt) REVERT: C 210 MET cc_start: 0.8294 (mtm) cc_final: 0.8086 (mtt) outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.1896 time to fit residues: 21.9909 Evaluate side-chains 79 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7851 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3312 Z= 0.195 Angle : 0.705 5.468 4503 Z= 0.397 Chirality : 0.054 0.150 543 Planarity : 0.003 0.014 558 Dihedral : 8.436 31.197 448 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 2.38 % Allowed : 11.11 % Favored : 86.51 % 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: -3.15 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 222 PHE 0.011 0.002 PHE B 171 TYR 0.019 0.002 TYR B 197 ARG 0.001 0.000 ARG B 140 *********************** 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 95 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.318 Fit side-chains REVERT: A 140 ARG cc_start: 0.8341 (mtp85) cc_final: 0.7512 (ttp-170) REVERT: A 206 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7615 (tt0) REVERT: B 140 ARG cc_start: 0.7730 (ttm110) cc_final: 0.7162 (mtp-110) REVERT: B 210 MET cc_start: 0.8180 (mtm) cc_final: 0.7952 (mtt) REVERT: C 140 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7506 (mmt180) REVERT: C 206 GLU cc_start: 0.7496 (tt0) cc_final: 0.6557 (tm-30) outliers start: 9 outliers final: 6 residues processed: 88 average time/residue: 0.1518 time to fit residues: 15.9213 Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 212 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.7960 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3312 Z= 0.273 Angle : 0.675 7.882 4503 Z= 0.373 Chirality : 0.054 0.152 543 Planarity : 0.003 0.013 558 Dihedral : 7.897 27.562 447 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 4.23 % Allowed : 13.23 % Favored : 82.54 % 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 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 239 PHE 0.010 0.002 PHE B 171 TYR 0.017 0.002 TYR A 143 ARG 0.001 0.000 ARG A 140 *********************** 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: 16 poor density : 80 time to evaluate : 0.363 Fit side-chains REVERT: A 124 LYS cc_start: 0.5656 (mmtt) cc_final: 0.4724 (mttt) REVERT: A 140 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7141 (ttp-170) REVERT: A 206 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7771 (tt0) REVERT: A 247 ARG cc_start: 0.8188 (ptm160) cc_final: 0.7877 (ttt180) REVERT: C 140 ARG cc_start: 0.8290 (mtp85) cc_final: 0.7503 (mmt180) REVERT: C 206 GLU cc_start: 0.7493 (tt0) cc_final: 0.6511 (tm-30) outliers start: 16 outliers final: 11 residues processed: 86 average time/residue: 0.1818 time to fit residues: 18.5278 Evaluate side-chains 81 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 229 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.0040 chunk 33 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7929 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3312 Z= 0.192 Angle : 0.602 6.014 4503 Z= 0.335 Chirality : 0.051 0.145 543 Planarity : 0.002 0.010 558 Dihedral : 7.401 26.918 447 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 5.29 % Allowed : 15.34 % Favored : 79.37 % 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: -3.23 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 239 PHE 0.009 0.001 PHE B 171 TYR 0.013 0.002 TYR C 143 ARG 0.001 0.000 ARG C 180 *********************** 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 89 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 0.352 Fit side-chains REVERT: A 124 LYS cc_start: 0.5912 (mmtt) cc_final: 0.5072 (mttt) REVERT: A 140 ARG cc_start: 0.8239 (mtp85) cc_final: 0.8017 (mtt-85) REVERT: A 148 ASN cc_start: 0.8018 (t0) cc_final: 0.7737 (t0) REVERT: A 161 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: A 247 ARG cc_start: 0.8099 (ptm160) cc_final: 0.7847 (ttt180) REVERT: C 140 ARG cc_start: 0.8293 (mtp85) cc_final: 0.7497 (mmt-90) REVERT: C 206 GLU cc_start: 0.7529 (tt0) cc_final: 0.6679 (tm-30) outliers start: 20 outliers final: 14 residues processed: 76 average time/residue: 0.1789 time to fit residues: 16.0882 Evaluate side-chains 82 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 247 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8033 moved from start: 0.3693 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= 0.365 Angle : 0.667 5.889 4503 Z= 0.369 Chirality : 0.053 0.147 543 Planarity : 0.003 0.011 558 Dihedral : 7.745 28.065 447 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 5.56 % Allowed : 16.40 % Favored : 78.04 % 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 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 239 PHE 0.011 0.002 PHE B 171 TYR 0.019 0.002 TYR C 143 ARG 0.002 0.000 ARG A 247 *********************** 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 96 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.390 Fit side-chains REVERT: A 124 LYS cc_start: 0.5875 (mmtt) cc_final: 0.4997 (mttt) REVERT: A 140 ARG cc_start: 0.8338 (mtp85) cc_final: 0.8133 (mtt-85) REVERT: A 148 ASN cc_start: 0.8116 (t0) cc_final: 0.7873 (t0) REVERT: A 205 GLU cc_start: 0.8193 (tp30) cc_final: 0.6828 (mp0) REVERT: C 140 ARG cc_start: 0.8309 (mtp85) cc_final: 0.8030 (mtt90) REVERT: C 206 GLU cc_start: 0.7583 (tt0) cc_final: 0.6690 (tm-30) outliers start: 21 outliers final: 17 residues processed: 82 average time/residue: 0.1798 time to fit residues: 17.4215 Evaluate side-chains 88 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 247 ARG 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: 0.0370 chunk 31 optimal weight: 0.0770 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7818 ------------------------------------------------------------------------------- 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: 0.7918 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3312 Z= 0.147 Angle : 0.571 5.452 4503 Z= 0.318 Chirality : 0.051 0.149 543 Planarity : 0.002 0.009 558 Dihedral : 7.109 26.547 447 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 5.56 % Allowed : 15.34 % Favored : 79.10 % 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: -3.26 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 222 PHE 0.008 0.001 PHE B 171 TYR 0.013 0.001 TYR C 211 ARG 0.001 0.000 ARG A 140 *********************** 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 96 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.6327 (mmtt) cc_final: 0.5452 (mttt) REVERT: A 205 GLU cc_start: 0.8152 (tp30) cc_final: 0.6859 (mp0) REVERT: C 140 ARG cc_start: 0.8275 (mtp85) cc_final: 0.8018 (mtt90) REVERT: C 206 GLU cc_start: 0.7528 (tt0) cc_final: 0.6652 (tm-30) outliers start: 21 outliers final: 13 residues processed: 83 average time/residue: 0.1796 time to fit residues: 17.9959 Evaluate side-chains 83 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 247 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 0.0970 chunk 23 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8075 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 3312 Z= 0.436 Angle : 0.694 6.080 4503 Z= 0.388 Chirality : 0.055 0.147 543 Planarity : 0.003 0.013 558 Dihedral : 7.840 29.557 447 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % Rotamer: Outliers : 4.76 % Allowed : 17.20 % Favored : 78.04 % 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: -3.52 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 239 PHE 0.013 0.002 PHE B 171 TYR 0.023 0.003 TYR C 143 ARG 0.002 0.000 ARG C 180 *********************** 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 97 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.422 Fit side-chains REVERT: A 124 LYS cc_start: 0.6017 (mmtt) cc_final: 0.5140 (mttt) REVERT: A 140 ARG cc_start: 0.8363 (mtp85) cc_final: 0.8122 (mtt-85) REVERT: A 205 GLU cc_start: 0.8162 (tp30) cc_final: 0.6795 (mp0) REVERT: C 140 ARG cc_start: 0.8311 (mtp85) cc_final: 0.8050 (mtt90) REVERT: C 206 GLU cc_start: 0.7591 (tt0) cc_final: 0.6656 (tm-30) outliers start: 18 outliers final: 16 residues processed: 87 average time/residue: 0.1827 time to fit residues: 18.6865 Evaluate side-chains 94 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 247 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8017 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3312 Z= 0.250 Angle : 0.620 5.959 4503 Z= 0.348 Chirality : 0.052 0.150 543 Planarity : 0.002 0.010 558 Dihedral : 7.449 29.522 447 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 4.23 % Allowed : 18.25 % Favored : 77.51 % 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: -3.46 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 239 PHE 0.010 0.002 PHE B 171 TYR 0.014 0.002 TYR C 211 ARG 0.002 0.000 ARG A 180 *********************** 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 94 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.5849 (mmtt) cc_final: 0.5078 (mttt) REVERT: A 205 GLU cc_start: 0.8125 (tp30) cc_final: 0.6834 (mp0) REVERT: C 140 ARG cc_start: 0.8311 (mtp85) cc_final: 0.8044 (mtt90) REVERT: C 206 GLU cc_start: 0.7569 (tt0) cc_final: 0.6668 (tm-30) outliers start: 16 outliers final: 14 residues processed: 84 average time/residue: 0.1749 time to fit residues: 17.4021 Evaluate side-chains 90 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 247 ARG 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: 0.6980 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.4980 chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7977 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3312 Z= 0.202 Angle : 0.601 6.406 4503 Z= 0.334 Chirality : 0.051 0.149 543 Planarity : 0.002 0.010 558 Dihedral : 7.192 28.481 447 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 4.23 % Allowed : 19.31 % Favored : 76.46 % 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 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 239 PHE 0.009 0.001 PHE B 171 TYR 0.013 0.001 TYR C 211 ARG 0.001 0.000 ARG A 140 *********************** 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 95 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.6105 (mmtt) cc_final: 0.5314 (mttt) REVERT: C 140 ARG cc_start: 0.8303 (mtp85) cc_final: 0.8024 (mtt90) REVERT: C 206 GLU cc_start: 0.7593 (tt0) cc_final: 0.6721 (tm-30) outliers start: 16 outliers final: 13 residues processed: 84 average time/residue: 0.1767 time to fit residues: 17.6588 Evaluate side-chains 89 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 247 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8087 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3312 Z= 0.472 Angle : 0.736 6.167 4503 Z= 0.409 Chirality : 0.055 0.159 543 Planarity : 0.003 0.016 558 Dihedral : 7.875 30.174 447 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 3.97 % Allowed : 20.11 % Favored : 75.93 % 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: -3.63 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 239 PHE 0.014 0.002 PHE B 171 TYR 0.022 0.003 TYR C 248 ARG 0.002 0.001 ARG C 180 ********************** 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 94 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.410 Fit side-chains REVERT: A 124 LYS cc_start: 0.6009 (mmtt) cc_final: 0.5132 (mttt) REVERT: A 140 ARG cc_start: 0.8382 (mtp85) cc_final: 0.8135 (mtt-85) REVERT: C 140 ARG cc_start: 0.8322 (mtp85) cc_final: 0.8027 (mtt90) REVERT: C 206 GLU cc_start: 0.7617 (tt0) cc_final: 0.6676 (tm-30) outliers start: 15 outliers final: 14 residues processed: 84 average time/residue: 0.1864 time to fit residues: 18.3998 Evaluate side-chains 93 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 247 ARG 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: 2.9990 chunk 1 optimal weight: 0.0870 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3833 r_free = 0.3833 target = 0.119407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.100891 restraints weight = 4216.924| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.17 r_work: 0.3522 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3312 Z= 0.238 Angle : 0.641 6.389 4503 Z= 0.357 Chirality : 0.052 0.151 543 Planarity : 0.002 0.011 558 Dihedral : 7.469 29.804 447 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 3.44 % Allowed : 21.16 % Favored : 75.40 % 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: -3.56 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 239 PHE 0.010 0.002 PHE B 171 TYR 0.014 0.002 TYR C 211 ARG 0.001 0.000 ARG A 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1314.52 seconds wall clock time: 24 minutes 44.76 seconds (1484.76 seconds total)