Starting phenix.real_space_refine on Sat Aug 3 17:25:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/08_2024/8ykw_39374_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/08_2024/8ykw_39374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/08_2024/8ykw_39374.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/08_2024/8ykw_39374.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/08_2024/8ykw_39374_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/08_2024/8ykw_39374_neut.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.081 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 55 5.16 5 C 5574 2.51 5 N 1481 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "R GLU 33": "OE1" <-> "OE2" Residue "R PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 153": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8718 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1713 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 210} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2560 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1719 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 440 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2278 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 271} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SIN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.82, per 1000 atoms: 0.55 Number of scatterers: 8718 At special positions: 0 Unit cell: (86.1, 119.72, 135.3, 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 55 16.00 O 1608 8.00 N 1481 7.00 C 5574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 268 " distance=2.30 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.4 seconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 39.2% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.746A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.407A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.161A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.951A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.701A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 11 through 24 Processing helix chain 'R' and resid 24 through 49 Processing helix chain 'R' and resid 56 through 74 Processing helix chain 'R' and resid 75 through 86 removed outlier: 4.008A pdb=" N LEU R 79 " --> pdb=" O THR R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 126 removed outlier: 3.664A pdb=" N ILE R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 134 Processing helix chain 'R' and resid 135 through 155 Processing helix chain 'R' and resid 156 through 158 No H-bonds generated for 'chain 'R' and resid 156 through 158' Processing helix chain 'R' and resid 180 through 196 removed outlier: 3.603A pdb=" N ILE R 186 " --> pdb=" O ASN R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 217 Processing helix chain 'R' and resid 227 through 260 removed outlier: 3.563A pdb=" N VAL R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) Proline residue: R 247 - end of helix Processing helix chain 'R' and resid 269 through 286 removed outlier: 3.534A pdb=" N ILE R 273 " --> pdb=" O THR R 269 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A) Proline residue: R 282 - end of helix Processing helix chain 'R' and resid 286 through 297 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 309 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.082A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.664A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.690A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.746A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.257A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.545A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.421A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.725A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.938A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.416A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.375A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.869A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1410 1.31 - 1.44: 2459 1.44 - 1.57: 4948 1.57 - 1.69: 2 1.69 - 1.82: 78 Bond restraints: 8897 Sorted by residual: bond pdb=" CA LEU E 233 " pdb=" C LEU E 233 " ideal model delta sigma weight residual 1.524 1.451 0.073 1.32e-02 5.74e+03 3.05e+01 bond pdb=" CA LEU E 237 " pdb=" C LEU E 237 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.30e-02 5.92e+03 2.37e+01 bond pdb=" CA VAL A 233 " pdb=" C VAL A 233 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.08e-02 8.57e+03 2.21e+01 bond pdb=" CA THR R 246 " pdb=" C THR R 246 " ideal model delta sigma weight residual 1.521 1.571 -0.049 1.17e-02 7.31e+03 1.77e+01 bond pdb=" C LEU E 237 " pdb=" O LEU E 237 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.23e-02 6.61e+03 1.53e+01 ... (remaining 8892 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.59: 281 107.59 - 114.75: 5199 114.75 - 121.91: 4778 121.91 - 129.08: 1741 129.08 - 136.24: 62 Bond angle restraints: 12061 Sorted by residual: angle pdb=" C LYS R 229 " pdb=" N PRO R 230 " pdb=" CA PRO R 230 " ideal model delta sigma weight residual 119.05 111.98 7.07 1.11e+00 8.12e-01 4.06e+01 angle pdb=" N GLN R 270 " pdb=" CA GLN R 270 " pdb=" C GLN R 270 " ideal model delta sigma weight residual 112.23 104.57 7.66 1.26e+00 6.30e-01 3.70e+01 angle pdb=" N LEU A 232 " pdb=" CA LEU A 232 " pdb=" C LEU A 232 " ideal model delta sigma weight residual 110.55 102.91 7.64 1.35e+00 5.49e-01 3.20e+01 angle pdb=" O LYS R 229 " pdb=" C LYS R 229 " pdb=" N PRO R 230 " ideal model delta sigma weight residual 120.48 124.76 -4.28 8.90e-01 1.26e+00 2.31e+01 angle pdb=" CA LYS R 229 " pdb=" C LYS R 229 " pdb=" N PRO R 230 " ideal model delta sigma weight residual 120.77 116.60 4.17 9.70e-01 1.06e+00 1.85e+01 ... (remaining 12056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4725 17.91 - 35.82: 410 35.82 - 53.73: 107 53.73 - 71.63: 14 71.63 - 89.54: 8 Dihedral angle restraints: 5264 sinusoidal: 1998 harmonic: 3266 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1182 0.055 - 0.109: 156 0.109 - 0.164: 37 0.164 - 0.219: 1 0.219 - 0.273: 4 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CA TYR E 235 " pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CB TYR E 235 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ILE R 278 " pdb=" N ILE R 278 " pdb=" C ILE R 278 " pdb=" CB ILE R 278 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA THR E 238 " pdb=" N THR E 238 " pdb=" C THR E 238 " pdb=" CB THR E 238 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1377 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 150 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO E 151 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 245 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C PHE R 245 " -0.040 2.00e-02 2.50e+03 pdb=" O PHE R 245 " 0.015 2.00e-02 2.50e+03 pdb=" N THR R 246 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 291 " -0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO R 292 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO R 292 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 292 " -0.031 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1688 2.77 - 3.30: 8501 3.30 - 3.84: 14751 3.84 - 4.37: 18209 4.37 - 4.90: 31450 Nonbonded interactions: 74599 Sorted by model distance: nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.239 3.040 nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.248 3.040 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.277 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.284 3.040 nonbonded pdb=" O ASN R 274 " pdb=" N TYR R 277 " model vdw 2.313 3.120 ... (remaining 74594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.190 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.004 0.073 8897 Z= 0.252 Angle : 0.652 11.238 12061 Z= 0.374 Chirality : 0.043 0.273 1380 Planarity : 0.005 0.068 1523 Dihedral : 14.747 89.543 3153 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.54 % Allowed : 15.09 % Favored : 84.38 % 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: 1.10 (0.26), residues: 1100 helix: 1.71 (0.27), residues: 383 sheet: 0.32 (0.29), residues: 307 loop : 0.27 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 88 HIS 0.005 0.001 HIS A 188 PHE 0.013 0.001 PHE R 34 TYR 0.016 0.001 TYR R 83 ARG 0.014 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 0.898 Fit side-chains REVERT: A 33 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7386 (mm-30) REVERT: B 46 ARG cc_start: 0.8073 (ptm160) cc_final: 0.7854 (ptm160) REVERT: B 219 ARG cc_start: 0.7946 (mmm160) cc_final: 0.7352 (mmt-90) REVERT: E 46 GLU cc_start: 0.8026 (tt0) cc_final: 0.7812 (tt0) REVERT: R 189 MET cc_start: 0.8267 (mmm) cc_final: 0.8018 (mmm) outliers start: 5 outliers final: 2 residues processed: 146 average time/residue: 1.3001 time to fit residues: 201.2855 Evaluate side-chains 121 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain E residue 193 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 255 ASN A 269 ASN A 331 ASN A 333 GLN B 75 GLN B 259 GLN E 77 ASN E 179 GLN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8897 Z= 0.213 Angle : 0.558 9.305 12061 Z= 0.300 Chirality : 0.043 0.153 1380 Planarity : 0.004 0.039 1523 Dihedral : 4.602 37.606 1221 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.59 % Allowed : 14.66 % Favored : 82.76 % 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: 1.60 (0.26), residues: 1100 helix: 2.31 (0.25), residues: 388 sheet: 0.43 (0.31), residues: 293 loop : 0.47 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.014 0.001 PHE A 274 TYR 0.022 0.001 TYR R 48 ARG 0.007 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 0.951 Fit side-chains REVERT: A 298 GLU cc_start: 0.8227 (tt0) cc_final: 0.7844 (tt0) REVERT: B 214 ARG cc_start: 0.8049 (mmt-90) cc_final: 0.7810 (mmp80) REVERT: B 219 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7286 (mmt-90) REVERT: B 267 ASP cc_start: 0.7765 (m-30) cc_final: 0.7444 (m-30) REVERT: E 46 GLU cc_start: 0.8034 (tt0) cc_final: 0.7807 (tt0) REVERT: E 229 CYS cc_start: 0.8429 (p) cc_final: 0.8165 (p) REVERT: R 189 MET cc_start: 0.8433 (mmm) cc_final: 0.8042 (mmm) REVERT: R 193 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7615 (tt) REVERT: R 253 ASN cc_start: 0.8743 (m-40) cc_final: 0.8382 (m-40) outliers start: 24 outliers final: 9 residues processed: 151 average time/residue: 1.2113 time to fit residues: 194.6736 Evaluate side-chains 129 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 193 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 311 ASN A 331 ASN B 75 GLN B 259 GLN E 39 GLN E 77 ASN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8897 Z= 0.401 Angle : 0.615 9.791 12061 Z= 0.327 Chirality : 0.046 0.162 1380 Planarity : 0.004 0.038 1523 Dihedral : 4.577 21.267 1218 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.20 % Allowed : 15.52 % Favored : 80.28 % 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: 1.46 (0.25), residues: 1100 helix: 2.24 (0.25), residues: 388 sheet: 0.41 (0.30), residues: 293 loop : 0.28 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS G 44 PHE 0.016 0.002 PHE R 115 TYR 0.019 0.002 TYR R 48 ARG 0.007 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 134 time to evaluate : 0.963 Fit side-chains REVERT: A 298 GLU cc_start: 0.8236 (tt0) cc_final: 0.7878 (tt0) REVERT: B 219 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7184 (mmt180) REVERT: E 46 GLU cc_start: 0.8128 (tt0) cc_final: 0.7903 (tt0) REVERT: E 183 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8180 (mt0) REVERT: E 244 LYS cc_start: 0.8362 (ttpp) cc_final: 0.8082 (tttm) REVERT: R 189 MET cc_start: 0.8494 (mmm) cc_final: 0.8090 (mmm) REVERT: R 193 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7695 (tt) REVERT: R 253 ASN cc_start: 0.8769 (m-40) cc_final: 0.8413 (m-40) outliers start: 39 outliers final: 17 residues processed: 153 average time/residue: 1.1746 time to fit residues: 191.9294 Evaluate side-chains 143 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 311 ASN A 331 ASN B 75 GLN B 237 ASN B 239 ASN B 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8897 Z= 0.218 Angle : 0.542 9.790 12061 Z= 0.288 Chirality : 0.043 0.155 1380 Planarity : 0.004 0.042 1523 Dihedral : 4.303 21.961 1218 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.56 % Allowed : 16.92 % Favored : 79.53 % 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: 1.58 (0.25), residues: 1100 helix: 2.48 (0.25), residues: 388 sheet: 0.45 (0.30), residues: 291 loop : 0.22 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.010 0.001 HIS B 266 PHE 0.018 0.001 PHE A 274 TYR 0.023 0.001 TYR R 48 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.061 Fit side-chains REVERT: A 298 GLU cc_start: 0.8220 (tt0) cc_final: 0.7864 (tt0) REVERT: B 219 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7200 (mmt180) REVERT: E 46 GLU cc_start: 0.8102 (tt0) cc_final: 0.7893 (tt0) REVERT: E 244 LYS cc_start: 0.8402 (ttpp) cc_final: 0.8135 (tttm) REVERT: R 189 MET cc_start: 0.8509 (mmm) cc_final: 0.8087 (mmm) REVERT: R 253 ASN cc_start: 0.8741 (m-40) cc_final: 0.8404 (m-40) outliers start: 33 outliers final: 18 residues processed: 152 average time/residue: 1.1419 time to fit residues: 185.5671 Evaluate side-chains 143 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 234 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9980 chunk 60 optimal weight: 0.0870 chunk 1 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 73 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 75 GLN B 259 GLN E 77 ASN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8897 Z= 0.170 Angle : 0.524 10.473 12061 Z= 0.276 Chirality : 0.041 0.160 1380 Planarity : 0.004 0.055 1523 Dihedral : 4.057 20.965 1218 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.69 % Allowed : 18.00 % Favored : 79.31 % 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: 1.67 (0.26), residues: 1100 helix: 2.63 (0.25), residues: 388 sheet: 0.44 (0.30), residues: 291 loop : 0.24 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.008 0.001 HIS B 266 PHE 0.019 0.001 PHE A 274 TYR 0.025 0.001 TYR R 48 ARG 0.004 0.000 ARG R 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 0.972 Fit side-chains REVERT: A 298 GLU cc_start: 0.8276 (tt0) cc_final: 0.7915 (tt0) REVERT: B 219 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7265 (mmt-90) REVERT: B 267 ASP cc_start: 0.7838 (m-30) cc_final: 0.7568 (m-30) REVERT: E 46 GLU cc_start: 0.8097 (tt0) cc_final: 0.7860 (tt0) REVERT: E 229 CYS cc_start: 0.8432 (p) cc_final: 0.8219 (p) REVERT: E 244 LYS cc_start: 0.8421 (ttpp) cc_final: 0.8161 (tttm) REVERT: R 189 MET cc_start: 0.8482 (mmm) cc_final: 0.8023 (mmm) REVERT: R 193 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7855 (tt) REVERT: R 253 ASN cc_start: 0.8775 (m-40) cc_final: 0.8415 (m-40) outliers start: 25 outliers final: 14 residues processed: 153 average time/residue: 1.1900 time to fit residues: 194.3948 Evaluate side-chains 144 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 193 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 75 GLN B 259 GLN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8897 Z= 0.293 Angle : 0.576 8.871 12061 Z= 0.301 Chirality : 0.044 0.223 1380 Planarity : 0.004 0.055 1523 Dihedral : 4.288 21.247 1218 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.34 % Allowed : 19.07 % Favored : 77.59 % 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: 1.59 (0.25), residues: 1100 helix: 2.55 (0.25), residues: 388 sheet: 0.45 (0.30), residues: 293 loop : 0.17 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS B 266 PHE 0.014 0.002 PHE A 196 TYR 0.026 0.001 TYR R 48 ARG 0.006 0.001 ARG R 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.984 Fit side-chains REVERT: A 298 GLU cc_start: 0.8289 (tt0) cc_final: 0.7950 (tt0) REVERT: B 153 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7701 (p0) REVERT: B 219 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7225 (mmt180) REVERT: B 267 ASP cc_start: 0.7893 (m-30) cc_final: 0.7661 (m-30) REVERT: E 46 GLU cc_start: 0.8123 (tt0) cc_final: 0.7894 (tt0) REVERT: E 160 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7664 (mmm-85) REVERT: E 183 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: E 244 LYS cc_start: 0.8443 (ttpp) cc_final: 0.8171 (tttm) REVERT: R 193 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7846 (tt) REVERT: R 253 ASN cc_start: 0.8808 (m-40) cc_final: 0.8549 (m-40) outliers start: 31 outliers final: 20 residues processed: 148 average time/residue: 1.1730 time to fit residues: 185.4688 Evaluate side-chains 147 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 234 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 89 optimal weight: 0.2980 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 331 ASN B 75 GLN E 77 ASN R 134 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8897 Z= 0.168 Angle : 0.531 8.716 12061 Z= 0.277 Chirality : 0.042 0.169 1380 Planarity : 0.004 0.040 1523 Dihedral : 4.045 22.277 1218 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.26 % Allowed : 20.15 % Favored : 77.59 % 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: 1.63 (0.26), residues: 1100 helix: 2.65 (0.25), residues: 389 sheet: 0.42 (0.30), residues: 283 loop : 0.15 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS B 266 PHE 0.009 0.001 PHE R 115 TYR 0.028 0.001 TYR R 48 ARG 0.005 0.000 ARG R 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.156 Fit side-chains REVERT: A 32 ARG cc_start: 0.8054 (mpt90) cc_final: 0.7834 (mpt90) REVERT: B 153 ASP cc_start: 0.8075 (m-30) cc_final: 0.7845 (p0) REVERT: B 219 ARG cc_start: 0.7936 (mmm160) cc_final: 0.7222 (mmt-90) REVERT: B 267 ASP cc_start: 0.7781 (m-30) cc_final: 0.7527 (m-30) REVERT: E 160 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7581 (tpp-160) REVERT: E 229 CYS cc_start: 0.8437 (p) cc_final: 0.8232 (p) REVERT: E 244 LYS cc_start: 0.8450 (ttpp) cc_final: 0.8199 (tttm) REVERT: R 217 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7657 (ttm170) REVERT: R 253 ASN cc_start: 0.8809 (m-40) cc_final: 0.8542 (m-40) outliers start: 21 outliers final: 12 residues processed: 146 average time/residue: 1.1662 time to fit residues: 181.8813 Evaluate side-chains 137 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 217 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.0030 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 0.0370 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 0.1980 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.2268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 269 ASN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 8897 Z= 0.140 Angle : 0.513 8.300 12061 Z= 0.267 Chirality : 0.041 0.161 1380 Planarity : 0.003 0.040 1523 Dihedral : 3.904 22.351 1218 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.62 % Allowed : 21.55 % Favored : 76.83 % 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: 1.76 (0.26), residues: 1100 helix: 2.81 (0.25), residues: 389 sheet: 0.46 (0.30), residues: 282 loop : 0.20 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS B 266 PHE 0.015 0.001 PHE A 274 TYR 0.030 0.001 TYR R 48 ARG 0.007 0.000 ARG R 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 0.889 Fit side-chains REVERT: A 32 ARG cc_start: 0.7904 (mpt90) cc_final: 0.7672 (mpt90) REVERT: A 298 GLU cc_start: 0.8275 (tt0) cc_final: 0.7998 (tt0) REVERT: B 219 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7207 (mmt-90) REVERT: B 267 ASP cc_start: 0.7711 (m-30) cc_final: 0.7430 (m-30) REVERT: E 160 ARG cc_start: 0.7819 (ttm-80) cc_final: 0.7557 (tpp-160) REVERT: E 244 LYS cc_start: 0.8407 (ttpp) cc_final: 0.8108 (tttm) REVERT: R 193 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7945 (tt) REVERT: R 253 ASN cc_start: 0.8781 (m-40) cc_final: 0.8514 (m-40) outliers start: 15 outliers final: 11 residues processed: 143 average time/residue: 1.1374 time to fit residues: 173.6501 Evaluate side-chains 138 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 193 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 93 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 259 GLN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8897 Z= 0.194 Angle : 0.547 8.248 12061 Z= 0.282 Chirality : 0.042 0.190 1380 Planarity : 0.003 0.039 1523 Dihedral : 3.997 22.196 1218 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.94 % Allowed : 21.55 % Favored : 76.51 % 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: 1.77 (0.26), residues: 1100 helix: 2.82 (0.25), residues: 388 sheet: 0.48 (0.31), residues: 279 loop : 0.19 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS B 266 PHE 0.011 0.001 PHE R 34 TYR 0.015 0.001 TYR R 248 ARG 0.007 0.000 ARG R 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.002 Fit side-chains REVERT: A 32 ARG cc_start: 0.7966 (mpt90) cc_final: 0.7732 (mpt90) REVERT: B 219 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7215 (mmt-90) REVERT: B 267 ASP cc_start: 0.7753 (m-30) cc_final: 0.7490 (m-30) REVERT: E 160 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7586 (tpp-160) REVERT: E 244 LYS cc_start: 0.8418 (ttpp) cc_final: 0.8081 (tttm) REVERT: R 193 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7968 (tt) REVERT: R 253 ASN cc_start: 0.8788 (m-40) cc_final: 0.8530 (m-40) outliers start: 18 outliers final: 14 residues processed: 139 average time/residue: 1.1497 time to fit residues: 170.9014 Evaluate side-chains 140 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 193 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.5980 chunk 72 optimal weight: 0.0770 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 0.0870 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 75 GLN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 8897 Z= 0.163 Angle : 0.526 8.512 12061 Z= 0.273 Chirality : 0.041 0.177 1380 Planarity : 0.003 0.039 1523 Dihedral : 3.913 22.107 1218 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.16 % Allowed : 21.77 % Favored : 76.08 % 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: 1.82 (0.26), residues: 1100 helix: 2.87 (0.25), residues: 388 sheet: 0.44 (0.30), residues: 286 loop : 0.25 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS B 266 PHE 0.009 0.001 PHE A 196 TYR 0.015 0.001 TYR R 248 ARG 0.007 0.000 ARG R 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.976 Fit side-chains REVERT: A 32 ARG cc_start: 0.7865 (mpt90) cc_final: 0.7630 (mpt90) REVERT: A 298 GLU cc_start: 0.8277 (tt0) cc_final: 0.8009 (tt0) REVERT: B 219 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7211 (mmt-90) REVERT: B 267 ASP cc_start: 0.7677 (m-30) cc_final: 0.7419 (m-30) REVERT: E 160 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7621 (tpp-160) REVERT: E 244 LYS cc_start: 0.8372 (ttpp) cc_final: 0.8104 (tttm) REVERT: R 64 ASN cc_start: 0.7958 (m110) cc_final: 0.7633 (m-40) REVERT: R 193 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8008 (tt) REVERT: R 253 ASN cc_start: 0.8761 (m-40) cc_final: 0.8491 (m-40) outliers start: 20 outliers final: 13 residues processed: 137 average time/residue: 1.1224 time to fit residues: 164.9194 Evaluate side-chains 140 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 193 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 36 optimal weight: 0.0570 chunk 89 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 311 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.161705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.111084 restraints weight = 9942.486| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.42 r_work: 0.3161 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8897 Z= 0.216 Angle : 0.559 8.413 12061 Z= 0.289 Chirality : 0.042 0.166 1380 Planarity : 0.004 0.037 1523 Dihedral : 4.024 22.157 1218 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.51 % Allowed : 22.63 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.26), residues: 1100 helix: 2.82 (0.25), residues: 387 sheet: 0.40 (0.30), residues: 287 loop : 0.23 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.006 0.001 HIS B 266 PHE 0.011 0.001 PHE A 196 TYR 0.015 0.001 TYR R 248 ARG 0.007 0.000 ARG R 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3711.85 seconds wall clock time: 65 minutes 39.33 seconds (3939.33 seconds total)