Starting phenix.real_space_refine on Fri Jul 19 17:43:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/07_2024/8ykw_39374_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/07_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_39374/07_2024/8ykw_39374.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/07_2024/8ykw_39374.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/07_2024/8ykw_39374_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/07_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.67, per 1000 atoms: 0.65 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: 3.60 Conformation dependent library (CDL) restraints added in 1.6 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: 1.16 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: 2.68 Time building geometry restraints manager: 3.93 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 2.440 nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.248 2.440 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.277 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.284 2.440 nonbonded pdb=" O ASN R 274 " pdb=" N TYR R 277 " model vdw 2.313 2.520 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 27.780 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.370 ------------------------------------------------------------------------------- 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 : 0.895 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: 1.3097 time to fit residues: 202.8202 Evaluate side-chains 121 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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: 5.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 255 ASN A 269 ASN A 331 ASN A 333 GLN B 75 GLN B 259 GLN E 3 GLN E 39 GLN E 77 ASN E 179 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8897 Z= 0.264 Angle : 0.567 9.113 12061 Z= 0.304 Chirality : 0.044 0.145 1380 Planarity : 0.004 0.040 1523 Dihedral : 4.605 33.843 1221 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.02 % Allowed : 14.55 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.26), residues: 1100 helix: 2.20 (0.25), residues: 388 sheet: 0.44 (0.31), residues: 293 loop : 0.43 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.014 0.001 PHE A 274 TYR 0.021 0.001 TYR R 48 ARG 0.008 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 165 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 0.962 Fit side-chains REVERT: A 33 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7453 (mm-30) REVERT: B 214 ARG cc_start: 0.8071 (mmt-90) cc_final: 0.7832 (mmp80) REVERT: B 219 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7243 (mpt180) REVERT: B 267 ASP cc_start: 0.7809 (m-30) cc_final: 0.7514 (m-30) REVERT: E 46 GLU cc_start: 0.7939 (tt0) cc_final: 0.7730 (tt0) REVERT: E 229 CYS cc_start: 0.8481 (p) cc_final: 0.8254 (p) REVERT: R 189 MET cc_start: 0.8436 (mmm) cc_final: 0.8074 (mmm) REVERT: R 193 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7616 (tt) REVERT: R 253 ASN cc_start: 0.8755 (m-40) cc_final: 0.8455 (m-40) outliers start: 28 outliers final: 14 residues processed: 151 average time/residue: 1.2552 time to fit residues: 201.5079 Evaluate side-chains 136 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 255 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 331 SER 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 G residue 52 THR Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 234 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.0010 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 3 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: 0.8299 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8897 Z= 0.176 Angle : 0.511 9.571 12061 Z= 0.271 Chirality : 0.042 0.151 1380 Planarity : 0.004 0.042 1523 Dihedral : 4.114 24.789 1218 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.16 % Allowed : 16.81 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.26), residues: 1100 helix: 2.60 (0.25), residues: 389 sheet: 0.63 (0.31), residues: 291 loop : 0.37 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.012 0.001 PHE R 34 TYR 0.023 0.001 TYR R 48 ARG 0.005 0.000 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 165 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 1.039 Fit side-chains REVERT: A 33 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 298 GLU cc_start: 0.8146 (tt0) cc_final: 0.7722 (tt0) REVERT: B 46 ARG cc_start: 0.8012 (ptm160) cc_final: 0.7772 (ptm160) REVERT: B 153 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7677 (p0) REVERT: B 219 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7230 (mpt180) REVERT: B 267 ASP cc_start: 0.7767 (m-30) cc_final: 0.7466 (m-30) REVERT: E 46 GLU cc_start: 0.7864 (tt0) cc_final: 0.7639 (tt0) REVERT: E 229 CYS cc_start: 0.8420 (p) cc_final: 0.8194 (p) REVERT: R 189 MET cc_start: 0.8488 (mmm) cc_final: 0.8119 (mmm) REVERT: R 253 ASN cc_start: 0.8708 (m-40) cc_final: 0.8410 (m-40) outliers start: 20 outliers final: 10 residues processed: 152 average time/residue: 1.1787 time to fit residues: 191.2112 Evaluate side-chains 135 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 153 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE 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 G residue 16 VAL Chi-restraints excluded: chain R residue 149 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 E 3 GLN E 77 ASN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8897 Z= 0.285 Angle : 0.555 8.846 12061 Z= 0.292 Chirality : 0.043 0.154 1380 Planarity : 0.004 0.049 1523 Dihedral : 4.264 20.726 1218 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.56 % Allowed : 16.49 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.26), residues: 1100 helix: 2.56 (0.25), residues: 389 sheet: 0.63 (0.30), residues: 293 loop : 0.30 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS G 44 PHE 0.014 0.002 PHE B 199 TYR 0.021 0.002 TYR R 48 ARG 0.005 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 171 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 0.946 Fit side-chains REVERT: A 33 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7447 (mm-30) REVERT: A 298 GLU cc_start: 0.8134 (tt0) cc_final: 0.7704 (tt0) REVERT: B 219 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7263 (mpt180) REVERT: E 160 ARG cc_start: 0.7873 (ttm110) cc_final: 0.7670 (ttm110) REVERT: E 183 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: R 189 MET cc_start: 0.8474 (mmm) cc_final: 0.8082 (mmm) REVERT: R 193 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7762 (tt) REVERT: R 217 ARG cc_start: 0.7583 (tpp-160) cc_final: 0.7369 (tpp-160) REVERT: R 253 ASN cc_start: 0.8718 (m-40) cc_final: 0.8438 (m-40) outliers start: 33 outliers final: 15 residues processed: 154 average time/residue: 1.1329 time to fit residues: 186.3899 Evaluate side-chains 149 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 ASP 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 B residue 331 SER 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 193 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 193 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 3 GLN E 77 ASN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8897 Z= 0.365 Angle : 0.584 8.575 12061 Z= 0.308 Chirality : 0.044 0.164 1380 Planarity : 0.004 0.045 1523 Dihedral : 4.423 21.467 1218 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.99 % Allowed : 18.32 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.25), residues: 1100 helix: 2.42 (0.25), residues: 388 sheet: 0.54 (0.30), residues: 293 loop : 0.20 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.007 0.001 HIS B 266 PHE 0.020 0.002 PHE A 274 TYR 0.021 0.002 TYR R 48 ARG 0.006 0.001 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 173 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 1.029 Fit side-chains REVERT: A 33 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7376 (mm-30) REVERT: A 298 GLU cc_start: 0.8172 (tt0) cc_final: 0.7794 (tt0) REVERT: B 219 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7287 (mpt180) REVERT: R 189 MET cc_start: 0.8501 (mmm) cc_final: 0.8088 (mmm) REVERT: R 193 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7788 (tt) REVERT: R 253 ASN cc_start: 0.8721 (m-40) cc_final: 0.8439 (m-40) outliers start: 37 outliers final: 23 residues processed: 157 average time/residue: 1.1007 time to fit residues: 185.2720 Evaluate side-chains 150 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 ASP 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 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL 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 B residue 331 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 THR 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 G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 79 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN B 75 GLN B 266 HIS E 3 GLN E 77 ASN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8897 Z= 0.258 Angle : 0.554 9.440 12061 Z= 0.290 Chirality : 0.043 0.162 1380 Planarity : 0.004 0.051 1523 Dihedral : 4.260 22.496 1218 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.20 % Allowed : 18.75 % Favored : 77.05 % 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: 1.62 (0.25), residues: 1100 helix: 2.51 (0.25), residues: 389 sheet: 0.53 (0.30), residues: 293 loop : 0.20 (0.31), residues: 418 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 0.021 0.001 PHE A 274 TYR 0.025 0.001 TYR R 48 ARG 0.007 0.001 ARG E 160 *********************** 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 171 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 0.932 Fit side-chains REVERT: A 32 ARG cc_start: 0.8017 (mtt90) cc_final: 0.7728 (mpt90) REVERT: A 33 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7389 (mm-30) REVERT: A 298 GLU cc_start: 0.8173 (tt0) cc_final: 0.7744 (tt0) REVERT: B 219 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7257 (mpt180) REVERT: R 189 MET cc_start: 0.8493 (mmm) cc_final: 0.8094 (mmm) REVERT: R 193 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7814 (tt) REVERT: R 253 ASN cc_start: 0.8757 (m-40) cc_final: 0.8495 (m-40) outliers start: 39 outliers final: 21 residues processed: 151 average time/residue: 1.1224 time to fit residues: 181.4941 Evaluate side-chains 148 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP 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 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 LEU 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 B residue 331 SER Chi-restraints excluded: chain E residue 11 LEU 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 193 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 79 LEU 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: 2.9990 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 0.0670 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN B 75 GLN B 175 GLN E 3 GLN E 77 ASN R 134 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8897 Z= 0.256 Angle : 0.540 8.926 12061 Z= 0.285 Chirality : 0.043 0.167 1380 Planarity : 0.004 0.044 1523 Dihedral : 4.219 22.694 1218 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.56 % Allowed : 19.61 % 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: 1.61 (0.26), residues: 1100 helix: 2.52 (0.25), residues: 389 sheet: 0.45 (0.30), residues: 295 loop : 0.23 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.023 0.001 PHE A 274 TYR 0.026 0.002 TYR R 48 ARG 0.007 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 162 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 1.052 Fit side-chains REVERT: A 32 ARG cc_start: 0.8018 (mtt90) cc_final: 0.7697 (mpt90) REVERT: A 33 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7409 (mm-30) REVERT: A 298 GLU cc_start: 0.8192 (tt0) cc_final: 0.7812 (tt0) REVERT: B 219 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7264 (mpt180) REVERT: E 160 ARG cc_start: 0.7877 (ttm110) cc_final: 0.7653 (ttm110) REVERT: R 189 MET cc_start: 0.8486 (mmm) cc_final: 0.8090 (mmm) REVERT: R 193 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7829 (tt) REVERT: R 253 ASN cc_start: 0.8756 (m-40) cc_final: 0.8514 (m-40) outliers start: 33 outliers final: 26 residues processed: 147 average time/residue: 1.1311 time to fit residues: 177.9106 Evaluate side-chains 156 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 ASP 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 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 LEU 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 B residue 331 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 THR 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 G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 98 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.0070 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN B 75 GLN E 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 8897 Z= 0.161 Angle : 0.524 10.606 12061 Z= 0.272 Chirality : 0.041 0.166 1380 Planarity : 0.004 0.051 1523 Dihedral : 4.065 22.931 1218 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.37 % Allowed : 21.34 % Favored : 76.29 % 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: 1.69 (0.26), residues: 1100 helix: 2.69 (0.26), residues: 390 sheet: 0.50 (0.30), residues: 289 loop : 0.14 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.002 0.001 HIS G 44 PHE 0.010 0.001 PHE B 199 TYR 0.031 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 162 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7952 (mtt90) cc_final: 0.7630 (mpt90) REVERT: A 33 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7442 (mm-30) REVERT: A 298 GLU cc_start: 0.8209 (tt0) cc_final: 0.7858 (tt0) REVERT: B 267 ASP cc_start: 0.7845 (m-30) cc_final: 0.7634 (m-30) REVERT: E 160 ARG cc_start: 0.7863 (ttm110) cc_final: 0.7646 (ttm110) REVERT: E 229 CYS cc_start: 0.8341 (p) cc_final: 0.8129 (p) REVERT: G 48 ASP cc_start: 0.8159 (t0) cc_final: 0.7913 (t0) REVERT: R 189 MET cc_start: 0.8493 (mmm) cc_final: 0.8035 (mmm) REVERT: R 253 ASN cc_start: 0.8716 (m-40) cc_final: 0.8463 (m-40) outliers start: 22 outliers final: 15 residues processed: 151 average time/residue: 1.1373 time to fit residues: 183.5905 Evaluate side-chains 145 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP 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 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 63 THR 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 56 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN B 75 GLN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8897 Z= 0.200 Angle : 0.534 8.524 12061 Z= 0.277 Chirality : 0.042 0.194 1380 Planarity : 0.004 0.052 1523 Dihedral : 4.046 23.071 1218 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.59 % Allowed : 21.34 % 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: 1.67 (0.26), residues: 1100 helix: 2.70 (0.25), residues: 388 sheet: 0.47 (0.30), residues: 291 loop : 0.13 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.012 0.001 PHE B 199 TYR 0.032 0.001 TYR R 48 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 153 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.023 Fit side-chains REVERT: A 33 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 298 GLU cc_start: 0.8204 (tt0) cc_final: 0.7871 (tt0) REVERT: B 219 ARG cc_start: 0.7929 (mmm160) cc_final: 0.7216 (mpt180) REVERT: B 267 ASP cc_start: 0.7887 (m-30) cc_final: 0.7677 (m-30) REVERT: E 160 ARG cc_start: 0.7839 (ttm110) cc_final: 0.7629 (ttm110) REVERT: G 48 ASP cc_start: 0.8229 (t0) cc_final: 0.7998 (t0) REVERT: R 189 MET cc_start: 0.8525 (mmm) cc_final: 0.8077 (mmm) REVERT: R 193 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7939 (tt) REVERT: R 253 ASN cc_start: 0.8710 (m-40) cc_final: 0.8482 (m-40) outliers start: 24 outliers final: 16 residues processed: 143 average time/residue: 1.1196 time to fit residues: 171.4516 Evaluate side-chains 143 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP 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 146 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 56 ASN 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: 2.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.0060 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN B 75 GLN E 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8897 Z= 0.178 Angle : 0.526 9.514 12061 Z= 0.271 Chirality : 0.041 0.172 1380 Planarity : 0.004 0.050 1523 Dihedral : 3.949 22.949 1218 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 1.72 (0.26), residues: 1100 helix: 2.75 (0.26), residues: 389 sheet: 0.46 (0.30), residues: 291 loop : 0.19 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.011 0.001 PHE B 199 TYR 0.032 0.001 TYR R 48 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 153 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.055 Fit side-chains REVERT: A 33 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7447 (mm-30) REVERT: A 298 GLU cc_start: 0.8205 (tt0) cc_final: 0.7951 (tt0) REVERT: B 219 ARG cc_start: 0.7933 (mmm160) cc_final: 0.7206 (mmt-90) REVERT: B 267 ASP cc_start: 0.7835 (m-30) cc_final: 0.7627 (m-30) REVERT: E 76 LYS cc_start: 0.8149 (mtmm) cc_final: 0.7917 (ptpp) REVERT: E 160 ARG cc_start: 0.7824 (ttm110) cc_final: 0.7619 (ttm110) REVERT: E 229 CYS cc_start: 0.8355 (p) cc_final: 0.8123 (p) REVERT: G 48 ASP cc_start: 0.8194 (t0) cc_final: 0.7960 (t0) REVERT: R 189 MET cc_start: 0.8531 (mmm) cc_final: 0.8096 (mmm) REVERT: R 193 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7939 (tt) REVERT: R 253 ASN cc_start: 0.8717 (m-40) cc_final: 0.8496 (m-40) outliers start: 20 outliers final: 18 residues processed: 145 average time/residue: 1.1848 time to fit residues: 183.8848 Evaluate side-chains 149 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP 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 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 56 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN B 75 GLN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.159932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110358 restraints weight = 9843.027| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.30 r_work: 0.3182 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 8897 Z= 0.304 Angle : 0.571 8.371 12061 Z= 0.298 Chirality : 0.043 0.168 1380 Planarity : 0.004 0.050 1523 Dihedral : 4.214 22.798 1218 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.16 % Allowed : 21.88 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.26), residues: 1100 helix: 2.61 (0.26), residues: 388 sheet: 0.47 (0.30), residues: 293 loop : 0.14 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS G 44 PHE 0.014 0.002 PHE B 199 TYR 0.030 0.002 TYR R 48 ARG 0.007 0.001 ARG R 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3725.44 seconds wall clock time: 65 minutes 53.87 seconds (3953.87 seconds total)