Starting phenix.real_space_refine on Wed Feb 14 00:33:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz4_32904/02_2024/7wz4_32904.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz4_32904/02_2024/7wz4_32904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz4_32904/02_2024/7wz4_32904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz4_32904/02_2024/7wz4_32904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz4_32904/02_2024/7wz4_32904.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz4_32904/02_2024/7wz4_32904.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 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 57 5.16 5 C 5185 2.51 5 N 1419 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 217": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 339": "NH1" <-> "NH2" Residue "R GLU 342": "OE1" <-> "OE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "S TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8187 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1692 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 3 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1715 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2577 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 4.64, per 1000 atoms: 0.57 Number of scatterers: 8187 At special positions: 0 Unit cell: (90.95, 119.85, 125.8, 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 57 16.00 O 1526 8.00 N 1419 7.00 C 5185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1994 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 37.2% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'R' and resid 34 through 59 removed outlier: 3.512A pdb=" N TYR R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER R 39 " --> pdb=" O SER R 35 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 63 Processing helix chain 'R' and resid 64 through 88 removed outlier: 3.819A pdb=" N PHE R 69 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET R 85 " --> pdb=" O CYS R 81 " (cutoff:3.500A) Proline residue: R 86 - end of helix Processing helix chain 'R' and resid 116 through 144 removed outlier: 3.591A pdb=" N CYS R 132 " --> pdb=" O LEU R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 153 Processing helix chain 'R' and resid 154 through 175 removed outlier: 3.743A pdb=" N TRP R 166 " --> pdb=" O LEU R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 227 removed outlier: 4.173A pdb=" N LEU R 195 " --> pdb=" O HIS R 191 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU R 196 " --> pdb=" O TYR R 192 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA R 197 " --> pdb=" O PRO R 193 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL R 216 " --> pdb=" O TYR R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 308 removed outlier: 3.652A pdb=" N LEU R 287 " --> pdb=" O GLY R 283 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 317 through 337 Proline residue: R 333 - end of helix Processing helix chain 'R' and resid 340 through 351 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.647A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.374A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.831A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.013A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.520A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.583A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.558A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.532A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.135A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.719A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.737A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.746A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.712A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.970A 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: 7.081A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.609A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.310A 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: 3.650A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.531A 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: 6.649A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.653A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.975A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.380A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.823A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1152 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: 3.05 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2671 1.34 - 1.46: 1981 1.46 - 1.58: 3611 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 8343 Sorted by residual: bond pdb=" N TRP R 179 " pdb=" CA TRP R 179 " ideal model delta sigma weight residual 1.455 1.481 -0.026 1.25e-02 6.40e+03 4.31e+00 bond pdb=" CA THR B 181 " pdb=" CB THR B 181 " ideal model delta sigma weight residual 1.527 1.562 -0.034 2.48e-02 1.63e+03 1.93e+00 bond pdb=" C TRP R 179 " pdb=" O TRP R 179 " ideal model delta sigma weight residual 1.234 1.244 -0.010 1.22e-02 6.72e+03 7.18e-01 bond pdb=" CA GLY B 41 " pdb=" C GLY B 41 " ideal model delta sigma weight residual 1.523 1.513 0.010 1.19e-02 7.06e+03 6.94e-01 bond pdb=" CB ASP G 26 " pdb=" CG ASP G 26 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.61e-01 ... (remaining 8338 not shown) Histogram of bond angle deviations from ideal: 100.12 - 106.94: 186 106.94 - 113.75: 4698 113.75 - 120.57: 3309 120.57 - 127.38: 3032 127.38 - 134.19: 85 Bond angle restraints: 11310 Sorted by residual: angle pdb=" N THR R 337 " pdb=" CA THR R 337 " pdb=" C THR R 337 " ideal model delta sigma weight residual 110.44 114.15 -3.71 1.20e+00 6.94e-01 9.57e+00 angle pdb=" CA TRP R 179 " pdb=" C TRP R 179 " pdb=" O TRP R 179 " ideal model delta sigma weight residual 120.99 117.82 3.17 1.12e+00 7.97e-01 8.01e+00 angle pdb=" CA LEU R 152 " pdb=" CB LEU R 152 " pdb=" CG LEU R 152 " ideal model delta sigma weight residual 116.30 125.68 -9.38 3.50e+00 8.16e-02 7.18e+00 angle pdb=" N ALA S 92 " pdb=" CA ALA S 92 " pdb=" C ALA S 92 " ideal model delta sigma weight residual 107.88 111.57 -3.69 1.41e+00 5.03e-01 6.85e+00 angle pdb=" C GLY S 197 " pdb=" N THR S 198 " pdb=" CA THR S 198 " ideal model delta sigma weight residual 123.05 126.89 -3.84 1.57e+00 4.06e-01 5.99e+00 ... (remaining 11305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 4544 17.44 - 34.88: 331 34.88 - 52.32: 62 52.32 - 69.76: 8 69.76 - 87.20: 6 Dihedral angle restraints: 4951 sinusoidal: 1858 harmonic: 3093 Sorted by residual: dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ARG S 179 " pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta harmonic sigma weight residual 180.00 162.59 17.41 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA LEU R 83 " pdb=" C LEU R 83 " pdb=" N TRP R 84 " pdb=" CA TRP R 84 " ideal model delta harmonic sigma weight residual 180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 4948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 822 0.032 - 0.065: 323 0.065 - 0.097: 98 0.097 - 0.129: 57 0.129 - 0.161: 5 Chirality restraints: 1305 Sorted by residual: chirality pdb=" CB THR B 181 " pdb=" CA THR B 181 " pdb=" OG1 THR B 181 " pdb=" CG2 THR B 181 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA MET R 85 " pdb=" N MET R 85 " pdb=" C MET R 85 " pdb=" CB MET R 85 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 1302 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 338 " 0.010 2.00e-02 2.50e+03 1.01e-02 2.56e+00 pdb=" CG TRP R 338 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP R 338 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 338 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 338 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 338 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 338 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 338 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 338 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 338 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.55e+00 pdb=" C THR B 87 " 0.022 2.00e-02 2.50e+03 pdb=" O THR B 87 " -0.008 2.00e-02 2.50e+03 pdb=" N ASN B 88 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO S 41 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " 0.017 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 78 2.66 - 3.22: 7228 3.22 - 3.78: 11695 3.78 - 4.34: 16121 4.34 - 4.90: 28264 Nonbonded interactions: 63386 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.096 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.101 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.141 2.440 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.280 2.440 nonbonded pdb=" NH2 ARG S 190 " pdb=" OD2 ASP S 211 " model vdw 2.282 2.520 ... (remaining 63381 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: 2.030 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: 0.010 Extract box with map and model: 7.330 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.430 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.003 0.039 8343 Z= 0.222 Angle : 0.590 9.377 11310 Z= 0.347 Chirality : 0.042 0.161 1305 Planarity : 0.003 0.031 1431 Dihedral : 12.942 87.201 2951 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.12 % Allowed : 0.23 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.09 (0.26), residues: 1051 helix: 2.46 (0.28), residues: 349 sheet: 0.58 (0.31), residues: 283 loop : -0.68 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 338 HIS 0.005 0.001 HIS B 142 PHE 0.011 0.001 PHE B 199 TYR 0.008 0.001 TYR B 105 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 0.905 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 155 ARG cc_start: 0.4093 (mmt180) cc_final: 0.3818 (mmt180) REVERT: R 217 ARG cc_start: 0.6608 (ttm-80) cc_final: 0.6404 (ptm160) REVERT: R 339 ARG cc_start: 0.8284 (mmm160) cc_final: 0.7705 (mmt-90) REVERT: A 26 ASP cc_start: 0.7396 (m-30) cc_final: 0.7170 (m-30) REVERT: A 308 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7592 (mt-10) REVERT: B 19 ARG cc_start: 0.7362 (ttm170) cc_final: 0.7070 (ttm110) REVERT: B 127 LYS cc_start: 0.8971 (mttm) cc_final: 0.8691 (mttt) REVERT: B 134 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7489 (mtp-110) REVERT: G 58 GLU cc_start: 0.7835 (pm20) cc_final: 0.6927 (mm-30) REVERT: S 211 ASP cc_start: 0.8392 (m-30) cc_final: 0.8109 (m-30) outliers start: 1 outliers final: 2 residues processed: 159 average time/residue: 1.2437 time to fit residues: 209.0943 Evaluate side-chains 130 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 179 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 0.0030 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 95 optimal weight: 0.4980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 32 GLN B 340 ASN S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8343 Z= 0.147 Angle : 0.491 8.648 11310 Z= 0.256 Chirality : 0.041 0.129 1305 Planarity : 0.003 0.029 1431 Dihedral : 4.450 48.889 1160 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.73 % Allowed : 10.96 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.41 (0.27), residues: 1051 helix: 2.87 (0.28), residues: 345 sheet: 0.69 (0.30), residues: 288 loop : -0.55 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 338 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR S 178 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.176 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 217 ARG cc_start: 0.6544 (ttm-80) cc_final: 0.6331 (ptm160) REVERT: R 339 ARG cc_start: 0.8347 (mmm160) cc_final: 0.7846 (mmt-90) REVERT: A 22 ASN cc_start: 0.7602 (m-40) cc_final: 0.7243 (m110) REVERT: A 51 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7755 (ttpp) REVERT: A 309 ASP cc_start: 0.8235 (p0) cc_final: 0.7899 (p0) REVERT: B 16 ASN cc_start: 0.6102 (m110) cc_final: 0.5885 (m-40) REVERT: B 19 ARG cc_start: 0.7416 (ttm170) cc_final: 0.7099 (ttm110) REVERT: B 127 LYS cc_start: 0.8877 (mttm) cc_final: 0.8573 (mttt) REVERT: B 134 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7487 (mtp-110) REVERT: B 175 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: G 58 GLU cc_start: 0.7673 (pm20) cc_final: 0.7206 (mm-30) REVERT: S 3 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7445 (pt0) outliers start: 15 outliers final: 5 residues processed: 136 average time/residue: 1.5866 time to fit residues: 227.9248 Evaluate side-chains 130 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 63 GLN R 67 ASN B 32 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8343 Z= 0.232 Angle : 0.513 7.847 11310 Z= 0.269 Chirality : 0.041 0.132 1305 Planarity : 0.003 0.028 1431 Dihedral : 4.579 59.450 1160 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.00 % Allowed : 12.57 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.35 (0.27), residues: 1051 helix: 2.91 (0.28), residues: 346 sheet: 0.48 (0.30), residues: 298 loop : -0.56 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.005 0.001 HIS B 142 PHE 0.015 0.002 PHE A 196 TYR 0.012 0.001 TYR B 105 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 0.960 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 344 ARG cc_start: 0.6305 (OUTLIER) cc_final: 0.5993 (mtt180) REVERT: A 22 ASN cc_start: 0.7550 (m-40) cc_final: 0.7229 (m110) REVERT: A 26 ASP cc_start: 0.7442 (m-30) cc_final: 0.7214 (m-30) REVERT: A 51 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7768 (ttpm) REVERT: A 251 ASP cc_start: 0.7905 (t0) cc_final: 0.7440 (t0) REVERT: A 309 ASP cc_start: 0.7972 (p0) cc_final: 0.7639 (p0) REVERT: B 19 ARG cc_start: 0.7406 (ttm170) cc_final: 0.7197 (ttm110) REVERT: B 127 LYS cc_start: 0.8960 (mttm) cc_final: 0.8601 (mttt) REVERT: B 134 ARG cc_start: 0.7788 (mtm110) cc_final: 0.7520 (mtp-110) REVERT: B 175 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: G 58 GLU cc_start: 0.7704 (pm20) cc_final: 0.7230 (mm-30) REVERT: S 3 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7459 (pt0) outliers start: 26 outliers final: 12 residues processed: 140 average time/residue: 1.4658 time to fit residues: 215.8975 Evaluate side-chains 137 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 221 VAL Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 63 GLN A 304 GLN B 16 ASN B 32 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 8343 Z= 0.467 Angle : 0.645 8.371 11310 Z= 0.338 Chirality : 0.046 0.143 1305 Planarity : 0.004 0.035 1431 Dihedral : 4.762 49.826 1157 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.04 % Allowed : 12.92 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1051 helix: 2.63 (0.28), residues: 345 sheet: 0.12 (0.30), residues: 303 loop : -0.78 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 47 HIS 0.008 0.002 HIS B 142 PHE 0.021 0.002 PHE A 196 TYR 0.018 0.002 TYR B 105 ARG 0.006 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 0.889 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 179 TRP cc_start: 0.7381 (OUTLIER) cc_final: 0.6885 (m-10) REVERT: R 344 ARG cc_start: 0.6298 (OUTLIER) cc_final: 0.5946 (mtt-85) REVERT: A 26 ASP cc_start: 0.7586 (m-30) cc_final: 0.7261 (m-30) REVERT: A 51 LYS cc_start: 0.8230 (ttmm) cc_final: 0.7836 (ttpm) REVERT: A 186 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7565 (mt-10) REVERT: A 251 ASP cc_start: 0.7952 (t0) cc_final: 0.7510 (t0) REVERT: A 309 ASP cc_start: 0.7928 (p0) cc_final: 0.7576 (p0) REVERT: B 19 ARG cc_start: 0.7406 (ttm170) cc_final: 0.7199 (ttm110) REVERT: B 46 ARG cc_start: 0.6629 (mtp85) cc_final: 0.6111 (ttp-170) REVERT: B 127 LYS cc_start: 0.9112 (mttm) cc_final: 0.8725 (mttt) REVERT: B 134 ARG cc_start: 0.7825 (mtm110) cc_final: 0.7564 (mtp-110) REVERT: B 175 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7447 (mp10) REVERT: G 58 GLU cc_start: 0.7723 (pm20) cc_final: 0.7256 (mm-30) REVERT: S 3 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7488 (pt0) REVERT: S 154 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8758 (tt) outliers start: 35 outliers final: 18 residues processed: 151 average time/residue: 1.3458 time to fit residues: 214.1860 Evaluate side-chains 149 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 221 VAL Chi-restraints excluded: chain R residue 297 THR Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 32 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8343 Z= 0.153 Angle : 0.480 8.177 11310 Z= 0.250 Chirality : 0.040 0.185 1305 Planarity : 0.003 0.035 1431 Dihedral : 4.135 48.271 1157 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.88 % Allowed : 15.80 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.32 (0.27), residues: 1051 helix: 3.04 (0.28), residues: 344 sheet: 0.40 (0.30), residues: 295 loop : -0.65 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.003 0.001 HIS R 131 PHE 0.014 0.001 PHE B 199 TYR 0.012 0.001 TYR S 178 ARG 0.006 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 0.876 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 344 ARG cc_start: 0.6263 (OUTLIER) cc_final: 0.5944 (mtt180) REVERT: A 22 ASN cc_start: 0.7567 (m-40) cc_final: 0.7270 (m110) REVERT: A 51 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7768 (ttpm) REVERT: A 186 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7620 (mt-10) REVERT: A 271 LYS cc_start: 0.7671 (ttmt) cc_final: 0.7093 (tttt) REVERT: B 19 ARG cc_start: 0.7288 (ttm170) cc_final: 0.7066 (ttm110) REVERT: B 127 LYS cc_start: 0.8920 (mttm) cc_final: 0.8546 (mttt) REVERT: B 134 ARG cc_start: 0.7670 (mtm110) cc_final: 0.7454 (mtp-110) REVERT: B 175 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7445 (mp10) REVERT: G 58 GLU cc_start: 0.7701 (pm20) cc_final: 0.7262 (mm-30) outliers start: 25 outliers final: 15 residues processed: 136 average time/residue: 1.4020 time to fit residues: 200.7593 Evaluate side-chains 134 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 32 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8343 Z= 0.158 Angle : 0.477 8.441 11310 Z= 0.249 Chirality : 0.040 0.150 1305 Planarity : 0.003 0.035 1431 Dihedral : 3.990 46.985 1157 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.46 % Allowed : 16.72 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.44 (0.27), residues: 1051 helix: 3.11 (0.28), residues: 345 sheet: 0.50 (0.30), residues: 290 loop : -0.57 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE B 199 TYR 0.011 0.001 TYR S 178 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 0.984 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 136 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7301 (mp) REVERT: R 344 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5969 (mtt180) REVERT: A 22 ASN cc_start: 0.7580 (m-40) cc_final: 0.7244 (m110) REVERT: A 26 ASP cc_start: 0.7454 (m-30) cc_final: 0.7204 (m-30) REVERT: A 51 LYS cc_start: 0.8231 (ttmm) cc_final: 0.7732 (ttpp) REVERT: A 251 ASP cc_start: 0.7851 (t0) cc_final: 0.7496 (t0) REVERT: A 271 LYS cc_start: 0.7488 (ttmt) cc_final: 0.7140 (tttt) REVERT: A 309 ASP cc_start: 0.7669 (p0) cc_final: 0.7331 (p0) REVERT: B 19 ARG cc_start: 0.7282 (ttm170) cc_final: 0.7061 (ttm110) REVERT: B 127 LYS cc_start: 0.8885 (mttm) cc_final: 0.8508 (mttt) REVERT: B 134 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7463 (mtp-110) REVERT: B 175 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7440 (mp10) REVERT: B 234 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8947 (m-80) REVERT: G 58 GLU cc_start: 0.7713 (pm20) cc_final: 0.7307 (mm-30) REVERT: S 3 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7413 (pt0) outliers start: 30 outliers final: 17 residues processed: 140 average time/residue: 1.3344 time to fit residues: 197.3860 Evaluate side-chains 142 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 0.0000 chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 32 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8343 Z= 0.147 Angle : 0.456 6.982 11310 Z= 0.240 Chirality : 0.040 0.150 1305 Planarity : 0.003 0.035 1431 Dihedral : 3.876 45.834 1157 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.11 % Allowed : 17.30 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.54 (0.27), residues: 1051 helix: 3.18 (0.28), residues: 345 sheet: 0.56 (0.31), residues: 290 loop : -0.50 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE B 199 TYR 0.011 0.001 TYR S 178 ARG 0.007 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 0.959 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 344 ARG cc_start: 0.6284 (OUTLIER) cc_final: 0.5971 (mtm180) REVERT: A 22 ASN cc_start: 0.7569 (m-40) cc_final: 0.7229 (m110) REVERT: A 26 ASP cc_start: 0.7433 (m-30) cc_final: 0.7160 (m-30) REVERT: A 251 ASP cc_start: 0.7822 (t0) cc_final: 0.7477 (t0) REVERT: A 304 GLN cc_start: 0.7536 (tt0) cc_final: 0.7297 (tt0) REVERT: A 309 ASP cc_start: 0.7611 (p0) cc_final: 0.7271 (p0) REVERT: B 19 ARG cc_start: 0.7275 (ttm170) cc_final: 0.7041 (ttm110) REVERT: B 127 LYS cc_start: 0.8839 (mttm) cc_final: 0.8445 (mttt) REVERT: B 130 GLU cc_start: 0.7922 (mp0) cc_final: 0.7694 (mp0) REVERT: B 134 ARG cc_start: 0.7665 (mtm110) cc_final: 0.7425 (mtp-110) REVERT: B 175 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7423 (mp10) REVERT: B 217 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7922 (pp-130) REVERT: B 234 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8921 (m-80) REVERT: G 58 GLU cc_start: 0.7719 (pm20) cc_final: 0.7313 (mm-30) outliers start: 27 outliers final: 16 residues processed: 139 average time/residue: 1.3255 time to fit residues: 194.8788 Evaluate side-chains 138 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 32 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8343 Z= 0.263 Angle : 0.527 8.869 11310 Z= 0.276 Chirality : 0.042 0.135 1305 Planarity : 0.003 0.036 1431 Dihedral : 3.975 23.227 1155 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.11 % Allowed : 18.11 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.40 (0.27), residues: 1051 helix: 3.10 (0.28), residues: 344 sheet: 0.44 (0.30), residues: 289 loop : -0.57 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.005 0.001 HIS B 142 PHE 0.014 0.002 PHE B 199 TYR 0.010 0.001 TYR S 178 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 0.919 Fit side-chains REVERT: R 344 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.5988 (mtt-85) REVERT: A 22 ASN cc_start: 0.7605 (m-40) cc_final: 0.7328 (m110) REVERT: A 186 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7654 (mt-10) REVERT: B 127 LYS cc_start: 0.8991 (mttm) cc_final: 0.8619 (mttt) REVERT: B 134 ARG cc_start: 0.7693 (mtm110) cc_final: 0.7479 (mtp-110) REVERT: B 175 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7417 (mp10) REVERT: B 234 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8942 (m-80) REVERT: G 21 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.6802 (ttt) REVERT: G 58 GLU cc_start: 0.7734 (pm20) cc_final: 0.7298 (mm-30) REVERT: S 3 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7362 (pt0) REVERT: S 154 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8747 (tt) outliers start: 27 outliers final: 15 residues processed: 135 average time/residue: 1.3744 time to fit residues: 195.4390 Evaluate side-chains 138 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 56 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 chunk 61 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 32 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8343 Z= 0.137 Angle : 0.453 6.671 11310 Z= 0.239 Chirality : 0.040 0.130 1305 Planarity : 0.003 0.034 1431 Dihedral : 3.636 20.474 1155 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.88 % Allowed : 18.22 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.53 (0.27), residues: 1051 helix: 3.21 (0.28), residues: 344 sheet: 0.51 (0.31), residues: 279 loop : -0.47 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.001 PHE B 199 TYR 0.011 0.001 TYR S 178 ARG 0.007 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 0.961 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 344 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5969 (mtm180) REVERT: A 22 ASN cc_start: 0.7560 (m-40) cc_final: 0.7208 (m110) REVERT: A 26 ASP cc_start: 0.7383 (m-30) cc_final: 0.7058 (m-30) REVERT: A 309 ASP cc_start: 0.7494 (p0) cc_final: 0.7144 (p0) REVERT: B 127 LYS cc_start: 0.8853 (mttm) cc_final: 0.8463 (mttt) REVERT: B 130 GLU cc_start: 0.7942 (mp0) cc_final: 0.7688 (mp0) REVERT: B 134 ARG cc_start: 0.7645 (mtm110) cc_final: 0.7425 (mtp-110) REVERT: B 175 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7417 (mp10) REVERT: B 234 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8897 (m-80) REVERT: G 21 MET cc_start: 0.7772 (mmt) cc_final: 0.6755 (ttt) REVERT: G 58 GLU cc_start: 0.7688 (pm20) cc_final: 0.7293 (mm-30) REVERT: S 3 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7324 (pt0) outliers start: 25 outliers final: 16 residues processed: 138 average time/residue: 1.3077 time to fit residues: 190.6032 Evaluate side-chains 141 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 221 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.0570 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 0.2980 chunk 96 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 32 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8343 Z= 0.150 Angle : 0.473 9.375 11310 Z= 0.247 Chirality : 0.040 0.127 1305 Planarity : 0.003 0.035 1431 Dihedral : 3.588 19.504 1155 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.77 % Allowed : 18.92 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.64 (0.27), residues: 1051 helix: 3.27 (0.28), residues: 343 sheet: 0.55 (0.31), residues: 288 loop : -0.39 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.001 PHE B 199 TYR 0.011 0.001 TYR S 178 ARG 0.007 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 0.904 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 344 ARG cc_start: 0.6255 (OUTLIER) cc_final: 0.5958 (mtm180) REVERT: A 22 ASN cc_start: 0.7565 (m-40) cc_final: 0.7218 (m110) REVERT: A 26 ASP cc_start: 0.7396 (m-30) cc_final: 0.7068 (m-30) REVERT: A 304 GLN cc_start: 0.7530 (tt0) cc_final: 0.7298 (tt0) REVERT: A 309 ASP cc_start: 0.7571 (p0) cc_final: 0.7223 (p0) REVERT: B 127 LYS cc_start: 0.8843 (mttm) cc_final: 0.8444 (mttt) REVERT: B 130 GLU cc_start: 0.7923 (mp0) cc_final: 0.7682 (mp0) REVERT: B 175 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7436 (mp10) REVERT: B 234 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8888 (m-80) REVERT: G 21 MET cc_start: 0.7793 (mmt) cc_final: 0.6780 (ttt) REVERT: G 58 GLU cc_start: 0.7680 (pm20) cc_final: 0.7304 (mm-30) outliers start: 24 outliers final: 15 residues processed: 135 average time/residue: 1.3162 time to fit residues: 187.7262 Evaluate side-chains 138 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 221 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 337 THR Chi-restraints excluded: chain R residue 344 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 32 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.159197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.106953 restraints weight = 9472.408| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.59 r_work: 0.3072 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8343 Z= 0.170 Angle : 0.477 6.669 11310 Z= 0.252 Chirality : 0.040 0.137 1305 Planarity : 0.003 0.035 1431 Dihedral : 3.631 19.820 1155 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.54 % Allowed : 19.15 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.27), residues: 1051 helix: 3.27 (0.28), residues: 343 sheet: 0.52 (0.31), residues: 288 loop : -0.43 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.013 0.001 PHE B 199 TYR 0.011 0.001 TYR S 178 ARG 0.007 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3866.79 seconds wall clock time: 69 minutes 10.51 seconds (4150.51 seconds total)