Starting phenix.real_space_refine on Wed Feb 12 01:22:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dhr_30682/02_2025/7dhr_30682.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dhr_30682/02_2025/7dhr_30682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dhr_30682/02_2025/7dhr_30682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dhr_30682/02_2025/7dhr_30682.map" model { file = "/net/cci-nas-00/data/ceres_data/7dhr_30682/02_2025/7dhr_30682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dhr_30682/02_2025/7dhr_30682.cif" } resolution = 3.8 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= 0.007 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 42 5.16 5 C 4538 2.51 5 N 1206 2.21 5 O 1271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7057 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1495 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 5 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2301 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 5, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 6, 'ARG:plan': 14, 'ASN:plan1': 4, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 169 Chain: "G" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 317 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "N" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 851 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "R" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2078 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 2 Unresolved non-hydrogen bonds: 229 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 149 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'5FW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.35, per 1000 atoms: 0.62 Number of scatterers: 7057 At special positions: 0 Unit cell: (82.134, 98.358, 120.666, 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 42 16.00 O 1271 8.00 N 1206 7.00 C 4538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 1.0 seconds 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 11 sheets defined 29.0% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 removed outlier: 3.592A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 32 Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.755A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.952A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 316' Processing helix chain 'A' and resid 331 through 345 removed outlier: 3.516A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.819A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 345 through 350' Processing helix chain 'A' and resid 372 through 390 removed outlier: 3.914A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 25 removed outlier: 3.721A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 34 through 44 removed outlier: 3.697A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.918A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 31 through 49 removed outlier: 3.520A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER R 41 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 70 Processing helix chain 'R' and resid 71 through 76 Processing helix chain 'R' and resid 77 through 86 removed outlier: 4.055A pdb=" N MET R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 93 removed outlier: 3.615A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS R 93 " --> pdb=" O PHE R 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 88 through 93' Processing helix chain 'R' and resid 105 through 116 removed outlier: 3.634A pdb=" N THR R 110 " --> pdb=" O CYS R 106 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU R 115 " --> pdb=" O SER R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 136 removed outlier: 3.523A pdb=" N ALA R 128 " --> pdb=" O LEU R 124 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA R 134 " --> pdb=" O ASP R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 159 Processing helix chain 'R' and resid 159 through 164 Processing helix chain 'R' and resid 198 through 203 Processing helix chain 'R' and resid 213 through 218 Processing helix chain 'R' and resid 219 through 221 No H-bonds generated for 'chain 'R' and resid 219 through 221' Processing helix chain 'R' and resid 222 through 227 Processing helix chain 'R' and resid 228 through 237 removed outlier: 4.395A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 286 removed outlier: 3.785A pdb=" N ALA R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 281 through 286' Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 294 through 299 removed outlier: 3.504A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 316 Processing helix chain 'R' and resid 317 through 326 removed outlier: 3.762A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix removed outlier: 3.623A pdb=" N TYR R 326 " --> pdb=" O ASN R 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 317 through 326' Processing helix chain 'R' and resid 329 through 336 removed outlier: 3.663A pdb=" N ARG R 333 " --> pdb=" O SER R 329 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE R 334 " --> pdb=" O PRO R 330 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA R 335 " --> pdb=" O ASP R 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 3.711A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.509A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.483A 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 62 removed outlier: 3.550A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.759A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 153 removed outlier: 6.870A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.519A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190 removed outlier: 4.826A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.720A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.619A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 17 through 21 Processing sheet with id=AB2, first strand: chain 'N' and resid 36 through 39 164 hydrogen bonds defined for protein. 426 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: 1.78 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2272 1.34 - 1.46: 1719 1.46 - 1.58: 3153 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 7202 Sorted by residual: bond pdb=" C VAL R 210 " pdb=" N PRO R 211 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.89e+00 bond pdb=" C LEU R 167 " pdb=" N PRO R 168 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.53e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.97e+00 bond pdb=" N THR R 189 " pdb=" CA THR R 189 " ideal model delta sigma weight residual 1.462 1.485 -0.023 1.54e-02 4.22e+03 2.23e+00 bond pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 1.458 1.476 -0.017 1.35e-02 5.49e+03 1.66e+00 ... (remaining 7197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 9490 1.94 - 3.88: 277 3.88 - 5.81: 55 5.81 - 7.75: 11 7.75 - 9.69: 8 Bond angle restraints: 9841 Sorted by residual: angle pdb=" N VAL R 152 " pdb=" CA VAL R 152 " pdb=" C VAL R 152 " ideal model delta sigma weight residual 111.81 107.54 4.27 8.60e-01 1.35e+00 2.47e+01 angle pdb=" C SER N 112 " pdb=" N THR N 113 " pdb=" CA THR N 113 " ideal model delta sigma weight residual 121.54 130.35 -8.81 1.91e+00 2.74e-01 2.13e+01 angle pdb=" N VAL R 31 " pdb=" CA VAL R 31 " pdb=" C VAL R 31 " ideal model delta sigma weight residual 113.42 108.46 4.96 1.17e+00 7.31e-01 1.80e+01 angle pdb=" C ARG R 304 " pdb=" N LYS R 305 " pdb=" CA LYS R 305 " ideal model delta sigma weight residual 121.54 128.97 -7.43 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 123.47 129.23 -5.76 1.53e+00 4.27e-01 1.42e+01 ... (remaining 9836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 3746 17.38 - 34.76: 340 34.76 - 52.14: 70 52.14 - 69.51: 8 69.51 - 86.89: 4 Dihedral angle restraints: 4168 sinusoidal: 1330 harmonic: 2838 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual -86.00 -11.85 -74.15 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" CA ASN R 51 " pdb=" C ASN R 51 " pdb=" N VAL R 52 " pdb=" CA VAL R 52 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA SER R 137 " pdb=" C SER R 137 " pdb=" N PRO R 138 " pdb=" CA PRO R 138 " ideal model delta harmonic sigma weight residual -180.00 -160.14 -19.86 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 977 0.064 - 0.128: 175 0.128 - 0.191: 26 0.191 - 0.255: 1 0.255 - 0.319: 1 Chirality restraints: 1180 Sorted by residual: chirality pdb=" CB ILE R 303 " pdb=" CA ILE R 303 " pdb=" CG1 ILE R 303 " pdb=" CG2 ILE R 303 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB ILE R 153 " pdb=" CA ILE R 153 " pdb=" CG1 ILE R 153 " pdb=" CG2 ILE R 153 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB VAL A 248 " pdb=" CA VAL A 248 " pdb=" CG1 VAL A 248 " pdb=" CG2 VAL A 248 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.28e-01 ... (remaining 1177 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " -0.049 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO R 323 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.047 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO B 236 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO R 211 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " -0.037 5.00e-02 4.00e+02 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2471 2.84 - 3.36: 5803 3.36 - 3.87: 10703 3.87 - 4.39: 11913 4.39 - 4.90: 21258 Nonbonded interactions: 52148 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.329 3.040 nonbonded pdb=" O SER B 84 " pdb=" OG SER B 84 " model vdw 2.336 3.040 nonbonded pdb=" OD2 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.343 3.040 nonbonded pdb=" OG SER R 207 " pdb=" OAC 5FW R 601 " model vdw 2.349 3.040 nonbonded pdb=" O PHE R 133 " pdb=" OG SER R 137 " model vdw 2.352 3.040 ... (remaining 52143 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 0.480 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.990 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 0.058 7202 Z= 0.262 Angle : 0.858 9.691 9841 Z= 0.470 Chirality : 0.052 0.319 1180 Planarity : 0.006 0.072 1240 Dihedral : 14.285 86.892 2318 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.06 % Favored : 90.83 % Rotamer: Outliers : 0.31 % Allowed : 9.71 % Favored : 89.98 % 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: -6.33 (0.18), residues: 949 helix: -5.10 (0.08), residues: 306 sheet: -3.66 (0.31), residues: 191 loop : -3.70 (0.22), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.013 0.002 PHE N 27 TYR 0.017 0.001 TYR B 59 ARG 0.005 0.001 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7889 (tttt) cc_final: 0.7687 (tttt) REVERT: A 343 ASP cc_start: 0.8084 (t70) cc_final: 0.7840 (t70) REVERT: B 99 TRP cc_start: 0.7046 (m-90) cc_final: 0.6773 (m-90) REVERT: R 279 MET cc_start: 0.8099 (tpt) cc_final: 0.7884 (tpt) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.2364 time to fit residues: 42.9315 Evaluate side-chains 112 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 74 optimal weight: 0.0770 chunk 28 optimal weight: 0.0010 chunk 45 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 overall best weight: 0.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 278 ASN A 384 GLN A 390 GLN B 183 HIS B 239 ASN B 266 HIS B 295 ASN G 24 ASN R 65 GLN R 229 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.170315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142090 restraints weight = 7616.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.140311 restraints weight = 8483.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141774 restraints weight = 8712.422| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7202 Z= 0.125 Angle : 0.533 5.564 9841 Z= 0.288 Chirality : 0.042 0.145 1180 Planarity : 0.004 0.058 1240 Dihedral : 5.461 59.717 1034 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.31 % Allowed : 14.95 % Favored : 82.74 % 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: -5.64 (0.20), residues: 949 helix: -4.25 (0.16), residues: 321 sheet: -3.53 (0.29), residues: 187 loop : -3.32 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS R 93 PHE 0.015 0.001 PHE N 29 TYR 0.010 0.001 TYR B 59 ARG 0.005 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 283 ARG cc_start: 0.7365 (ttp-110) cc_final: 0.7110 (ttp-110) REVERT: R 36 MET cc_start: 0.7012 (tpp) cc_final: 0.6770 (tpp) REVERT: R 38 ILE cc_start: 0.8476 (mt) cc_final: 0.8245 (mt) REVERT: R 156 MET cc_start: 0.6670 (ttm) cc_final: 0.6230 (tmm) outliers start: 15 outliers final: 7 residues processed: 131 average time/residue: 0.1969 time to fit residues: 34.4709 Evaluate side-chains 111 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 216 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 65 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 68 optimal weight: 0.0470 chunk 28 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.0060 chunk 20 optimal weight: 9.9990 overall best weight: 1.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN A 390 GLN B 183 HIS B 225 HIS G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN R 229 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.158496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.129826 restraints weight = 7974.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129124 restraints weight = 9433.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130854 restraints weight = 8691.442| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7202 Z= 0.256 Angle : 0.578 6.016 9841 Z= 0.312 Chirality : 0.044 0.138 1180 Planarity : 0.004 0.053 1240 Dihedral : 5.798 59.608 1034 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.77 % Allowed : 17.72 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.17 (0.22), residues: 949 helix: -3.69 (0.20), residues: 326 sheet: -3.39 (0.31), residues: 178 loop : -3.14 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.023 0.002 PHE A 212 TYR 0.013 0.001 TYR B 59 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.727 Fit side-chains REVERT: A 283 ARG cc_start: 0.7304 (ttp-110) cc_final: 0.7091 (ttp-110) REVERT: A 343 ASP cc_start: 0.8319 (t70) cc_final: 0.8093 (t70) REVERT: N 33 LYS cc_start: 0.8174 (tttm) cc_final: 0.7932 (tttm) REVERT: R 36 MET cc_start: 0.7050 (tpp) cc_final: 0.6805 (tpp) outliers start: 18 outliers final: 10 residues processed: 132 average time/residue: 0.2041 time to fit residues: 35.9320 Evaluate side-chains 124 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.153428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.124764 restraints weight = 8150.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123573 restraints weight = 10044.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125039 restraints weight = 10063.166| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7202 Z= 0.399 Angle : 0.672 7.078 9841 Z= 0.362 Chirality : 0.046 0.145 1180 Planarity : 0.005 0.058 1240 Dihedral : 6.409 56.325 1034 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 3.70 % Allowed : 19.26 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.06 (0.23), residues: 949 helix: -3.59 (0.21), residues: 322 sheet: -3.38 (0.32), residues: 179 loop : -3.07 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.021 0.002 PHE N 108 TYR 0.014 0.002 TYR N 32 ARG 0.004 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 36 MET cc_start: 0.6961 (tpp) cc_final: 0.6740 (tpp) REVERT: R 82 MET cc_start: 0.7973 (mtp) cc_final: 0.7760 (mtp) outliers start: 24 outliers final: 18 residues processed: 139 average time/residue: 0.1813 time to fit residues: 34.0101 Evaluate side-chains 135 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 0.0670 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 271 ASN G 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.159752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131775 restraints weight = 7712.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131512 restraints weight = 8590.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132571 restraints weight = 8176.843| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7202 Z= 0.155 Angle : 0.538 5.839 9841 Z= 0.290 Chirality : 0.042 0.138 1180 Planarity : 0.004 0.055 1240 Dihedral : 5.512 57.235 1034 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.24 % Allowed : 20.96 % Favored : 75.81 % 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: -4.63 (0.24), residues: 949 helix: -3.15 (0.24), residues: 321 sheet: -3.28 (0.33), residues: 177 loop : -2.82 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.021 0.001 PHE A 212 TYR 0.014 0.001 TYR A 360 ARG 0.004 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.938 Fit side-chains REVERT: A 270 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8139 (tt) REVERT: N 83 MET cc_start: 0.5765 (tpt) cc_final: 0.5486 (tpt) REVERT: R 38 ILE cc_start: 0.8478 (mt) cc_final: 0.8251 (mt) outliers start: 21 outliers final: 11 residues processed: 136 average time/residue: 0.2015 time to fit residues: 37.0131 Evaluate side-chains 125 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 87 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.162978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.133434 restraints weight = 7840.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.133904 restraints weight = 8934.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134584 restraints weight = 7118.267| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7202 Z= 0.145 Angle : 0.541 9.489 9841 Z= 0.285 Chirality : 0.042 0.135 1180 Planarity : 0.004 0.052 1240 Dihedral : 5.131 58.578 1034 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.08 % Allowed : 21.11 % Favored : 75.81 % 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: -4.32 (0.25), residues: 949 helix: -2.83 (0.25), residues: 319 sheet: -3.20 (0.33), residues: 176 loop : -2.65 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.019 0.001 PHE A 212 TYR 0.013 0.001 TYR A 360 ARG 0.007 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8055 (tt) REVERT: B 45 MET cc_start: 0.8277 (mtm) cc_final: 0.8016 (mtm) REVERT: R 38 ILE cc_start: 0.8578 (mt) cc_final: 0.8359 (mt) REVERT: R 275 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7913 (mt) outliers start: 20 outliers final: 14 residues processed: 126 average time/residue: 0.1959 time to fit residues: 33.2673 Evaluate side-chains 124 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.163034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.133295 restraints weight = 7776.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133669 restraints weight = 8722.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134955 restraints weight = 7136.927| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7202 Z= 0.160 Angle : 0.539 8.697 9841 Z= 0.286 Chirality : 0.042 0.134 1180 Planarity : 0.003 0.052 1240 Dihedral : 5.076 59.455 1034 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.08 % Allowed : 22.34 % Favored : 74.58 % 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: -4.12 (0.25), residues: 949 helix: -2.62 (0.26), residues: 319 sheet: -3.13 (0.33), residues: 177 loop : -2.55 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.023 0.001 PHE A 212 TYR 0.011 0.001 TYR A 360 ARG 0.007 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8167 (tt) REVERT: B 45 MET cc_start: 0.8278 (mtm) cc_final: 0.8057 (mtm) REVERT: R 38 ILE cc_start: 0.8545 (mt) cc_final: 0.8271 (mt) outliers start: 20 outliers final: 13 residues processed: 122 average time/residue: 0.1983 time to fit residues: 32.3770 Evaluate side-chains 121 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 73 optimal weight: 0.0970 chunk 94 optimal weight: 0.0670 chunk 48 optimal weight: 0.0060 chunk 38 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 0.1980 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.2532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 183 HIS B 340 ASN G 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.169023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146273 restraints weight = 7695.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.142594 restraints weight = 12243.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.144483 restraints weight = 12136.482| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7202 Z= 0.118 Angle : 0.506 8.200 9841 Z= 0.267 Chirality : 0.041 0.139 1180 Planarity : 0.003 0.051 1240 Dihedral : 4.629 56.597 1034 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.62 % Allowed : 22.03 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.25), residues: 949 helix: -2.51 (0.26), residues: 334 sheet: -2.85 (0.32), residues: 190 loop : -2.42 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 82 HIS 0.002 0.000 HIS A 357 PHE 0.020 0.001 PHE A 212 TYR 0.011 0.001 TYR A 360 ARG 0.005 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7418 (mppt) cc_final: 0.7199 (mptt) REVERT: A 270 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8272 (tt) REVERT: B 52 ARG cc_start: 0.7521 (ptp-110) cc_final: 0.7219 (ptp90) REVERT: B 117 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7934 (mt) REVERT: R 38 ILE cc_start: 0.8386 (mt) cc_final: 0.8125 (mt) REVERT: R 156 MET cc_start: 0.6622 (ttm) cc_final: 0.6309 (tmm) REVERT: R 279 MET cc_start: 0.6875 (tpt) cc_final: 0.6576 (ttt) outliers start: 17 outliers final: 10 residues processed: 129 average time/residue: 0.1855 time to fit residues: 32.2887 Evaluate side-chains 117 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 37 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.162514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132992 restraints weight = 7887.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133247 restraints weight = 8939.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134471 restraints weight = 7888.745| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7202 Z= 0.207 Angle : 0.549 7.385 9841 Z= 0.289 Chirality : 0.043 0.136 1180 Planarity : 0.003 0.050 1240 Dihedral : 4.912 54.502 1034 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.77 % Allowed : 22.50 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.25), residues: 949 helix: -2.39 (0.27), residues: 326 sheet: -2.81 (0.33), residues: 175 loop : -2.44 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.018 0.001 PHE A 212 TYR 0.010 0.001 TYR A 360 ARG 0.006 0.001 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8116 (tt) REVERT: N 83 MET cc_start: 0.5748 (tpt) cc_final: 0.5532 (tpt) REVERT: R 38 ILE cc_start: 0.8562 (mt) cc_final: 0.8286 (mt) REVERT: R 279 MET cc_start: 0.6828 (tpt) cc_final: 0.6514 (ttt) outliers start: 18 outliers final: 9 residues processed: 125 average time/residue: 0.1862 time to fit residues: 31.8807 Evaluate side-chains 118 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 8 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.166512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.136954 restraints weight = 7943.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.137042 restraints weight = 9056.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138419 restraints weight = 7569.693| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7202 Z= 0.147 Angle : 0.531 7.518 9841 Z= 0.277 Chirality : 0.042 0.137 1180 Planarity : 0.003 0.052 1240 Dihedral : 4.727 53.517 1034 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.69 % Allowed : 23.88 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.26), residues: 949 helix: -2.27 (0.27), residues: 333 sheet: -2.62 (0.34), residues: 173 loop : -2.43 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.019 0.001 PHE A 212 TYR 0.013 0.001 TYR A 360 ARG 0.006 0.000 ARG R 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7388 (mppt) cc_final: 0.7160 (mptt) REVERT: A 270 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8141 (tt) REVERT: N 83 MET cc_start: 0.5769 (tpt) cc_final: 0.5369 (tpt) REVERT: R 38 ILE cc_start: 0.8548 (mt) cc_final: 0.8289 (mt) outliers start: 11 outliers final: 9 residues processed: 118 average time/residue: 0.1789 time to fit residues: 29.1157 Evaluate side-chains 118 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 43 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.0050 chunk 56 optimal weight: 3.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.166824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.140150 restraints weight = 7748.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.138410 restraints weight = 10562.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.139590 restraints weight = 10160.275| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7202 Z= 0.142 Angle : 0.525 7.631 9841 Z= 0.273 Chirality : 0.042 0.137 1180 Planarity : 0.003 0.050 1240 Dihedral : 4.562 50.045 1034 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.69 % Allowed : 24.04 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.26), residues: 949 helix: -2.08 (0.28), residues: 320 sheet: -2.49 (0.34), residues: 183 loop : -2.33 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.018 0.001 PHE A 212 TYR 0.013 0.001 TYR A 360 ARG 0.006 0.000 ARG R 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2239.92 seconds wall clock time: 40 minutes 55.64 seconds (2455.64 seconds total)