Starting phenix.real_space_refine on Wed Mar 12 00:58:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dhr_30682/03_2025/7dhr_30682.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dhr_30682/03_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_30682/03_2025/7dhr_30682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dhr_30682/03_2025/7dhr_30682.map" model { file = "/net/cci-nas-00/data/ceres_data/7dhr_30682/03_2025/7dhr_30682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dhr_30682/03_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-5624/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: 4.63, per 1000 atoms: 0.66 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: 1.69 Conformation dependent library (CDL) restraints added in 1.1 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: 0.83 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: 1.70 Time building geometry restraints manager: 1.97 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: 0.000 Normalize map: mean=0, sd=1: 0.270 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.780 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.420 ------------------------------------------------------------------------------- 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 : 0.787 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: 0.2244 time to fit residues: 40.6362 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 : 0.751 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.4786 ------------------------------------------------------------------------------- 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 225 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.168758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.141696 restraints weight = 7650.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139750 restraints weight = 9648.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.141832 restraints weight = 9214.548| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7202 Z= 0.132 Angle : 0.534 5.572 9841 Z= 0.289 Chirality : 0.042 0.143 1180 Planarity : 0.004 0.058 1240 Dihedral : 5.486 58.619 1034 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.31 % Allowed : 14.48 % Favored : 83.20 % 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: -4.24 (0.16), residues: 321 sheet: -3.57 (0.29), residues: 188 loop : -3.31 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 93 PHE 0.014 0.001 PHE N 29 TYR 0.011 0.001 TYR B 59 ARG 0.005 0.000 ARG B 137 *********************** 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 135 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 283 ARG cc_start: 0.7337 (ttp-110) cc_final: 0.7088 (ttp-110) REVERT: B 61 MET cc_start: 0.8896 (ppp) cc_final: 0.8687 (ppp) REVERT: B 99 TRP cc_start: 0.7008 (m-90) cc_final: 0.6787 (m-90) REVERT: B 117 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8018 (tt) REVERT: N 33 LYS cc_start: 0.8039 (tttm) cc_final: 0.7779 (tttm) REVERT: R 36 MET cc_start: 0.7003 (tpp) cc_final: 0.6774 (tpp) REVERT: R 38 ILE cc_start: 0.8470 (mt) cc_final: 0.8233 (mt) outliers start: 15 outliers final: 8 residues processed: 130 average time/residue: 0.1876 time to fit residues: 32.7609 Evaluate side-chains 113 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 117 LEU 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 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: 5.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 0.0000 chunk 78 optimal weight: 0.3980 chunk 60 optimal weight: 0.0570 chunk 20 optimal weight: 9.9990 overall best weight: 0.6904 ------------------------------------------------------------------------------- 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 G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.167330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136758 restraints weight = 7792.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137952 restraints weight = 6592.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.139025 restraints weight = 5862.824| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7202 Z= 0.141 Angle : 0.503 5.550 9841 Z= 0.273 Chirality : 0.041 0.130 1180 Planarity : 0.004 0.052 1240 Dihedral : 5.154 56.276 1034 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.62 % Allowed : 17.10 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.06 (0.22), residues: 949 helix: -3.61 (0.21), residues: 327 sheet: -3.32 (0.30), residues: 189 loop : -3.02 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.026 0.001 PHE A 212 TYR 0.014 0.001 TYR B 289 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 126 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.703 Fit side-chains REVERT: B 117 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7712 (mp) REVERT: B 258 ASP cc_start: 0.7641 (m-30) cc_final: 0.6680 (t0) REVERT: N 33 LYS cc_start: 0.7930 (tttm) cc_final: 0.7687 (tttm) REVERT: R 38 ILE cc_start: 0.8635 (mt) cc_final: 0.8381 (mt) REVERT: R 156 MET cc_start: 0.6613 (ttm) cc_final: 0.6062 (tmm) outliers start: 17 outliers final: 9 residues processed: 120 average time/residue: 0.1921 time to fit residues: 30.7421 Evaluate side-chains 117 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 117 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 13 optimal weight: 40.0000 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.163765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134787 restraints weight = 7869.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133211 restraints weight = 8288.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134787 restraints weight = 7554.331| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7202 Z= 0.180 Angle : 0.519 5.570 9841 Z= 0.281 Chirality : 0.042 0.125 1180 Planarity : 0.003 0.050 1240 Dihedral : 5.139 55.236 1034 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.24 % Allowed : 18.03 % Favored : 78.74 % 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: -4.66 (0.23), residues: 949 helix: -3.22 (0.23), residues: 322 sheet: -3.16 (0.32), residues: 176 loop : -2.86 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.020 0.001 PHE A 212 TYR 0.014 0.001 TYR B 59 ARG 0.002 0.000 ARG B 137 *********************** 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 132 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8157 (tt) REVERT: A 291 LEU cc_start: 0.7155 (mt) cc_final: 0.6954 (mt) REVERT: B 45 MET cc_start: 0.8257 (mtm) cc_final: 0.7976 (mtm) REVERT: N 33 LYS cc_start: 0.7966 (tttm) cc_final: 0.7720 (tttm) REVERT: R 38 ILE cc_start: 0.8616 (mt) cc_final: 0.8371 (mt) REVERT: R 156 MET cc_start: 0.6752 (ttm) cc_final: 0.6204 (tmm) outliers start: 21 outliers final: 11 residues processed: 126 average time/residue: 0.1937 time to fit residues: 32.8297 Evaluate side-chains 116 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 93 ILE Chi-restraints excluded: chain B residue 147 SER 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 R residue 184 CYS Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.159936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.132773 restraints weight = 7727.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131879 restraints weight = 8941.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132796 restraints weight = 8931.076| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7202 Z= 0.206 Angle : 0.540 6.775 9841 Z= 0.290 Chirality : 0.043 0.130 1180 Planarity : 0.003 0.050 1240 Dihedral : 5.232 54.584 1034 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.93 % Allowed : 19.72 % Favored : 77.35 % 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: -4.47 (0.24), residues: 949 helix: -3.01 (0.24), residues: 322 sheet: -3.07 (0.33), residues: 177 loop : -2.79 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE A 212 TYR 0.009 0.001 TYR B 289 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 133 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8148 (tt) REVERT: A 291 LEU cc_start: 0.7282 (mt) cc_final: 0.7069 (mt) REVERT: B 45 MET cc_start: 0.8299 (mtm) cc_final: 0.8036 (mtm) outliers start: 19 outliers final: 17 residues processed: 126 average time/residue: 0.1768 time to fit residues: 30.2922 Evaluate side-chains 123 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 93 ILE Chi-restraints excluded: chain B residue 147 SER 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 N residue 79 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 0.0970 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.162483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.133481 restraints weight = 7702.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134271 restraints weight = 8526.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.135345 restraints weight = 6726.194| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2388 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= 0.148 Angle : 0.504 5.973 9841 Z= 0.271 Chirality : 0.042 0.135 1180 Planarity : 0.003 0.051 1240 Dihedral : 4.909 52.834 1034 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.54 % Allowed : 20.18 % Favored : 76.27 % 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: -4.21 (0.25), residues: 949 helix: -2.73 (0.26), residues: 322 sheet: -2.97 (0.33), residues: 176 loop : -2.67 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE A 212 TYR 0.015 0.001 TYR A 360 ARG 0.002 0.000 ARG B 137 *********************** 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 135 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8180 (tt) REVERT: B 45 MET cc_start: 0.8245 (mtm) cc_final: 0.7994 (mtm) REVERT: R 38 ILE cc_start: 0.8550 (mt) cc_final: 0.8257 (mt) REVERT: R 156 MET cc_start: 0.6713 (ttm) cc_final: 0.6177 (tmm) outliers start: 23 outliers final: 15 residues processed: 128 average time/residue: 0.1920 time to fit residues: 32.8351 Evaluate side-chains 121 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 147 SER 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 G residue 22 GLU 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 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: 0.4980 chunk 25 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.0670 chunk 28 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 267 GLN A 271 ASN G 24 ASN N 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.168587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.145085 restraints weight = 7725.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.143242 restraints weight = 12365.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145224 restraints weight = 11551.847| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2653 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= 0.120 Angle : 0.503 9.895 9841 Z= 0.265 Chirality : 0.041 0.137 1180 Planarity : 0.003 0.050 1240 Dihedral : 4.494 47.326 1034 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.24 % Allowed : 20.80 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.25), residues: 949 helix: -2.48 (0.27), residues: 328 sheet: -2.76 (0.33), residues: 185 loop : -2.58 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP B 82 HIS 0.002 0.000 HIS A 357 PHE 0.024 0.001 PHE A 212 TYR 0.014 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 134 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7348 (mppt) cc_final: 0.7029 (mmtm) REVERT: A 270 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8324 (tt) REVERT: A 291 LEU cc_start: 0.7265 (mt) cc_final: 0.7046 (mt) REVERT: B 45 MET cc_start: 0.8157 (mtm) cc_final: 0.7955 (mtm) REVERT: R 38 ILE cc_start: 0.8419 (mt) cc_final: 0.8142 (mt) REVERT: R 156 MET cc_start: 0.6529 (ttm) cc_final: 0.6291 (tmm) outliers start: 21 outliers final: 13 residues processed: 129 average time/residue: 0.1786 time to fit residues: 31.3631 Evaluate side-chains 118 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 147 SER 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 G residue 22 GLU 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 275 LEU Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 73 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN G 24 ASN N 53 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.162845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133919 restraints weight = 7667.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.134220 restraints weight = 8611.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135277 restraints weight = 7335.251| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7202 Z= 0.173 Angle : 0.522 9.559 9841 Z= 0.276 Chirality : 0.042 0.129 1180 Planarity : 0.003 0.050 1240 Dihedral : 4.615 43.176 1034 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.77 % Allowed : 21.11 % Favored : 76.12 % 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: -3.88 (0.25), residues: 949 helix: -2.37 (0.27), residues: 330 sheet: -2.65 (0.34), residues: 182 loop : -2.59 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.020 0.001 PHE A 212 TYR 0.012 0.001 TYR A 360 ARG 0.006 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 122 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8101 (tt) REVERT: A 291 LEU cc_start: 0.7248 (mt) cc_final: 0.6996 (mt) REVERT: B 45 MET cc_start: 0.8236 (mtm) cc_final: 0.8007 (mtm) REVERT: R 38 ILE cc_start: 0.8537 (mt) cc_final: 0.8260 (mt) REVERT: R 156 MET cc_start: 0.6573 (ttm) cc_final: 0.6302 (tmm) outliers start: 18 outliers final: 14 residues processed: 115 average time/residue: 0.1723 time to fit residues: 27.3725 Evaluate side-chains 114 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 29 THR Chi-restraints excluded: chain B residue 147 SER 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 154 ILE Chi-restraints excluded: chain R residue 184 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.163537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.134262 restraints weight = 7732.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.134096 restraints weight = 9409.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.135138 restraints weight = 7613.875| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2731 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= 0.162 Angle : 0.512 9.250 9841 Z= 0.272 Chirality : 0.042 0.131 1180 Planarity : 0.003 0.050 1240 Dihedral : 4.536 39.853 1034 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % 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: -3.73 (0.25), residues: 949 helix: -2.21 (0.28), residues: 322 sheet: -2.61 (0.33), residues: 189 loop : -2.51 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.020 0.001 PHE A 212 TYR 0.013 0.001 TYR B 289 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 121 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8107 (tt) REVERT: A 291 LEU cc_start: 0.7128 (mt) cc_final: 0.6857 (mt) REVERT: B 45 MET cc_start: 0.8300 (mtm) cc_final: 0.8089 (mtm) REVERT: R 38 ILE cc_start: 0.8533 (mt) cc_final: 0.8265 (mt) REVERT: R 156 MET cc_start: 0.6618 (ttm) cc_final: 0.6308 (tmm) outliers start: 18 outliers final: 16 residues processed: 115 average time/residue: 0.1695 time to fit residues: 26.9365 Evaluate side-chains 117 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 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 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 147 SER 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 73 THR Chi-restraints excluded: chain R residue 154 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 275 LEU Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 8 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 0.0040 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN G 24 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.163945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134790 restraints weight = 7826.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.134266 restraints weight = 9176.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135770 restraints weight = 8593.448| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7202 Z= 0.156 Angle : 0.523 9.036 9841 Z= 0.275 Chirality : 0.042 0.132 1180 Planarity : 0.003 0.050 1240 Dihedral : 4.503 36.932 1034 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.62 % Allowed : 22.96 % 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: -3.61 (0.26), residues: 949 helix: -2.12 (0.28), residues: 327 sheet: -2.56 (0.34), residues: 183 loop : -2.42 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.021 0.001 PHE A 212 TYR 0.012 0.001 TYR B 289 ARG 0.006 0.001 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 119 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8085 (tt) REVERT: A 291 LEU cc_start: 0.7244 (mt) cc_final: 0.6965 (mt) REVERT: R 38 ILE cc_start: 0.8517 (mt) cc_final: 0.8250 (mt) REVERT: R 156 MET cc_start: 0.6651 (ttm) cc_final: 0.6334 (tmm) REVERT: R 279 MET cc_start: 0.6585 (tpt) cc_final: 0.6186 (ttt) outliers start: 17 outliers final: 14 residues processed: 113 average time/residue: 0.1690 time to fit residues: 26.4102 Evaluate side-chains 113 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 147 SER 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 73 THR Chi-restraints excluded: chain R residue 154 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 275 LEU Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 43 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 56 optimal weight: 5.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN G 24 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.164354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.136922 restraints weight = 7615.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.135877 restraints weight = 9960.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.136807 restraints weight = 9396.876| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7202 Z= 0.159 Angle : 0.523 8.902 9841 Z= 0.275 Chirality : 0.042 0.131 1180 Planarity : 0.003 0.050 1240 Dihedral : 4.445 33.533 1034 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.62 % Allowed : 23.42 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.26), residues: 949 helix: -2.05 (0.28), residues: 327 sheet: -2.43 (0.35), residues: 192 loop : -2.41 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.020 0.001 PHE A 212 TYR 0.013 0.001 TYR B 289 ARG 0.006 0.001 ARG R 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2251.52 seconds wall clock time: 39 minutes 56.50 seconds (2396.50 seconds total)