Starting phenix.real_space_refine on Wed Sep 25 15:29:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6os9_20180/09_2024/6os9_20180.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6os9_20180/09_2024/6os9_20180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6os9_20180/09_2024/6os9_20180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6os9_20180/09_2024/6os9_20180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6os9_20180/09_2024/6os9_20180.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6os9_20180/09_2024/6os9_20180.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2127 atoms to isotropic. 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 61 5.16 5 C 5711 2.51 5 N 1528 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8969 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2415 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1751 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 5.24, per 1000 atoms: 0.58 Number of scatterers: 8969 At special positions: 0 Unit cell: (102.82, 121.9, 119.78, 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 61 16.00 O 1669 8.00 N 1528 7.00 C 5711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " 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: 2.07 Conformation dependent library (CDL) restraints added in 1.0 seconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 39.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'R' and resid 51 through 55 removed outlier: 3.607A pdb=" N LEU R 54 " --> pdb=" O SER R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 91 Processing helix chain 'R' and resid 97 through 128 removed outlier: 4.228A pdb=" N VAL R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) Proline residue: R 121 - end of helix removed outlier: 3.620A pdb=" N TYR R 125 " --> pdb=" O PRO R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 172 removed outlier: 3.514A pdb=" N GLY R 140 " --> pdb=" O PHE R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 180 Processing helix chain 'R' and resid 181 through 199 Processing helix chain 'R' and resid 201 through 206 removed outlier: 4.131A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 201 through 206' Processing helix chain 'R' and resid 229 through 245 removed outlier: 4.185A pdb=" N VAL R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 272 Processing helix chain 'R' and resid 295 through 329 removed outlier: 3.568A pdb=" N ARG R 299 " --> pdb=" O VAL R 295 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG R 306 " --> pdb=" O VAL R 302 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 366 Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 367 through 369 No H-bonds generated for 'chain 'R' and resid 367 through 369' Processing helix chain 'R' and resid 370 through 375 removed outlier: 4.507A pdb=" N ILE R 374 " --> pdb=" O ASN R 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.946A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.720A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.365A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.855A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.622A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.694A pdb=" N SER D 55 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 52 through 56' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'R' and resid 209 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.960A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.862A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.701A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.654A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.588A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.590A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 5.979A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.688A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.700A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.700A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 130 removed outlier: 3.702A pdb=" N ALA D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.692A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2828 1.34 - 1.46: 2369 1.46 - 1.59: 3873 1.59 - 1.72: 0 1.72 - 1.84: 90 Bond restraints: 9160 Sorted by residual: bond pdb=" C MET R 120 " pdb=" N PRO R 121 " ideal model delta sigma weight residual 1.336 1.376 -0.041 1.23e-02 6.61e+03 1.09e+01 bond pdb=" CG1 ILE B 80 " pdb=" CD1 ILE B 80 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.48e+00 bond pdb=" CB VAL R 159 " pdb=" CG1 VAL R 159 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.02e+00 bond pdb=" CG LEU B 146 " pdb=" CD1 LEU B 146 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.15e+00 bond pdb=" CB VAL R 313 " pdb=" CG2 VAL R 313 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.98e+00 ... (remaining 9155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 12071 2.73 - 5.46: 297 5.46 - 8.20: 36 8.20 - 10.93: 8 10.93 - 13.66: 7 Bond angle restraints: 12419 Sorted by residual: angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 135.20 -13.66 1.91e+00 2.74e-01 5.11e+01 angle pdb=" C SER B 227 " pdb=" N ASP B 228 " pdb=" CA ASP B 228 " ideal model delta sigma weight residual 120.90 127.76 -6.86 1.41e+00 5.03e-01 2.37e+01 angle pdb=" C HIS B 142 " pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta sigma weight residual 122.46 129.15 -6.69 1.41e+00 5.03e-01 2.25e+01 angle pdb=" CA ARG D 206 " pdb=" CB ARG D 206 " pdb=" CG ARG D 206 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" C TYR D 178 " pdb=" N ARG D 179 " pdb=" CA ARG D 179 " ideal model delta sigma weight residual 122.19 127.99 -5.80 1.41e+00 5.03e-01 1.69e+01 ... (remaining 12414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 5128 16.05 - 32.10: 236 32.10 - 48.16: 42 48.16 - 64.21: 4 64.21 - 80.26: 7 Dihedral angle restraints: 5417 sinusoidal: 2069 harmonic: 3348 Sorted by residual: dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual -86.00 -166.26 80.26 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 165.73 -72.73 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 5414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1091 0.068 - 0.136: 282 0.136 - 0.204: 32 0.204 - 0.272: 9 0.272 - 0.340: 4 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CG LEU D 162 " pdb=" CB LEU D 162 " pdb=" CD1 LEU D 162 " pdb=" CD2 LEU D 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB VAL B 90 " pdb=" CA VAL B 90 " pdb=" CG1 VAL B 90 " pdb=" CG2 VAL B 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB ILE D 100 " pdb=" CA ILE D 100 " pdb=" CG1 ILE D 100 " pdb=" CG2 ILE D 100 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 1415 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 142 " 0.026 2.00e-02 2.50e+03 2.67e-02 1.07e+01 pdb=" CG HIS B 142 " -0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS B 142 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS B 142 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS B 142 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS B 142 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 111 " -0.023 2.00e-02 2.50e+03 1.75e-02 7.67e+00 pdb=" CG TRP D 111 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP D 111 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP D 111 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 111 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 111 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 111 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 111 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 111 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 111 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 227 " -0.006 2.00e-02 2.50e+03 1.71e-02 5.13e+00 pdb=" CG PHE D 227 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE D 227 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE D 227 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 227 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE D 227 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 227 " -0.002 2.00e-02 2.50e+03 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1880 2.77 - 3.30: 7993 3.30 - 3.84: 14878 3.84 - 4.37: 17205 4.37 - 4.90: 30523 Nonbonded interactions: 72479 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.240 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR D 163 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.270 3.040 nonbonded pdb=" O ILE D 126 " pdb=" OG1 THR D 226 " model vdw 2.286 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.290 3.040 ... (remaining 72474 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.520 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.010 0.091 9160 Z= 0.668 Angle : 1.083 13.659 12419 Z= 0.579 Chirality : 0.062 0.340 1418 Planarity : 0.006 0.051 1566 Dihedral : 10.142 77.253 3248 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.21 % Allowed : 4.13 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.70 (0.21), residues: 1132 helix: -1.48 (0.20), residues: 391 sheet: -1.61 (0.28), residues: 286 loop : -2.01 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP D 111 HIS 0.028 0.004 HIS B 142 PHE 0.037 0.004 PHE A 199 TYR 0.036 0.004 TYR B 111 ARG 0.010 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 1.108 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 205 PHE cc_start: 0.7011 (p90) cc_final: 0.6554 (m-80) REVERT: R 210 GLN cc_start: 0.8365 (tt0) cc_final: 0.8125 (tt0) REVERT: R 232 THR cc_start: 0.7968 (m) cc_final: 0.7466 (m) REVERT: R 325 MET cc_start: 0.8262 (ttm) cc_final: 0.8000 (ttm) REVERT: A 49 ILE cc_start: 0.8426 (mt) cc_final: 0.8223 (OUTLIER) REVERT: B 12 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8271 (tp30) REVERT: B 170 ASP cc_start: 0.7912 (t70) cc_final: 0.7592 (t70) REVERT: B 188 MET cc_start: 0.8426 (mmm) cc_final: 0.8158 (mmp) REVERT: D 46 GLU cc_start: 0.8046 (tt0) cc_final: 0.7838 (tt0) outliers start: 2 outliers final: 4 residues processed: 225 average time/residue: 1.2317 time to fit residues: 295.1366 Evaluate side-chains 152 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 24 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 255 ASN A 306 GLN B 88 ASN B 91 HIS B 259 GLN B 311 HIS D 130 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9160 Z= 0.199 Angle : 0.644 8.119 12419 Z= 0.339 Chirality : 0.043 0.138 1418 Planarity : 0.004 0.042 1566 Dihedral : 5.088 25.857 1252 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.51 % Allowed : 13.31 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1132 helix: 0.46 (0.25), residues: 392 sheet: -1.02 (0.28), residues: 292 loop : -1.51 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 111 HIS 0.014 0.001 HIS B 142 PHE 0.012 0.002 PHE R 188 TYR 0.017 0.002 TYR A 296 ARG 0.011 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 182 time to evaluate : 1.080 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 124 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8600 (mm) REVERT: A 24 ARG cc_start: 0.7721 (mtt180) cc_final: 0.7198 (mtm110) REVERT: A 49 ILE cc_start: 0.8349 (mt) cc_final: 0.7930 (mp) REVERT: A 53 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7043 (mpt) REVERT: B 12 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8416 (tm-30) REVERT: B 226 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: B 280 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7866 (tttp) REVERT: C 20 LYS cc_start: 0.8383 (ptmt) cc_final: 0.8110 (pttt) REVERT: D 46 GLU cc_start: 0.8068 (tt0) cc_final: 0.7798 (tt0) outliers start: 34 outliers final: 10 residues processed: 195 average time/residue: 1.1641 time to fit residues: 242.1154 Evaluate side-chains 157 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 186 LYS Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain D residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 90 optimal weight: 0.1980 chunk 34 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 294 ASN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9160 Z= 0.238 Angle : 0.633 8.666 12419 Z= 0.328 Chirality : 0.044 0.178 1418 Planarity : 0.004 0.040 1566 Dihedral : 4.817 29.106 1252 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.92 % Allowed : 15.69 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.25), residues: 1132 helix: 1.14 (0.26), residues: 395 sheet: -0.81 (0.29), residues: 294 loop : -1.14 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 111 HIS 0.016 0.001 HIS B 142 PHE 0.022 0.002 PHE D 68 TYR 0.015 0.002 TYR A 296 ARG 0.008 0.001 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 155 time to evaluate : 1.102 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7574 (mpt) cc_final: 0.7059 (mpt) REVERT: B 12 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8529 (tm-30) REVERT: B 45 MET cc_start: 0.8148 (mtm) cc_final: 0.7887 (ptp) REVERT: B 217 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.6785 (pmm) REVERT: B 280 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7733 (tttp) REVERT: C 20 LYS cc_start: 0.8404 (ptmt) cc_final: 0.8119 (pttt) REVERT: D 46 GLU cc_start: 0.7991 (tt0) cc_final: 0.7706 (tt0) REVERT: D 183 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8882 (mp) outliers start: 38 outliers final: 13 residues processed: 175 average time/residue: 1.1813 time to fit residues: 220.8231 Evaluate side-chains 155 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9160 Z= 0.228 Angle : 0.621 8.348 12419 Z= 0.319 Chirality : 0.043 0.159 1418 Planarity : 0.004 0.044 1566 Dihedral : 4.660 30.315 1252 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.92 % Allowed : 17.03 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1132 helix: 1.47 (0.26), residues: 394 sheet: -0.71 (0.29), residues: 301 loop : -0.93 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 111 HIS 0.014 0.001 HIS B 142 PHE 0.014 0.002 PHE D 68 TYR 0.017 0.002 TYR A 296 ARG 0.009 0.001 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 1.075 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: R 123 GLU cc_start: 0.8049 (tt0) cc_final: 0.7840 (tt0) REVERT: R 354 TYR cc_start: 0.7690 (m-10) cc_final: 0.7473 (m-10) REVERT: A 244 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.6904 (m90) REVERT: B 12 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8411 (tm-30) REVERT: B 217 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.6769 (pmm) REVERT: B 226 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: B 280 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7762 (tttp) REVERT: C 20 LYS cc_start: 0.8334 (ptmt) cc_final: 0.7971 (pttt) REVERT: D 46 GLU cc_start: 0.7991 (tt0) cc_final: 0.7680 (tt0) outliers start: 38 outliers final: 16 residues processed: 177 average time/residue: 1.2205 time to fit residues: 230.3008 Evaluate side-chains 161 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 51 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9160 Z= 0.170 Angle : 0.606 10.118 12419 Z= 0.309 Chirality : 0.043 0.228 1418 Planarity : 0.004 0.043 1566 Dihedral : 4.412 25.129 1250 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.61 % Allowed : 18.68 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1132 helix: 1.62 (0.26), residues: 399 sheet: -0.41 (0.30), residues: 297 loop : -0.88 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.010 0.001 HIS B 142 PHE 0.014 0.001 PHE D 68 TYR 0.017 0.001 TYR A 296 ARG 0.010 0.001 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 1.069 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 210 GLN cc_start: 0.7799 (tt0) cc_final: 0.7520 (tt0) REVERT: A 244 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.6874 (m90) REVERT: A 253 ILE cc_start: 0.8667 (tp) cc_final: 0.8290 (pp) REVERT: A 313 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6824 (ptp-170) REVERT: B 8 ARG cc_start: 0.7091 (mtt90) cc_final: 0.6852 (mtp85) REVERT: B 20 ASP cc_start: 0.8411 (t0) cc_final: 0.8199 (t0) REVERT: B 226 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: B 266 HIS cc_start: 0.8201 (t-90) cc_final: 0.7940 (t-90) REVERT: B 280 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7554 (tttp) REVERT: C 20 LYS cc_start: 0.8231 (ptmt) cc_final: 0.7961 (pttt) REVERT: D 46 GLU cc_start: 0.8098 (tt0) cc_final: 0.7792 (tt0) outliers start: 35 outliers final: 11 residues processed: 180 average time/residue: 1.1275 time to fit residues: 217.1179 Evaluate side-chains 160 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 HIS ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 306 GLN B 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9160 Z= 0.388 Angle : 0.709 9.580 12419 Z= 0.362 Chirality : 0.046 0.209 1418 Planarity : 0.004 0.055 1566 Dihedral : 4.831 39.745 1250 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.75 % Allowed : 19.20 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1132 helix: 1.37 (0.26), residues: 400 sheet: -0.42 (0.30), residues: 294 loop : -0.83 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.018 0.001 HIS B 142 PHE 0.020 0.002 PHE D 68 TYR 0.026 0.002 TYR B 105 ARG 0.011 0.001 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 153 time to evaluate : 1.051 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 244 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.7015 (m90) REVERT: A 313 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6946 (ptp-170) REVERT: B 146 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8268 (mt) REVERT: B 217 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.6993 (pmm) REVERT: B 226 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: B 266 HIS cc_start: 0.8285 (t-90) cc_final: 0.8019 (t-90) REVERT: C 20 LYS cc_start: 0.8285 (ptmt) cc_final: 0.7942 (pttt) REVERT: D 46 GLU cc_start: 0.8134 (tt0) cc_final: 0.7885 (tt0) REVERT: D 93 MET cc_start: 0.8087 (tpp) cc_final: 0.7722 (ttt) outliers start: 46 outliers final: 25 residues processed: 183 average time/residue: 1.1499 time to fit residues: 224.9894 Evaluate side-chains 168 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain R residue 357 SER Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 172 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9160 Z= 0.206 Angle : 0.661 10.595 12419 Z= 0.332 Chirality : 0.043 0.245 1418 Planarity : 0.004 0.052 1566 Dihedral : 4.541 29.236 1250 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.30 % Allowed : 21.57 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1132 helix: 1.58 (0.26), residues: 400 sheet: -0.29 (0.30), residues: 303 loop : -0.76 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.014 0.001 HIS B 142 PHE 0.015 0.001 PHE D 68 TYR 0.025 0.001 TYR A 296 ARG 0.012 0.001 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 1.049 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 210 GLN cc_start: 0.7770 (tt0) cc_final: 0.7488 (tt0) REVERT: R 269 GLN cc_start: 0.7881 (pt0) cc_final: 0.7640 (pt0) REVERT: A 244 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.6876 (m90) REVERT: A 253 ILE cc_start: 0.8697 (tp) cc_final: 0.8382 (pp) REVERT: A 313 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6858 (ptp-170) REVERT: C 20 LYS cc_start: 0.8246 (ptmt) cc_final: 0.7881 (pttt) REVERT: D 11 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7211 (mp) REVERT: D 46 GLU cc_start: 0.8100 (tt0) cc_final: 0.7839 (tt0) REVERT: D 93 MET cc_start: 0.8071 (tpp) cc_final: 0.7748 (ttt) outliers start: 32 outliers final: 15 residues processed: 162 average time/residue: 1.1416 time to fit residues: 197.9559 Evaluate side-chains 158 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9160 Z= 0.251 Angle : 0.685 9.281 12419 Z= 0.346 Chirality : 0.044 0.184 1418 Planarity : 0.004 0.059 1566 Dihedral : 4.489 31.424 1248 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.41 % Allowed : 21.78 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1132 helix: 1.58 (0.26), residues: 400 sheet: -0.21 (0.31), residues: 293 loop : -0.77 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.014 0.001 HIS B 142 PHE 0.016 0.002 PHE D 68 TYR 0.022 0.002 TYR A 296 ARG 0.013 0.001 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 1.078 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 210 GLN cc_start: 0.7812 (tt0) cc_final: 0.7555 (tt0) REVERT: R 222 LEU cc_start: 0.7908 (mm) cc_final: 0.7648 (mt) REVERT: R 269 GLN cc_start: 0.7882 (pt0) cc_final: 0.7639 (pt0) REVERT: A 244 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.6840 (m90) REVERT: A 253 ILE cc_start: 0.8717 (tp) cc_final: 0.8348 (pp) REVERT: B 226 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: C 20 LYS cc_start: 0.8209 (ptmt) cc_final: 0.7876 (pttt) REVERT: D 46 GLU cc_start: 0.8063 (tt0) cc_final: 0.7813 (tt0) REVERT: D 76 LYS cc_start: 0.8165 (mtmm) cc_final: 0.7927 (pmtt) REVERT: D 93 MET cc_start: 0.8094 (tpp) cc_final: 0.7802 (ttt) outliers start: 33 outliers final: 21 residues processed: 163 average time/residue: 1.1927 time to fit residues: 207.6082 Evaluate side-chains 160 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 172 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9160 Z= 0.228 Angle : 0.683 13.623 12419 Z= 0.341 Chirality : 0.044 0.352 1418 Planarity : 0.004 0.061 1566 Dihedral : 4.417 30.443 1248 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.68 % Allowed : 23.32 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.26), residues: 1132 helix: 1.59 (0.26), residues: 400 sheet: -0.21 (0.31), residues: 302 loop : -0.71 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.012 0.001 HIS B 142 PHE 0.016 0.001 PHE D 68 TYR 0.019 0.001 TYR A 296 ARG 0.013 0.001 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.058 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 222 LEU cc_start: 0.7893 (mm) cc_final: 0.7675 (mt) REVERT: R 269 GLN cc_start: 0.7851 (pt0) cc_final: 0.7638 (pt0) REVERT: A 244 HIS cc_start: 0.7727 (OUTLIER) cc_final: 0.6737 (m90) REVERT: A 253 ILE cc_start: 0.8692 (tp) cc_final: 0.8348 (pp) REVERT: B 146 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8137 (mt) REVERT: B 226 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: C 20 LYS cc_start: 0.8245 (ptmt) cc_final: 0.7916 (pttt) REVERT: D 46 GLU cc_start: 0.8008 (tt0) cc_final: 0.7739 (tt0) REVERT: D 93 MET cc_start: 0.8046 (tpp) cc_final: 0.7788 (ttt) outliers start: 26 outliers final: 19 residues processed: 158 average time/residue: 1.1463 time to fit residues: 193.5752 Evaluate side-chains 159 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 172 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9160 Z= 0.209 Angle : 0.665 12.391 12419 Z= 0.336 Chirality : 0.043 0.159 1418 Planarity : 0.004 0.065 1566 Dihedral : 4.311 28.001 1248 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.48 % Allowed : 23.32 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1132 helix: 1.67 (0.26), residues: 399 sheet: -0.08 (0.32), residues: 276 loop : -0.69 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 316 HIS 0.011 0.001 HIS B 142 PHE 0.016 0.001 PHE R 74 TYR 0.018 0.001 TYR A 296 ARG 0.015 0.001 ARG D 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 0.996 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 210 GLN cc_start: 0.7690 (tt0) cc_final: 0.7415 (tt0) REVERT: A 244 HIS cc_start: 0.7685 (t70) cc_final: 0.6735 (m90) REVERT: A 253 ILE cc_start: 0.8676 (tp) cc_final: 0.8316 (pp) REVERT: A 279 LYS cc_start: 0.7826 (mtmt) cc_final: 0.7598 (tmmt) REVERT: B 146 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8144 (mp) REVERT: C 20 LYS cc_start: 0.8145 (ptmt) cc_final: 0.7813 (pttt) REVERT: D 46 GLU cc_start: 0.7981 (tt0) cc_final: 0.7713 (tt0) REVERT: D 93 MET cc_start: 0.7960 (tpp) cc_final: 0.7754 (ttt) outliers start: 24 outliers final: 19 residues processed: 161 average time/residue: 1.1736 time to fit residues: 202.1398 Evaluate side-chains 158 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 172 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.0040 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.137015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.103984 restraints weight = 13513.279| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.55 r_work: 0.3338 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9160 Z= 0.198 Angle : 0.675 11.616 12419 Z= 0.337 Chirality : 0.043 0.263 1418 Planarity : 0.004 0.065 1566 Dihedral : 4.263 27.559 1248 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.37 % Allowed : 23.94 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1132 helix: 1.71 (0.26), residues: 398 sheet: 0.05 (0.33), residues: 270 loop : -0.67 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 316 HIS 0.010 0.001 HIS B 142 PHE 0.021 0.001 PHE R 74 TYR 0.015 0.001 TYR A 296 ARG 0.014 0.001 ARG D 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3990.92 seconds wall clock time: 70 minutes 17.44 seconds (4217.44 seconds total)