Starting phenix.real_space_refine on Fri Jun 6 00:16:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wvu_32858/06_2025/7wvu_32858.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wvu_32858/06_2025/7wvu_32858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wvu_32858/06_2025/7wvu_32858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wvu_32858/06_2025/7wvu_32858.map" model { file = "/net/cci-nas-00/data/ceres_data/7wvu_32858/06_2025/7wvu_32858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wvu_32858/06_2025/7wvu_32858.cif" } resolution = 3.3 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= 0.004 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 50 5.16 5 C 4405 2.51 5 N 1157 2.21 5 O 1250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6862 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2279 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 12, 'TRANS': 285} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1714 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2457 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 382 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Classifications: {'peptide': 3} Modifications used: {'COO': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.70, per 1000 atoms: 0.68 Number of scatterers: 6862 At special positions: 0 Unit cell: (113.905, 117.04, 80.465, 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 50 16.00 O 1250 8.00 N 1157 7.00 C 4405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.03 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: 1.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1710 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 48.8% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'R' and resid 21 through 53 Processing helix chain 'R' and resid 58 through 88 removed outlier: 3.514A pdb=" N PHE R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) Proline residue: R 79 - end of helix removed outlier: 3.644A pdb=" N ARG R 84 " --> pdb=" O PHE R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 removed outlier: 3.808A pdb=" N ASP R 106 " --> pdb=" O PHE R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 136 Processing helix chain 'R' and resid 138 through 163 removed outlier: 3.659A pdb=" N ILE R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY R 148 " --> pdb=" O LYS R 144 " (cutoff:3.500A) Proline residue: R 149 - end of helix Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 186 through 211 Processing helix chain 'R' and resid 212 through 231 Processing helix chain 'R' and resid 237 through 267 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 272 Processing helix chain 'R' and resid 276 through 302 removed outlier: 3.632A pdb=" N ASN R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 316 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.600A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 4.070A pdb=" N CYS A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 218 removed outlier: 4.128A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.886A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.768A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.885A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.367A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.663A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.606A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.620A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.509A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 320 " --> pdb=" O ILE A 264 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.762A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.815A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.618A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 4.191A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.624A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 5.922A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1110 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: 2.01 Time building geometry restraints manager: 2.00 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: 2206 1.34 - 1.46: 1622 1.46 - 1.58: 3108 1.58 - 1.70: 0 1.70 - 1.81: 70 Bond restraints: 7006 Sorted by residual: bond pdb=" SD FME L 1 " pdb=" CE FME L 1 " ideal model delta sigma weight residual 1.805 1.752 0.053 2.00e-02 2.50e+03 7.06e+00 bond pdb=" CG FME L 1 " pdb=" SD FME L 1 " ideal model delta sigma weight residual 1.817 1.772 0.045 2.00e-02 2.50e+03 5.03e+00 bond pdb=" N FME L 1 " pdb=" CN FME L 1 " ideal model delta sigma weight residual 1.335 1.375 -0.040 2.00e-02 2.50e+03 3.97e+00 bond pdb=" N FME L 1 " pdb=" CA FME L 1 " ideal model delta sigma weight residual 1.458 1.436 0.022 1.90e-02 2.77e+03 1.33e+00 bond pdb=" C ALA R 212 " pdb=" N PRO R 213 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.09e+00 ... (remaining 7001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 9410 1.65 - 3.30: 99 3.30 - 4.94: 15 4.94 - 6.59: 5 6.59 - 8.24: 1 Bond angle restraints: 9530 Sorted by residual: angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 127.78 -6.24 1.91e+00 2.74e-01 1.07e+01 angle pdb=" CA LEU R 39 " pdb=" CB LEU R 39 " pdb=" CG LEU R 39 " ideal model delta sigma weight residual 116.30 124.54 -8.24 3.50e+00 8.16e-02 5.54e+00 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 125.96 -4.42 1.91e+00 2.74e-01 5.36e+00 angle pdb=" C PHE R 102 " pdb=" N THR R 103 " pdb=" CA THR R 103 " ideal model delta sigma weight residual 121.64 117.20 4.44 2.13e+00 2.20e-01 4.34e+00 angle pdb=" CB GLN A 333 " pdb=" CG GLN A 333 " pdb=" CD GLN A 333 " ideal model delta sigma weight residual 112.60 115.84 -3.24 1.70e+00 3.46e-01 3.63e+00 ... (remaining 9525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 3749 17.71 - 35.41: 280 35.41 - 53.12: 60 53.12 - 70.82: 6 70.82 - 88.52: 5 Dihedral angle restraints: 4100 sinusoidal: 1466 harmonic: 2634 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -171.88 85.88 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CG ARG B 150 " pdb=" CD ARG B 150 " pdb=" NE ARG B 150 " pdb=" CZ ARG B 150 " ideal model delta sinusoidal sigma weight residual -90.00 -130.97 40.97 2 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CA ARG R 269 " pdb=" CB ARG R 269 " pdb=" CG ARG R 269 " pdb=" CD ARG R 269 " ideal model delta sinusoidal sigma weight residual 180.00 127.00 53.00 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 4097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 725 0.029 - 0.058: 262 0.058 - 0.087: 86 0.087 - 0.117: 47 0.117 - 0.146: 6 Chirality restraints: 1126 Sorted by residual: chirality pdb=" CB VAL R 164 " pdb=" CA VAL R 164 " pdb=" CG1 VAL R 164 " pdb=" CG2 VAL R 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1123 not shown) Planarity restraints: 1199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.061 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO B 236 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 148 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO R 149 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 149 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 149 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 287 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 288 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " 0.021 5.00e-02 4.00e+02 ... (remaining 1196 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 932 2.76 - 3.29: 6734 3.29 - 3.83: 11596 3.83 - 4.36: 12952 4.36 - 4.90: 23359 Nonbonded interactions: 55573 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR R 257 " pdb=" O LEU L 2 " model vdw 2.267 3.040 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.304 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.311 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.333 3.040 ... (remaining 55568 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 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: 1.160 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: 19.760 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 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 : 0.002 0.053 7007 Z= 0.109 Angle : 0.466 8.238 9532 Z= 0.252 Chirality : 0.038 0.146 1126 Planarity : 0.004 0.092 1199 Dihedral : 13.254 88.524 2387 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.98 (0.29), residues: 894 helix: 2.27 (0.26), residues: 397 sheet: 0.29 (0.43), residues: 155 loop : -1.17 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 49 HIS 0.001 0.000 HIS R 229 PHE 0.009 0.001 PHE B 151 TYR 0.005 0.001 TYR B 264 ARG 0.008 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.18822 ( 388) hydrogen bonds : angle 6.66226 ( 1110) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.43387 ( 2) covalent geometry : bond 0.00211 ( 7006) covalent geometry : angle 0.46625 ( 9530) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.691 Fit side-chains REVERT: B 191 SER cc_start: 0.8220 (p) cc_final: 0.8020 (p) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1628 time to fit residues: 30.6450 Evaluate side-chains 111 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 0.0060 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.0370 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 0.1980 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.184149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.146698 restraints weight = 6982.771| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.13 r_work: 0.3627 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7007 Z= 0.109 Angle : 0.500 6.849 9532 Z= 0.260 Chirality : 0.040 0.134 1126 Planarity : 0.004 0.063 1199 Dihedral : 4.287 76.711 963 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.28 % Allowed : 9.97 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.29), residues: 894 helix: 2.45 (0.26), residues: 402 sheet: 0.15 (0.41), residues: 161 loop : -1.09 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.012 0.001 PHE R 93 TYR 0.010 0.001 TYR A 296 ARG 0.006 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 388) hydrogen bonds : angle 4.92115 ( 1110) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.28023 ( 2) covalent geometry : bond 0.00222 ( 7006) covalent geometry : angle 0.50033 ( 9530) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.743 Fit side-chains REVERT: A 20 ASP cc_start: 0.7999 (t0) cc_final: 0.7670 (m-30) outliers start: 9 outliers final: 4 residues processed: 123 average time/residue: 0.1504 time to fit residues: 26.3955 Evaluate side-chains 110 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.162963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.123253 restraints weight = 7457.119| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.06 r_work: 0.3323 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 7007 Z= 0.317 Angle : 0.697 10.403 9532 Z= 0.358 Chirality : 0.046 0.179 1126 Planarity : 0.005 0.050 1199 Dihedral : 5.326 85.792 963 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.42 % Allowed : 11.54 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.28), residues: 894 helix: 1.77 (0.26), residues: 396 sheet: -0.39 (0.40), residues: 166 loop : -1.21 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 339 HIS 0.005 0.001 HIS A 213 PHE 0.020 0.002 PHE R 96 TYR 0.017 0.002 TYR R 221 ARG 0.004 0.001 ARG R 123 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 388) hydrogen bonds : angle 5.21904 ( 1110) SS BOND : bond 0.00221 ( 1) SS BOND : angle 0.78240 ( 2) covalent geometry : bond 0.00736 ( 7006) covalent geometry : angle 0.69714 ( 9530) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.702 Fit side-chains REVERT: R 87 MET cc_start: 0.5590 (mmt) cc_final: 0.5272 (mmt) REVERT: R 152 MET cc_start: 0.7318 (tpt) cc_final: 0.7050 (tpt) REVERT: A 20 ASP cc_start: 0.8159 (t0) cc_final: 0.7954 (m-30) REVERT: B 259 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7306 (pm20) REVERT: B 262 MET cc_start: 0.7472 (mmt) cc_final: 0.6925 (mmt) outliers start: 24 outliers final: 16 residues processed: 142 average time/residue: 0.1508 time to fit residues: 30.6128 Evaluate side-chains 124 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 163 ARG Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 7 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 57 HIS R 258 GLN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 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 = 0.4044 r_free = 0.4044 target = 0.168576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128328 restraints weight = 7327.179| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.95 r_work: 0.3401 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7007 Z= 0.143 Angle : 0.562 9.058 9532 Z= 0.282 Chirality : 0.041 0.145 1126 Planarity : 0.004 0.047 1199 Dihedral : 4.798 74.465 963 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.99 % Allowed : 15.10 % Favored : 81.91 % 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: 0.56 (0.28), residues: 894 helix: 1.95 (0.26), residues: 396 sheet: -0.49 (0.40), residues: 159 loop : -1.09 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 339 HIS 0.003 0.001 HIS B 54 PHE 0.011 0.001 PHE B 292 TYR 0.011 0.001 TYR B 59 ARG 0.003 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 388) hydrogen bonds : angle 4.92817 ( 1110) SS BOND : bond 0.00058 ( 1) SS BOND : angle 0.21779 ( 2) covalent geometry : bond 0.00320 ( 7006) covalent geometry : angle 0.56206 ( 9530) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.754 Fit side-chains REVERT: R 54 ARG cc_start: 0.7376 (mmm-85) cc_final: 0.7080 (mmp80) REVERT: R 152 MET cc_start: 0.7022 (tpt) cc_final: 0.6797 (tpt) REVERT: R 276 TYR cc_start: 0.6942 (m-10) cc_final: 0.6628 (m-80) REVERT: B 261 LEU cc_start: 0.7630 (mt) cc_final: 0.7284 (mt) REVERT: B 262 MET cc_start: 0.7406 (mmt) cc_final: 0.6941 (mmt) outliers start: 21 outliers final: 16 residues processed: 123 average time/residue: 0.1493 time to fit residues: 26.3246 Evaluate side-chains 125 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 55 optimal weight: 0.9990 chunk 80 optimal weight: 0.0170 chunk 51 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.168675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.129121 restraints weight = 7259.748| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.05 r_work: 0.3392 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7007 Z= 0.143 Angle : 0.549 8.055 9532 Z= 0.274 Chirality : 0.041 0.135 1126 Planarity : 0.003 0.046 1199 Dihedral : 4.738 74.716 963 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.85 % Allowed : 15.81 % Favored : 80.34 % 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: 0.57 (0.28), residues: 894 helix: 2.02 (0.26), residues: 396 sheet: -0.65 (0.40), residues: 159 loop : -1.09 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 339 HIS 0.002 0.001 HIS B 311 PHE 0.013 0.001 PHE B 292 TYR 0.015 0.001 TYR B 59 ARG 0.005 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 388) hydrogen bonds : angle 4.83587 ( 1110) SS BOND : bond 0.00017 ( 1) SS BOND : angle 0.19514 ( 2) covalent geometry : bond 0.00327 ( 7006) covalent geometry : angle 0.54862 ( 9530) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.737 Fit side-chains REVERT: R 54 ARG cc_start: 0.7444 (mmm-85) cc_final: 0.7187 (mmp80) REVERT: R 152 MET cc_start: 0.7119 (tpt) cc_final: 0.6908 (tpt) REVERT: R 229 HIS cc_start: 0.7263 (OUTLIER) cc_final: 0.6758 (t-90) REVERT: R 276 TYR cc_start: 0.6929 (m-10) cc_final: 0.6606 (m-80) REVERT: A 198 MET cc_start: 0.8560 (mtt) cc_final: 0.8197 (mtt) REVERT: B 259 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.6469 (pm20) REVERT: B 262 MET cc_start: 0.7394 (mmt) cc_final: 0.6887 (mmt) outliers start: 27 outliers final: 19 residues processed: 127 average time/residue: 0.1439 time to fit residues: 26.2470 Evaluate side-chains 121 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 20.0000 chunk 67 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.168967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.129226 restraints weight = 7317.917| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.93 r_work: 0.3413 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7007 Z= 0.142 Angle : 0.539 7.908 9532 Z= 0.271 Chirality : 0.040 0.132 1126 Planarity : 0.003 0.046 1199 Dihedral : 4.710 74.806 963 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.13 % Allowed : 17.52 % Favored : 79.34 % 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: 0.60 (0.29), residues: 894 helix: 2.06 (0.26), residues: 397 sheet: -0.72 (0.40), residues: 159 loop : -1.04 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 339 HIS 0.002 0.001 HIS B 311 PHE 0.012 0.001 PHE B 292 TYR 0.011 0.001 TYR R 257 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 388) hydrogen bonds : angle 4.78829 ( 1110) SS BOND : bond 0.00018 ( 1) SS BOND : angle 0.15441 ( 2) covalent geometry : bond 0.00323 ( 7006) covalent geometry : angle 0.53945 ( 9530) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.682 Fit side-chains REVERT: R 54 ARG cc_start: 0.7419 (mmm-85) cc_final: 0.6722 (mmt180) REVERT: R 152 MET cc_start: 0.7135 (tpt) cc_final: 0.6931 (tpt) REVERT: R 229 HIS cc_start: 0.7238 (OUTLIER) cc_final: 0.6689 (t-90) REVERT: A 29 LYS cc_start: 0.7699 (ttmt) cc_final: 0.7333 (tptt) REVERT: B 127 LYS cc_start: 0.8506 (mmtt) cc_final: 0.8264 (mmtp) REVERT: B 262 MET cc_start: 0.7328 (mmt) cc_final: 0.6984 (mmt) outliers start: 22 outliers final: 21 residues processed: 116 average time/residue: 0.1400 time to fit residues: 23.8304 Evaluate side-chains 122 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.164287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123568 restraints weight = 7309.927| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.05 r_work: 0.3332 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7007 Z= 0.217 Angle : 0.605 9.339 9532 Z= 0.305 Chirality : 0.043 0.143 1126 Planarity : 0.004 0.046 1199 Dihedral : 5.010 78.348 963 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.13 % Allowed : 17.09 % Favored : 78.77 % 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: 0.34 (0.28), residues: 894 helix: 1.88 (0.26), residues: 396 sheet: -0.92 (0.40), residues: 155 loop : -1.18 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 339 HIS 0.003 0.001 HIS B 311 PHE 0.017 0.002 PHE B 292 TYR 0.011 0.002 TYR B 264 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 388) hydrogen bonds : angle 4.98477 ( 1110) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.25271 ( 2) covalent geometry : bond 0.00504 ( 7006) covalent geometry : angle 0.60513 ( 9530) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.812 Fit side-chains REVERT: R 54 ARG cc_start: 0.7349 (mmm-85) cc_final: 0.7142 (mmp80) REVERT: R 85 LYS cc_start: 0.7574 (tptm) cc_final: 0.7175 (tptp) REVERT: R 152 MET cc_start: 0.7343 (tpt) cc_final: 0.7122 (tpt) REVERT: R 229 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.6869 (t-90) REVERT: R 276 TYR cc_start: 0.6998 (m-10) cc_final: 0.6658 (m-80) REVERT: B 127 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8298 (mmtp) REVERT: B 259 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.6484 (pm20) REVERT: B 262 MET cc_start: 0.7496 (mmt) cc_final: 0.7144 (mmt) outliers start: 29 outliers final: 25 residues processed: 129 average time/residue: 0.2012 time to fit residues: 37.4142 Evaluate side-chains 132 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 61 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.167810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128683 restraints weight = 7279.514| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.11 r_work: 0.3391 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7007 Z= 0.143 Angle : 0.561 8.831 9532 Z= 0.280 Chirality : 0.041 0.134 1126 Planarity : 0.003 0.046 1199 Dihedral : 4.823 74.829 963 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.56 % Allowed : 18.66 % Favored : 77.78 % 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: 0.48 (0.29), residues: 894 helix: 1.93 (0.26), residues: 397 sheet: -0.84 (0.40), residues: 159 loop : -1.04 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 339 HIS 0.003 0.001 HIS B 54 PHE 0.012 0.001 PHE B 292 TYR 0.014 0.001 TYR A 296 ARG 0.003 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 388) hydrogen bonds : angle 4.84692 ( 1110) SS BOND : bond 0.00019 ( 1) SS BOND : angle 0.04673 ( 2) covalent geometry : bond 0.00326 ( 7006) covalent geometry : angle 0.56114 ( 9530) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.100 Fit side-chains REVERT: R 54 ARG cc_start: 0.7365 (mmm-85) cc_final: 0.7135 (mmp80) REVERT: R 85 LYS cc_start: 0.7484 (tptm) cc_final: 0.7098 (tptp) REVERT: R 152 MET cc_start: 0.7267 (tpt) cc_final: 0.7064 (tpt) REVERT: R 229 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.6737 (t-90) REVERT: A 29 LYS cc_start: 0.7674 (ttmt) cc_final: 0.7315 (tptt) REVERT: A 53 MET cc_start: 0.6270 (pmm) cc_final: 0.5377 (pmm) REVERT: A 323 PHE cc_start: 0.7657 (m-10) cc_final: 0.7392 (m-10) REVERT: B 127 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8335 (mmtp) REVERT: B 262 MET cc_start: 0.7381 (mmt) cc_final: 0.7017 (mmt) outliers start: 25 outliers final: 22 residues processed: 123 average time/residue: 0.2395 time to fit residues: 44.1889 Evaluate side-chains 126 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 17 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 0.0370 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.169652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129542 restraints weight = 7306.690| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.97 r_work: 0.3411 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7007 Z= 0.132 Angle : 0.544 8.812 9532 Z= 0.273 Chirality : 0.041 0.135 1126 Planarity : 0.003 0.046 1199 Dihedral : 4.709 73.505 963 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.56 % Allowed : 18.38 % Favored : 78.06 % 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: 0.52 (0.29), residues: 894 helix: 1.97 (0.26), residues: 397 sheet: -0.85 (0.39), residues: 160 loop : -1.01 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 339 HIS 0.002 0.001 HIS B 54 PHE 0.011 0.001 PHE B 292 TYR 0.013 0.001 TYR A 296 ARG 0.003 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 388) hydrogen bonds : angle 4.74431 ( 1110) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.07670 ( 2) covalent geometry : bond 0.00299 ( 7006) covalent geometry : angle 0.54405 ( 9530) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 1.132 Fit side-chains REVERT: R 54 ARG cc_start: 0.7368 (mmm-85) cc_final: 0.7114 (mmp80) REVERT: R 82 MET cc_start: 0.7060 (mmm) cc_final: 0.6778 (mmm) REVERT: R 85 LYS cc_start: 0.7446 (tptm) cc_final: 0.7065 (tptp) REVERT: R 152 MET cc_start: 0.7215 (tpt) cc_final: 0.6909 (tpt) REVERT: R 229 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.6710 (t-90) REVERT: A 29 LYS cc_start: 0.7654 (ttmt) cc_final: 0.7294 (tptt) REVERT: A 53 MET cc_start: 0.6281 (pmm) cc_final: 0.5438 (pmm) REVERT: A 323 PHE cc_start: 0.7583 (m-10) cc_final: 0.7286 (m-10) REVERT: B 127 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8364 (mmtp) REVERT: B 262 MET cc_start: 0.7382 (mmt) cc_final: 0.6891 (mmt) outliers start: 25 outliers final: 22 residues processed: 119 average time/residue: 0.2382 time to fit residues: 41.4808 Evaluate side-chains 126 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.167669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.128081 restraints weight = 7404.226| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.10 r_work: 0.3359 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7007 Z= 0.169 Angle : 0.575 8.958 9532 Z= 0.288 Chirality : 0.042 0.134 1126 Planarity : 0.004 0.045 1199 Dihedral : 4.811 75.149 963 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.42 % Allowed : 18.66 % Favored : 77.92 % 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: 0.46 (0.29), residues: 894 helix: 1.94 (0.26), residues: 397 sheet: -0.93 (0.39), residues: 159 loop : -1.04 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 339 HIS 0.002 0.001 HIS B 311 PHE 0.014 0.001 PHE B 292 TYR 0.012 0.001 TYR A 296 ARG 0.003 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 388) hydrogen bonds : angle 4.82785 ( 1110) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.16550 ( 2) covalent geometry : bond 0.00391 ( 7006) covalent geometry : angle 0.57478 ( 9530) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.805 Fit side-chains REVERT: R 54 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.7143 (mmp80) REVERT: R 82 MET cc_start: 0.7054 (mmm) cc_final: 0.6791 (mmm) REVERT: R 85 LYS cc_start: 0.7500 (tptm) cc_final: 0.7105 (tptp) REVERT: R 146 ILE cc_start: 0.8481 (mm) cc_final: 0.8088 (tt) REVERT: R 152 MET cc_start: 0.7312 (tpt) cc_final: 0.7014 (tpt) REVERT: R 229 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.6813 (t-90) REVERT: A 29 LYS cc_start: 0.7689 (ttmt) cc_final: 0.7288 (tptt) REVERT: A 53 MET cc_start: 0.6316 (pmm) cc_final: 0.5386 (pmm) REVERT: A 323 PHE cc_start: 0.7634 (m-10) cc_final: 0.7317 (m-10) REVERT: B 75 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8316 (mm-40) REVERT: B 127 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8359 (mmtp) REVERT: B 262 MET cc_start: 0.7431 (mmt) cc_final: 0.6940 (mmt) REVERT: B 336 LEU cc_start: 0.8757 (tt) cc_final: 0.8556 (tt) outliers start: 24 outliers final: 23 residues processed: 121 average time/residue: 0.1732 time to fit residues: 31.2103 Evaluate side-chains 128 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 28 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 27 optimal weight: 0.0060 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 57 HIS ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.170790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.131079 restraints weight = 7255.024| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.10 r_work: 0.3425 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7007 Z= 0.117 Angle : 0.538 8.930 9532 Z= 0.267 Chirality : 0.040 0.138 1126 Planarity : 0.003 0.046 1199 Dihedral : 4.569 71.918 963 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.42 % Allowed : 19.37 % Favored : 77.21 % 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: 0.53 (0.29), residues: 894 helix: 2.02 (0.26), residues: 399 sheet: -1.04 (0.39), residues: 160 loop : -0.96 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 339 HIS 0.003 0.001 HIS B 54 PHE 0.010 0.001 PHE B 292 TYR 0.012 0.001 TYR A 296 ARG 0.003 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 388) hydrogen bonds : angle 4.64239 ( 1110) SS BOND : bond 0.00017 ( 1) SS BOND : angle 0.10235 ( 2) covalent geometry : bond 0.00258 ( 7006) covalent geometry : angle 0.53844 ( 9530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4561.47 seconds wall clock time: 81 minutes 54.43 seconds (4914.43 seconds total)