Starting phenix.real_space_refine on Thu Feb 13 10:23:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ijd_35485/02_2025/8ijd_35485_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ijd_35485/02_2025/8ijd_35485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ijd_35485/02_2025/8ijd_35485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ijd_35485/02_2025/8ijd_35485.map" model { file = "/net/cci-nas-00/data/ceres_data/8ijd_35485/02_2025/8ijd_35485_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ijd_35485/02_2025/8ijd_35485_neut.cif" } resolution = 3.25 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= 0.015 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 64 5.16 5 C 5544 2.51 5 N 1489 2.21 5 O 1627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8724 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2183 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 8, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 136 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1695 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'FI7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.18, per 1000 atoms: 0.59 Number of scatterers: 8724 At special positions: 0 Unit cell: (88.81, 120.35, 126.16, 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 64 16.00 O 1627 8.00 N 1489 7.00 C 5544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.02 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.07 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=1.85 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 2.16 Conformation dependent library (CDL) restraints added in 1.0 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.2% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 23 through 55 removed outlier: 4.124A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 60 through 89 removed outlier: 3.591A pdb=" N LEU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Proline residue: A 81 - end of helix removed outlier: 3.594A pdb=" N ARG A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 131 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 140 through 164 removed outlier: 5.068A pdb=" N HIS A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.548A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 223 through 261 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 268 through 288 removed outlier: 4.421A pdb=" N VAL A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.928A pdb=" N VAL A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.881A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 32 removed outlier: 3.710A pdb=" N ARG C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 51 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.995A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.719A pdb=" N ASP C 231 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.675A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.554A pdb=" N CYS C 286 " --> pdb=" O LEU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 Processing helix chain 'C' and resid 329 through 351 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.162A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.656A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.699A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.018A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.120A 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 Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.651A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.977A 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: 6.074A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.421A 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: 3.778A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 191 removed outlier: 3.635A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 268 " --> pdb=" O HIS C 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.423A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.423A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 4.040A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1260 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: 2.62 Time building geometry restraints manager: 2.50 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: 2810 1.34 - 1.47: 2251 1.47 - 1.60: 3757 1.60 - 1.73: 2 1.73 - 1.86: 91 Bond restraints: 8911 Sorted by residual: bond pdb=" C20 FI7 A 401 " pdb=" C21 FI7 A 401 " ideal model delta sigma weight residual 1.355 1.543 -0.188 2.00e-02 2.50e+03 8.86e+01 bond pdb=" N ASN A 17 " pdb=" CA ASN A 17 " ideal model delta sigma weight residual 1.463 1.377 0.086 1.47e-02 4.63e+03 3.39e+01 bond pdb=" CA LYS A 16 " pdb=" C LYS A 16 " ideal model delta sigma weight residual 1.523 1.421 0.103 1.80e-02 3.09e+03 3.25e+01 bond pdb=" CA CYS A 18 " pdb=" C CYS A 18 " ideal model delta sigma weight residual 1.522 1.586 -0.063 1.20e-02 6.94e+03 2.78e+01 bond pdb=" ND1 HIS B 91 " pdb=" CE1 HIS B 91 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.76e+01 ... (remaining 8906 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.78: 11967 4.78 - 9.56: 102 9.56 - 14.34: 16 14.34 - 19.12: 8 19.12 - 23.90: 3 Bond angle restraints: 12096 Sorted by residual: angle pdb=" N SER A 181 " pdb=" CA SER A 181 " pdb=" C SER A 181 " ideal model delta sigma weight residual 109.24 85.34 23.90 1.63e+00 3.76e-01 2.15e+02 angle pdb=" N CYS A 18 " pdb=" CA CYS A 18 " pdb=" C CYS A 18 " ideal model delta sigma weight residual 108.14 129.66 -21.52 1.52e+00 4.33e-01 2.00e+02 angle pdb=" N ARG A 222 " pdb=" CA ARG A 222 " pdb=" C ARG A 222 " ideal model delta sigma weight residual 111.28 125.75 -14.47 1.09e+00 8.42e-01 1.76e+02 angle pdb=" C GLU A 12 " pdb=" CA GLU A 12 " pdb=" CB GLU A 12 " ideal model delta sigma weight residual 112.09 91.90 20.19 1.54e+00 4.22e-01 1.72e+02 angle pdb=" N GLN A 170 " pdb=" CA GLN A 170 " pdb=" C GLN A 170 " ideal model delta sigma weight residual 109.96 90.98 18.98 1.50e+00 4.44e-01 1.60e+02 ... (remaining 12091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4545 17.86 - 35.71: 560 35.71 - 53.57: 135 53.57 - 71.42: 21 71.42 - 89.28: 14 Dihedral angle restraints: 5275 sinusoidal: 1984 harmonic: 3291 Sorted by residual: dihedral pdb=" C GLU A 12 " pdb=" N GLU A 12 " pdb=" CA GLU A 12 " pdb=" CB GLU A 12 " ideal model delta harmonic sigma weight residual -122.60 -97.82 -24.78 0 2.50e+00 1.60e-01 9.83e+01 dihedral pdb=" C PHE A 180 " pdb=" N PHE A 180 " pdb=" CA PHE A 180 " pdb=" CB PHE A 180 " ideal model delta harmonic sigma weight residual -122.60 -97.85 -24.75 0 2.50e+00 1.60e-01 9.80e+01 dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 177 " pdb=" CB CYS A 177 " ideal model delta sinusoidal sigma weight residual 93.00 176.96 -83.96 1 1.00e+01 1.00e-02 8.59e+01 ... (remaining 5272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 1350 0.165 - 0.329: 17 0.329 - 0.494: 3 0.494 - 0.658: 3 0.658 - 0.823: 1 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA ASP A 221 " pdb=" N ASP A 221 " pdb=" C ASP A 221 " pdb=" CB ASP A 221 " both_signs ideal model delta sigma weight residual False 2.51 1.69 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" CA CYS A 177 " pdb=" N CYS A 177 " pdb=" C CYS A 177 " pdb=" CB CYS A 177 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.02e+00 chirality pdb=" CA GLU A 12 " pdb=" N GLU A 12 " pdb=" C GLU A 12 " pdb=" CB GLU A 12 " both_signs ideal model delta sigma weight residual False 2.51 3.07 -0.56 2.00e-01 2.50e+01 7.86e+00 ... (remaining 1371 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 FI7 A 401 " -0.093 2.00e-02 2.50e+03 1.21e-01 1.83e+02 pdb=" C17 FI7 A 401 " 0.017 2.00e-02 2.50e+03 pdb=" C20 FI7 A 401 " -0.143 2.00e-02 2.50e+03 pdb=" N19 FI7 A 401 " 0.208 2.00e-02 2.50e+03 pdb=" O18 FI7 A 401 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 15 " 0.038 2.00e-02 2.50e+03 8.63e-02 7.45e+01 pdb=" C LYS A 15 " -0.149 2.00e-02 2.50e+03 pdb=" O LYS A 15 " 0.061 2.00e-02 2.50e+03 pdb=" N LYS A 16 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 284 " 0.085 2.00e-02 2.50e+03 5.15e-02 5.30e+01 pdb=" CG TYR A 284 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 284 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 284 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 284 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 284 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 284 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 284 " 0.088 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 60 2.43 - 3.05: 5795 3.05 - 3.66: 14021 3.66 - 4.28: 20090 4.28 - 4.90: 33333 Nonbonded interactions: 73299 Sorted by model distance: nonbonded pdb=" O ILE A 182 " pdb=" CG1 ILE A 182 " model vdw 1.812 3.440 nonbonded pdb=" O ILE A 182 " pdb=" CD1 ILE A 182 " model vdw 1.865 3.460 nonbonded pdb=" OG SER A 298 " pdb=" O GLY C 352 " model vdw 1.963 3.040 nonbonded pdb=" O ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.106 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.125 3.040 ... (remaining 73294 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: 1.320 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: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.240 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.008 0.188 8911 Z= 0.492 Angle : 1.204 23.902 12096 Z= 0.725 Chirality : 0.066 0.823 1374 Planarity : 0.008 0.122 1540 Dihedral : 16.918 89.280 3132 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.30 % Allowed : 30.85 % Favored : 66.85 % Cbeta Deviations : 0.94 % Peptide Plane: Cis-proline : 3.23 % 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: -0.43 (0.26), residues: 1120 helix: 0.46 (0.27), residues: 368 sheet: 0.03 (0.32), residues: 273 loop : -0.99 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP A 91 HIS 0.006 0.001 HIS A 259 PHE 0.050 0.002 PHE A 277 TYR 0.088 0.003 TYR A 284 ARG 0.008 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.8382 (tmm) cc_final: 0.7819 (tmm) REVERT: A 137 ASN cc_start: 0.8762 (m-40) cc_final: 0.8550 (m110) REVERT: A 217 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8847 (tm-30) REVERT: C 294 ASN cc_start: 0.8170 (m-40) cc_final: 0.7963 (t0) REVERT: C 350 ASP cc_start: 0.8947 (t0) cc_final: 0.8741 (m-30) REVERT: G 27 ARG cc_start: 0.8342 (tpp80) cc_final: 0.7778 (tpp80) REVERT: S 190 ARG cc_start: 0.7867 (mtp180) cc_final: 0.7517 (mtp180) outliers start: 21 outliers final: 9 residues processed: 194 average time/residue: 0.2452 time to fit residues: 63.1262 Evaluate side-chains 174 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 91 HIS B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN S 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.100050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.069935 restraints weight = 20160.923| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.92 r_work: 0.2824 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8911 Z= 0.357 Angle : 0.719 9.491 12096 Z= 0.374 Chirality : 0.046 0.167 1374 Planarity : 0.005 0.060 1540 Dihedral : 8.227 71.566 1266 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.92 % Allowed : 26.04 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.06 (0.26), residues: 1120 helix: 1.14 (0.27), residues: 371 sheet: 0.11 (0.33), residues: 266 loop : -1.03 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP S 164 HIS 0.014 0.001 HIS A 189 PHE 0.020 0.002 PHE A 180 TYR 0.021 0.002 TYR S 178 ARG 0.005 0.001 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.9054 (tmm) cc_final: 0.8759 (tmm) REVERT: A 112 GLN cc_start: 0.8563 (tp40) cc_final: 0.8215 (tp40) REVERT: A 217 GLN cc_start: 0.9190 (tm-30) cc_final: 0.8789 (tm-30) REVERT: A 238 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8986 (tp) REVERT: C 308 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.8884 (mt-10) REVERT: G 27 ARG cc_start: 0.8380 (tpp80) cc_final: 0.7949 (tpp80) REVERT: G 48 ASP cc_start: 0.8279 (t0) cc_final: 0.8008 (t0) REVERT: S 87 ARG cc_start: 0.7787 (mpp80) cc_final: 0.7557 (mpp80) REVERT: S 180 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8429 (ptt) outliers start: 45 outliers final: 24 residues processed: 204 average time/residue: 0.2318 time to fit residues: 63.3315 Evaluate side-chains 183 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.100981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.070908 restraints weight = 20418.980| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.97 r_work: 0.2846 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8911 Z= 0.248 Angle : 0.667 8.566 12096 Z= 0.349 Chirality : 0.045 0.174 1374 Planarity : 0.004 0.048 1540 Dihedral : 7.785 71.461 1259 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 5.03 % Allowed : 26.37 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.02 (0.26), residues: 1120 helix: 1.29 (0.27), residues: 370 sheet: 0.11 (0.32), residues: 268 loop : -1.03 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP S 164 HIS 0.010 0.001 HIS A 189 PHE 0.013 0.001 PHE A 180 TYR 0.018 0.001 TYR S 178 ARG 0.005 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8653 (m) cc_final: 0.8227 (m) REVERT: A 109 MET cc_start: 0.9073 (tmm) cc_final: 0.8840 (tmm) REVERT: A 112 GLN cc_start: 0.8541 (tp40) cc_final: 0.8170 (tp40) REVERT: A 137 ASN cc_start: 0.8731 (m-40) cc_final: 0.8002 (m110) REVERT: C 294 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7993 (t0) REVERT: C 308 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.8884 (mt-10) REVERT: C 331 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8281 (p0) REVERT: G 27 ARG cc_start: 0.8368 (tpp80) cc_final: 0.7897 (tpp80) REVERT: S 87 ARG cc_start: 0.7708 (mpp80) cc_final: 0.7382 (mpp80) REVERT: S 89 GLU cc_start: 0.8791 (pm20) cc_final: 0.8585 (pm20) REVERT: S 180 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8087 (ptm) REVERT: S 206 ARG cc_start: 0.8684 (tpp80) cc_final: 0.8007 (tpp80) REVERT: S 208 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8309 (pm20) REVERT: S 219 GLN cc_start: 0.9426 (pp30) cc_final: 0.9173 (pp30) outliers start: 46 outliers final: 25 residues processed: 209 average time/residue: 0.2359 time to fit residues: 65.6031 Evaluate side-chains 193 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN C 331 ASN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.099814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.070026 restraints weight = 20511.796| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.87 r_work: 0.2829 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8911 Z= 0.301 Angle : 0.678 8.521 12096 Z= 0.353 Chirality : 0.045 0.155 1374 Planarity : 0.004 0.047 1540 Dihedral : 7.625 71.367 1258 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 6.46 % Allowed : 25.49 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1120 helix: 1.36 (0.27), residues: 370 sheet: 0.07 (0.32), residues: 268 loop : -1.04 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP S 164 HIS 0.008 0.001 HIS A 259 PHE 0.016 0.001 PHE A 180 TYR 0.018 0.001 TYR S 178 ARG 0.005 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 171 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8717 (m) cc_final: 0.8320 (m) REVERT: A 109 MET cc_start: 0.8980 (tmm) cc_final: 0.8757 (tmm) REVERT: A 112 GLN cc_start: 0.8512 (tp40) cc_final: 0.8158 (tp40) REVERT: A 137 ASN cc_start: 0.8787 (m-40) cc_final: 0.8024 (m110) REVERT: A 238 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8957 (tp) REVERT: B 97 SER cc_start: 0.9178 (OUTLIER) cc_final: 0.8821 (p) REVERT: C 294 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.8017 (t0) REVERT: C 308 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8867 (mt-10) REVERT: C 317 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8039 (ttmt) REVERT: G 27 ARG cc_start: 0.8316 (tpp80) cc_final: 0.7787 (tpp80) REVERT: S 82 GLN cc_start: 0.8855 (mm110) cc_final: 0.8539 (mm-40) REVERT: S 87 ARG cc_start: 0.7696 (mpp80) cc_final: 0.7448 (mpp80) REVERT: S 180 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8130 (ptm) REVERT: S 206 ARG cc_start: 0.8768 (tpp80) cc_final: 0.8111 (tpp80) REVERT: S 208 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8292 (pm20) REVERT: S 219 GLN cc_start: 0.9442 (pp30) cc_final: 0.9089 (pp30) REVERT: S 232 LYS cc_start: 0.8716 (tppt) cc_final: 0.8404 (tppt) outliers start: 59 outliers final: 30 residues processed: 216 average time/residue: 0.2404 time to fit residues: 69.0762 Evaluate side-chains 199 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.100338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.070188 restraints weight = 20362.476| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.99 r_work: 0.2843 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8911 Z= 0.242 Angle : 0.674 14.099 12096 Z= 0.344 Chirality : 0.045 0.157 1374 Planarity : 0.004 0.049 1540 Dihedral : 7.372 70.854 1257 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 5.69 % Allowed : 26.26 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.14 (0.26), residues: 1120 helix: 1.55 (0.27), residues: 370 sheet: 0.16 (0.32), residues: 268 loop : -1.10 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP S 164 HIS 0.007 0.001 HIS A 259 PHE 0.018 0.001 PHE A 186 TYR 0.016 0.001 TYR S 178 ARG 0.007 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8685 (m) cc_final: 0.8296 (m) REVERT: A 109 MET cc_start: 0.9011 (tmm) cc_final: 0.8795 (tmm) REVERT: A 112 GLN cc_start: 0.8551 (tp40) cc_final: 0.8180 (tp40) REVERT: A 137 ASN cc_start: 0.8795 (m-40) cc_final: 0.8039 (m110) REVERT: A 181 SER cc_start: 0.9282 (m) cc_final: 0.8962 (p) REVERT: A 182 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8276 (pt) REVERT: A 238 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.9015 (tp) REVERT: B 97 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8837 (p) REVERT: B 228 ASP cc_start: 0.8409 (m-30) cc_final: 0.7770 (m-30) REVERT: C 308 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8877 (mt-10) REVERT: C 317 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8060 (ttmt) REVERT: G 27 ARG cc_start: 0.8311 (tpp80) cc_final: 0.7624 (tpp80) REVERT: G 38 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8788 (ppp) REVERT: S 87 ARG cc_start: 0.7761 (mpp80) cc_final: 0.7236 (mpp80) REVERT: S 180 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8139 (ptm) REVERT: S 206 ARG cc_start: 0.8868 (tpp80) cc_final: 0.8173 (tpp80) REVERT: S 208 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8229 (pm20) REVERT: S 219 GLN cc_start: 0.9408 (pp30) cc_final: 0.9098 (pp30) REVERT: S 232 LYS cc_start: 0.8727 (tppt) cc_final: 0.8439 (tppt) outliers start: 52 outliers final: 30 residues processed: 219 average time/residue: 0.2434 time to fit residues: 70.9959 Evaluate side-chains 206 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** 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 = 0.3523 r_free = 0.3523 target = 0.097971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.067892 restraints weight = 20527.258| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.89 r_work: 0.2793 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8911 Z= 0.377 Angle : 0.727 11.257 12096 Z= 0.373 Chirality : 0.046 0.142 1374 Planarity : 0.004 0.051 1540 Dihedral : 7.414 70.555 1257 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 5.58 % Allowed : 27.24 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1120 helix: 1.51 (0.27), residues: 371 sheet: 0.01 (0.32), residues: 275 loop : -1.04 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP S 164 HIS 0.008 0.001 HIS A 161 PHE 0.013 0.002 PHE A 197 TYR 0.018 0.002 TYR S 223 ARG 0.006 0.001 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 1.110 Fit side-chains REVERT: A 79 CYS cc_start: 0.8913 (m) cc_final: 0.8491 (m) REVERT: A 109 MET cc_start: 0.8980 (tmm) cc_final: 0.8585 (tmm) REVERT: A 112 GLN cc_start: 0.8592 (tp40) cc_final: 0.8226 (tp40) REVERT: A 181 SER cc_start: 0.9228 (m) cc_final: 0.8911 (p) REVERT: A 182 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8136 (pt) REVERT: A 238 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9074 (tp) REVERT: B 97 SER cc_start: 0.9222 (OUTLIER) cc_final: 0.8883 (p) REVERT: B 297 TRP cc_start: 0.9241 (m100) cc_final: 0.8823 (m100) REVERT: C 308 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.8895 (mt-10) REVERT: C 317 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8202 (ttmt) REVERT: G 27 ARG cc_start: 0.8386 (tpp80) cc_final: 0.7796 (tpp80) REVERT: G 38 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8839 (ppp) REVERT: S 39 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7600 (tp40) REVERT: S 43 LYS cc_start: 0.9462 (mmmm) cc_final: 0.9208 (mmtm) REVERT: S 87 ARG cc_start: 0.7882 (mpp80) cc_final: 0.7235 (mpp80) REVERT: S 89 GLU cc_start: 0.8950 (pm20) cc_final: 0.8698 (pm20) REVERT: S 180 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8195 (ptm) REVERT: S 206 ARG cc_start: 0.8911 (tpp80) cc_final: 0.8328 (tpp80) REVERT: S 232 LYS cc_start: 0.8816 (tppt) cc_final: 0.8569 (tppt) outliers start: 51 outliers final: 34 residues processed: 204 average time/residue: 0.2392 time to fit residues: 64.9874 Evaluate side-chains 197 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 80 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 3 optimal weight: 30.0000 chunk 41 optimal weight: 0.0070 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 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 = 0.3565 r_free = 0.3565 target = 0.100621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.070702 restraints weight = 20645.367| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 4.01 r_work: 0.2842 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8911 Z= 0.218 Angle : 0.694 10.596 12096 Z= 0.351 Chirality : 0.045 0.146 1374 Planarity : 0.004 0.048 1540 Dihedral : 7.225 69.742 1257 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 5.36 % Allowed : 27.13 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.18 (0.26), residues: 1120 helix: 1.60 (0.27), residues: 370 sheet: 0.15 (0.32), residues: 272 loop : -1.08 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP S 164 HIS 0.007 0.001 HIS A 259 PHE 0.021 0.001 PHE C 274 TYR 0.015 0.001 TYR S 223 ARG 0.007 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8881 (m) cc_final: 0.8406 (m) REVERT: A 109 MET cc_start: 0.8984 (tmm) cc_final: 0.8349 (tmm) REVERT: A 112 GLN cc_start: 0.8484 (tp40) cc_final: 0.8113 (tp40) REVERT: A 181 SER cc_start: 0.9233 (m) cc_final: 0.8897 (p) REVERT: A 182 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7707 (pt) REVERT: A 238 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.9037 (tp) REVERT: B 97 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8827 (p) REVERT: B 145 TYR cc_start: 0.9222 (p90) cc_final: 0.8825 (p90) REVERT: B 228 ASP cc_start: 0.8391 (m-30) cc_final: 0.7801 (m-30) REVERT: B 297 TRP cc_start: 0.9160 (m100) cc_final: 0.8836 (m100) REVERT: C 308 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8896 (mt-10) REVERT: C 317 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8007 (ttmt) REVERT: G 27 ARG cc_start: 0.8356 (tpp80) cc_final: 0.7548 (tpp80) REVERT: S 39 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7614 (tp40) REVERT: S 87 ARG cc_start: 0.7780 (mpp80) cc_final: 0.7179 (mpp80) REVERT: S 89 GLU cc_start: 0.8946 (pm20) cc_final: 0.8700 (pm20) REVERT: S 206 ARG cc_start: 0.8852 (tpp80) cc_final: 0.8612 (tpp80) REVERT: S 211 ASP cc_start: 0.9230 (m-30) cc_final: 0.8898 (m-30) REVERT: S 219 GLN cc_start: 0.9395 (pp30) cc_final: 0.9102 (pp30) REVERT: S 232 LYS cc_start: 0.8889 (tppt) cc_final: 0.8569 (tppt) outliers start: 49 outliers final: 31 residues processed: 212 average time/residue: 0.2362 time to fit residues: 66.8831 Evaluate side-chains 200 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.0670 chunk 16 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.100552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.070648 restraints weight = 20719.515| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 4.00 r_work: 0.2847 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8911 Z= 0.236 Angle : 0.739 10.451 12096 Z= 0.370 Chirality : 0.046 0.157 1374 Planarity : 0.004 0.047 1540 Dihedral : 7.207 69.511 1257 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 5.03 % Allowed : 27.79 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.20 (0.26), residues: 1120 helix: 1.55 (0.27), residues: 371 sheet: 0.15 (0.32), residues: 274 loop : -1.01 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP S 164 HIS 0.007 0.001 HIS A 259 PHE 0.011 0.001 PHE A 197 TYR 0.016 0.001 TYR S 223 ARG 0.007 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 167 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8870 (m) cc_final: 0.8399 (m) REVERT: A 109 MET cc_start: 0.8981 (tmm) cc_final: 0.8336 (tmm) REVERT: A 112 GLN cc_start: 0.8507 (tp40) cc_final: 0.8149 (tp40) REVERT: A 181 SER cc_start: 0.9177 (m) cc_final: 0.8803 (p) REVERT: A 182 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7341 (pt) REVERT: A 238 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9047 (tp) REVERT: B 97 SER cc_start: 0.9184 (OUTLIER) cc_final: 0.8821 (p) REVERT: B 145 TYR cc_start: 0.9235 (p90) cc_final: 0.8833 (p90) REVERT: B 228 ASP cc_start: 0.8359 (m-30) cc_final: 0.7778 (m-30) REVERT: B 262 MET cc_start: 0.8638 (tpt) cc_final: 0.8183 (mmm) REVERT: B 297 TRP cc_start: 0.9171 (m100) cc_final: 0.8835 (m100) REVERT: C 308 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8849 (mt-10) REVERT: C 317 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8014 (ttmt) REVERT: G 27 ARG cc_start: 0.8345 (tpp80) cc_final: 0.7534 (tpp80) REVERT: G 38 MET cc_start: 0.8837 (ppp) cc_final: 0.8530 (ppp) REVERT: S 39 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7583 (tp40) REVERT: S 206 ARG cc_start: 0.8832 (tpp80) cc_final: 0.8623 (tpp80) REVERT: S 211 ASP cc_start: 0.9212 (m-30) cc_final: 0.8894 (m-30) REVERT: S 219 GLN cc_start: 0.9399 (pp30) cc_final: 0.9089 (pp30) REVERT: S 232 LYS cc_start: 0.8980 (tppt) cc_final: 0.8679 (tppt) outliers start: 46 outliers final: 34 residues processed: 204 average time/residue: 0.2408 time to fit residues: 65.5871 Evaluate side-chains 199 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 0.0000 chunk 71 optimal weight: 0.5980 chunk 83 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 104 optimal weight: 0.3980 chunk 95 optimal weight: 0.3980 chunk 42 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 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 = 0.3600 r_free = 0.3600 target = 0.102646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.072878 restraints weight = 20449.407| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 4.00 r_work: 0.2890 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8911 Z= 0.204 Angle : 0.761 11.071 12096 Z= 0.380 Chirality : 0.046 0.160 1374 Planarity : 0.004 0.045 1540 Dihedral : 7.323 69.527 1257 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 3.72 % Allowed : 29.54 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.21 (0.26), residues: 1120 helix: 1.51 (0.27), residues: 371 sheet: 0.22 (0.32), residues: 272 loop : -0.98 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 164 HIS 0.007 0.001 HIS A 259 PHE 0.029 0.001 PHE A 180 TYR 0.013 0.001 TYR C 302 ARG 0.008 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8895 (m) cc_final: 0.8461 (m) REVERT: A 109 MET cc_start: 0.8971 (tmm) cc_final: 0.8337 (tmm) REVERT: A 138 LYS cc_start: 0.9508 (mtmm) cc_final: 0.9212 (mtmm) REVERT: A 181 SER cc_start: 0.9059 (m) cc_final: 0.8613 (p) REVERT: A 182 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.6892 (pt) REVERT: A 238 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8941 (tp) REVERT: B 145 TYR cc_start: 0.9189 (p90) cc_final: 0.8894 (p90) REVERT: B 186 ASP cc_start: 0.8212 (m-30) cc_final: 0.7819 (m-30) REVERT: B 228 ASP cc_start: 0.8279 (m-30) cc_final: 0.7711 (m-30) REVERT: B 262 MET cc_start: 0.8647 (tpt) cc_final: 0.8197 (mmm) REVERT: B 297 TRP cc_start: 0.9048 (m100) cc_final: 0.8738 (m100) REVERT: C 308 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.8824 (mt-10) REVERT: C 313 ARG cc_start: 0.8981 (mpp80) cc_final: 0.8511 (mtm-85) REVERT: G 27 ARG cc_start: 0.8287 (tpp80) cc_final: 0.7486 (tpp80) REVERT: S 18 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6837 (ttp80) REVERT: S 39 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7433 (tp40) REVERT: S 82 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8277 (mm-40) REVERT: S 206 ARG cc_start: 0.8850 (tpp80) cc_final: 0.8642 (tpp80) REVERT: S 211 ASP cc_start: 0.9226 (m-30) cc_final: 0.8940 (m-30) REVERT: S 219 GLN cc_start: 0.9379 (pp30) cc_final: 0.9115 (pp30) REVERT: S 232 LYS cc_start: 0.8975 (tppt) cc_final: 0.8674 (tppt) outliers start: 34 outliers final: 25 residues processed: 209 average time/residue: 0.2315 time to fit residues: 64.2242 Evaluate side-chains 197 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.099461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.069319 restraints weight = 20669.502| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.90 r_work: 0.2823 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8911 Z= 0.349 Angle : 0.800 11.681 12096 Z= 0.400 Chirality : 0.047 0.177 1374 Planarity : 0.004 0.047 1540 Dihedral : 7.276 71.609 1254 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 3.72 % Allowed : 30.63 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.21 (0.26), residues: 1120 helix: 1.51 (0.27), residues: 372 sheet: 0.17 (0.32), residues: 269 loop : -0.95 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP S 164 HIS 0.008 0.001 HIS A 161 PHE 0.048 0.002 PHE S 68 TYR 0.016 0.002 TYR S 223 ARG 0.008 0.001 ARG S 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8988 (m) cc_final: 0.8616 (m) REVERT: A 138 LYS cc_start: 0.9490 (mtmm) cc_final: 0.9205 (mtmm) REVERT: A 181 SER cc_start: 0.9063 (m) cc_final: 0.8616 (p) REVERT: A 182 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7081 (pt) REVERT: A 238 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9069 (tp) REVERT: B 228 ASP cc_start: 0.8338 (m-30) cc_final: 0.7768 (m-30) REVERT: B 262 MET cc_start: 0.8717 (tpt) cc_final: 0.8404 (mmm) REVERT: B 297 TRP cc_start: 0.9182 (m100) cc_final: 0.8811 (m100) REVERT: C 308 GLU cc_start: 0.9304 (OUTLIER) cc_final: 0.8856 (mt-10) REVERT: G 27 ARG cc_start: 0.8396 (tpp80) cc_final: 0.7580 (tpp80) REVERT: S 39 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7533 (tp40) REVERT: S 82 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8205 (mm-40) REVERT: S 211 ASP cc_start: 0.9253 (m-30) cc_final: 0.8882 (m-30) REVERT: S 219 GLN cc_start: 0.9390 (pp30) cc_final: 0.9041 (pp30) REVERT: S 232 LYS cc_start: 0.9002 (tppt) cc_final: 0.8737 (tppt) outliers start: 34 outliers final: 27 residues processed: 191 average time/residue: 0.2523 time to fit residues: 65.3346 Evaluate side-chains 193 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.099682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.069576 restraints weight = 20666.595| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.92 r_work: 0.2826 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.197 8911 Z= 0.343 Angle : 1.056 59.199 12096 Z= 0.584 Chirality : 0.047 0.272 1374 Planarity : 0.004 0.046 1540 Dihedral : 7.283 71.609 1254 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 3.94 % Allowed : 31.07 % Favored : 64.99 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.23 % 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: 0.20 (0.26), residues: 1120 helix: 1.52 (0.27), residues: 372 sheet: 0.15 (0.32), residues: 269 loop : -0.96 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP S 164 HIS 0.007 0.001 HIS A 259 PHE 0.038 0.002 PHE S 68 TYR 0.016 0.002 TYR S 223 ARG 0.005 0.001 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4748.84 seconds wall clock time: 84 minutes 53.80 seconds (5093.80 seconds total)