Starting phenix.real_space_refine on Tue Apr 29 20:15:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ijd_35485/04_2025/8ijd_35485_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ijd_35485/04_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_35485/04_2025/8ijd_35485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ijd_35485/04_2025/8ijd_35485.map" model { file = "/net/cci-nas-00/data/ceres_data/8ijd_35485/04_2025/8ijd_35485_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ijd_35485/04_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.79, per 1000 atoms: 0.66 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: 2.39 Conformation dependent library (CDL) restraints added in 1.1 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: 1.10 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: 2.70 Time building geometry restraints manager: 2.74 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: 1.300 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.990 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.960 ------------------------------------------------------------------------------- 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 8916 Z= 0.425 Angle : 1.283 33.887 12106 Z= 0.754 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 Details of bonding type rmsd hydrogen bonds : bond 0.13843 ( 445) hydrogen bonds : angle 6.73379 ( 1260) SS BOND : bond 0.08506 ( 5) SS BOND : angle 15.41118 ( 10) covalent geometry : bond 0.00756 ( 8911) covalent geometry : angle 1.20420 (12096) *********************** 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 : 0.911 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: 0.2363 time to fit residues: 61.0124 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 : 1.112 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.100010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.070197 restraints weight = 20175.215| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.83 r_work: 0.2832 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8916 Z= 0.242 Angle : 0.722 9.440 12106 Z= 0.376 Chirality : 0.046 0.163 1374 Planarity : 0.005 0.061 1540 Dihedral : 8.227 71.573 1266 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.92 % Allowed : 25.93 % Favored : 69.15 % 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 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 445) hydrogen bonds : angle 5.23454 ( 1260) SS BOND : bond 0.00728 ( 5) SS BOND : angle 2.27649 ( 10) covalent geometry : bond 0.00547 ( 8911) covalent geometry : angle 0.71923 (12096) *********************** 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 : 0.998 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.9025 (tmm) cc_final: 0.8725 (tmm) REVERT: A 112 GLN cc_start: 0.8519 (tp40) cc_final: 0.8174 (tp40) REVERT: A 217 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8787 (tm-30) REVERT: A 238 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8976 (tp) REVERT: B 187 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8798 (t) REVERT: C 308 GLU cc_start: 0.9306 (OUTLIER) cc_final: 0.8870 (mt-10) REVERT: G 27 ARG cc_start: 0.8367 (tpp80) cc_final: 0.7932 (tpp80) REVERT: G 48 ASP cc_start: 0.8268 (t0) cc_final: 0.7995 (t0) REVERT: S 87 ARG cc_start: 0.7764 (mpp80) cc_final: 0.7535 (mpp80) REVERT: S 180 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8410 (ptt) outliers start: 45 outliers final: 24 residues processed: 204 average time/residue: 0.2308 time to fit residues: 63.3030 Evaluate side-chains 184 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 187 VAL 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: 10.0000 chunk 5 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.100853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.070810 restraints weight = 20427.067| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.96 r_work: 0.2843 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8916 Z= 0.173 Angle : 0.666 8.530 12106 Z= 0.348 Chirality : 0.045 0.164 1374 Planarity : 0.004 0.050 1540 Dihedral : 7.768 71.456 1259 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.14 % Allowed : 26.26 % 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: 1.30 (0.27), residues: 370 sheet: 0.11 (0.32), residues: 268 loop : -1.04 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP S 164 HIS 0.010 0.001 HIS A 189 PHE 0.012 0.001 PHE A 10 TYR 0.018 0.001 TYR S 178 ARG 0.005 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 445) hydrogen bonds : angle 5.04963 ( 1260) SS BOND : bond 0.00696 ( 5) SS BOND : angle 1.73997 ( 10) covalent geometry : bond 0.00389 ( 8911) covalent geometry : angle 0.66426 (12096) *********************** 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 221 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8650 (m) cc_final: 0.8231 (m) REVERT: A 109 MET cc_start: 0.9072 (tmm) cc_final: 0.8835 (tmm) REVERT: A 112 GLN cc_start: 0.8543 (tp40) cc_final: 0.8174 (tp40) REVERT: A 137 ASN cc_start: 0.8758 (m-40) cc_final: 0.8027 (m110) REVERT: C 294 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7907 (t0) REVERT: C 308 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8879 (mt-10) REVERT: G 27 ARG cc_start: 0.8366 (tpp80) cc_final: 0.7891 (tpp80) REVERT: S 87 ARG cc_start: 0.7702 (mpp80) cc_final: 0.7370 (mpp80) REVERT: S 89 GLU cc_start: 0.8794 (pm20) cc_final: 0.8582 (pm20) REVERT: S 180 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8122 (ptm) REVERT: S 206 ARG cc_start: 0.8696 (tpp80) cc_final: 0.8015 (tpp80) REVERT: S 208 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8311 (pm20) REVERT: S 219 GLN cc_start: 0.9423 (pp30) cc_final: 0.9167 (pp30) outliers start: 47 outliers final: 25 residues processed: 207 average time/residue: 0.2218 time to fit residues: 61.5225 Evaluate side-chains 192 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 259 GLN C 331 ASN S 82 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.099723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.069476 restraints weight = 20513.575| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.96 r_work: 0.2815 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8916 Z= 0.212 Angle : 0.681 8.521 12106 Z= 0.354 Chirality : 0.045 0.157 1374 Planarity : 0.004 0.048 1540 Dihedral : 7.486 71.345 1257 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 6.67 % Allowed : 25.71 % Favored : 67.61 % 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: 0.04 (0.26), residues: 1120 helix: 1.37 (0.27), residues: 370 sheet: 0.10 (0.32), residues: 267 loop : -1.05 (0.29), residues: 483 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 0.012 0.001 PHE A 197 TYR 0.018 0.001 TYR S 178 ARG 0.006 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 445) hydrogen bonds : angle 4.97349 ( 1260) SS BOND : bond 0.00352 ( 5) SS BOND : angle 1.70826 ( 10) covalent geometry : bond 0.00481 ( 8911) covalent geometry : angle 0.67913 (12096) *********************** 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 232 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 171 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8742 (m) cc_final: 0.8347 (m) REVERT: A 109 MET cc_start: 0.9024 (tmm) cc_final: 0.8805 (tmm) REVERT: A 112 GLN cc_start: 0.8556 (tp40) cc_final: 0.8201 (tp40) REVERT: A 137 ASN cc_start: 0.8786 (m-40) cc_final: 0.8021 (m110) REVERT: A 238 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8966 (tp) REVERT: B 97 SER cc_start: 0.9192 (OUTLIER) cc_final: 0.8836 (p) REVERT: C 294 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.8038 (t0) REVERT: C 308 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.8889 (mt-10) REVERT: C 317 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8075 (ttmt) REVERT: G 27 ARG cc_start: 0.8337 (tpp80) cc_final: 0.7808 (tpp80) REVERT: S 87 ARG cc_start: 0.7732 (mpp80) cc_final: 0.7493 (mpp80) REVERT: S 180 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8151 (ptm) REVERT: S 206 ARG cc_start: 0.8777 (tpp80) cc_final: 0.8104 (tpp80) REVERT: S 208 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: S 219 GLN cc_start: 0.9429 (pp30) cc_final: 0.9103 (pp30) REVERT: S 232 LYS cc_start: 0.8731 (tppt) cc_final: 0.8414 (tppt) outliers start: 61 outliers final: 32 residues processed: 217 average time/residue: 0.2452 time to fit residues: 71.1595 Evaluate side-chains 198 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 155 THR 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: 0.8980 chunk 83 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 82 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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** ** 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 = 0.098178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.067986 restraints weight = 20449.115| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.91 r_work: 0.2795 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8916 Z= 0.266 Angle : 0.714 13.764 12106 Z= 0.367 Chirality : 0.046 0.150 1374 Planarity : 0.004 0.052 1540 Dihedral : 7.468 70.856 1257 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.36 % Favored : 94.55 % Rotamer: Outliers : 6.78 % Allowed : 25.27 % Favored : 67.94 % 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: 0.05 (0.26), residues: 1120 helix: 1.49 (0.27), residues: 371 sheet: -0.06 (0.31), residues: 275 loop : -1.06 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP S 164 HIS 0.007 0.001 HIS A 259 PHE 0.015 0.002 PHE A 197 TYR 0.019 0.002 TYR S 223 ARG 0.007 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 445) hydrogen bonds : angle 4.99049 ( 1260) SS BOND : bond 0.00501 ( 5) SS BOND : angle 1.07433 ( 10) covalent geometry : bond 0.00600 ( 8911) covalent geometry : angle 0.71332 (12096) *********************** 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 231 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8752 (m) cc_final: 0.8404 (m) REVERT: A 109 MET cc_start: 0.9026 (tmm) cc_final: 0.8322 (tmm) REVERT: A 112 GLN cc_start: 0.8605 (tp40) cc_final: 0.8249 (tp40) REVERT: A 137 ASN cc_start: 0.8811 (m-40) cc_final: 0.8051 (m110) REVERT: A 181 SER cc_start: 0.9242 (m) cc_final: 0.8880 (p) REVERT: A 182 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8357 (pt) REVERT: A 238 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9065 (tp) REVERT: B 97 SER cc_start: 0.9244 (OUTLIER) cc_final: 0.8905 (p) REVERT: B 297 TRP cc_start: 0.9234 (m100) cc_final: 0.8823 (m100) REVERT: C 308 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.8883 (mt-10) REVERT: C 317 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8202 (ttmt) REVERT: G 27 ARG cc_start: 0.8345 (tpp80) cc_final: 0.7817 (tpp80) REVERT: S 82 GLN cc_start: 0.8597 (mm110) cc_final: 0.8306 (mm-40) REVERT: S 87 ARG cc_start: 0.7801 (mpp80) cc_final: 0.7237 (mpp80) REVERT: S 206 ARG cc_start: 0.8878 (tpp80) cc_final: 0.8274 (tpp80) REVERT: S 208 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8330 (pm20) REVERT: S 232 LYS cc_start: 0.8756 (tppt) cc_final: 0.8530 (tppt) outliers start: 62 outliers final: 38 residues processed: 214 average time/residue: 0.2372 time to fit residues: 68.3599 Evaluate side-chains 205 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 155 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 23 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 143 VAL Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 203 THR 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: 2.9990 chunk 84 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.099478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.069435 restraints weight = 20398.585| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.96 r_work: 0.2821 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8916 Z= 0.180 Angle : 0.694 11.493 12106 Z= 0.353 Chirality : 0.045 0.146 1374 Planarity : 0.004 0.049 1540 Dihedral : 7.454 69.872 1257 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 5.25 % Allowed : 26.59 % Favored : 68.16 % 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: 0.12 (0.26), residues: 1120 helix: 1.58 (0.27), residues: 370 sheet: 0.10 (0.32), residues: 264 loop : -1.11 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP S 164 HIS 0.008 0.001 HIS A 259 PHE 0.019 0.001 PHE A 180 TYR 0.017 0.002 TYR S 223 ARG 0.006 0.001 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 445) hydrogen bonds : angle 4.86936 ( 1260) SS BOND : bond 0.00478 ( 5) SS BOND : angle 0.95252 ( 10) covalent geometry : bond 0.00409 ( 8911) covalent geometry : angle 0.69326 (12096) *********************** 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 230 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8858 (m) cc_final: 0.8406 (m) REVERT: A 109 MET cc_start: 0.8995 (tmm) cc_final: 0.8324 (tmm) REVERT: A 112 GLN cc_start: 0.8511 (tp40) cc_final: 0.8150 (tp40) REVERT: A 137 ASN cc_start: 0.8814 (m-40) cc_final: 0.8010 (m110) REVERT: A 181 SER cc_start: 0.9230 (m) cc_final: 0.8893 (p) REVERT: A 182 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8117 (pt) REVERT: A 238 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9069 (tp) REVERT: B 97 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8868 (p) REVERT: B 228 ASP cc_start: 0.8407 (m-30) cc_final: 0.7774 (m-30) REVERT: B 297 TRP cc_start: 0.9185 (m100) cc_final: 0.8811 (m100) REVERT: C 308 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8880 (mt-10) REVERT: C 317 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8091 (ttmt) REVERT: G 27 ARG cc_start: 0.8355 (tpp80) cc_final: 0.7523 (tpp80) REVERT: S 39 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7617 (tp40) REVERT: S 43 LYS cc_start: 0.9490 (mmmm) cc_final: 0.9206 (mmtm) REVERT: S 82 GLN cc_start: 0.8699 (mm110) cc_final: 0.8487 (mm-40) REVERT: S 87 ARG cc_start: 0.7819 (mpp80) cc_final: 0.7229 (mpp80) REVERT: S 89 GLU cc_start: 0.8936 (pm20) cc_final: 0.8702 (pm20) REVERT: S 206 ARG cc_start: 0.8938 (tpp80) cc_final: 0.8297 (tpp80) REVERT: S 208 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8239 (pm20) REVERT: S 219 GLN cc_start: 0.9409 (pp30) cc_final: 0.9088 (pp30) REVERT: S 232 LYS cc_start: 0.8874 (tppt) cc_final: 0.8571 (tppt) outliers start: 48 outliers final: 34 residues processed: 216 average time/residue: 0.2345 time to fit residues: 67.2639 Evaluate side-chains 201 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 143 THR Chi-restraints excluded: chain A residue 155 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 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 19 LEU 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 208 GLU 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: 7.9990 chunk 38 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 3 optimal weight: 30.0000 chunk 41 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.100469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.070645 restraints weight = 20648.248| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.99 r_work: 0.2842 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8916 Z= 0.149 Angle : 0.705 10.610 12106 Z= 0.356 Chirality : 0.045 0.149 1374 Planarity : 0.004 0.047 1540 Dihedral : 7.408 69.785 1257 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.82 % Favored : 95.09 % Rotamer: Outliers : 5.14 % Allowed : 27.46 % Favored : 67.40 % 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: 371 sheet: 0.23 (0.32), residues: 263 loop : -1.13 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 164 HIS 0.008 0.001 HIS A 161 PHE 0.022 0.001 PHE C 274 TYR 0.016 0.001 TYR S 223 ARG 0.007 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 445) hydrogen bonds : angle 4.79836 ( 1260) SS BOND : bond 0.00453 ( 5) SS BOND : angle 1.14501 ( 10) covalent geometry : bond 0.00340 ( 8911) covalent geometry : angle 0.70443 (12096) *********************** 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 223 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8878 (m) cc_final: 0.8428 (m) REVERT: A 109 MET cc_start: 0.9001 (tmm) cc_final: 0.8355 (tmm) REVERT: A 112 GLN cc_start: 0.8486 (tp40) cc_final: 0.8114 (tp40) REVERT: A 181 SER cc_start: 0.9237 (m) cc_final: 0.8880 (p) REVERT: A 182 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7669 (pt) REVERT: A 238 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9038 (tp) REVERT: B 97 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8834 (p) REVERT: B 228 ASP cc_start: 0.8375 (m-30) cc_final: 0.7788 (m-30) REVERT: B 297 TRP cc_start: 0.9176 (m100) cc_final: 0.8834 (m100) REVERT: C 308 GLU cc_start: 0.9324 (OUTLIER) cc_final: 0.8903 (mt-10) REVERT: C 317 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8021 (ttmt) REVERT: G 27 ARG cc_start: 0.8355 (tpp80) cc_final: 0.7544 (tpp80) REVERT: G 38 MET cc_start: 0.8830 (ppp) cc_final: 0.8505 (ppp) REVERT: S 39 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7597 (tp40) REVERT: S 82 GLN cc_start: 0.8652 (mm110) cc_final: 0.8368 (mm-40) REVERT: S 87 ARG cc_start: 0.7774 (mpp80) cc_final: 0.7106 (mpp80) REVERT: S 168 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8900 (mtm-85) REVERT: S 206 ARG cc_start: 0.8924 (tpp80) cc_final: 0.8336 (tpp80) REVERT: S 208 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8189 (pm20) REVERT: S 211 ASP cc_start: 0.9218 (m-30) cc_final: 0.8907 (m-30) REVERT: S 219 GLN cc_start: 0.9405 (pp30) cc_final: 0.9097 (pp30) REVERT: S 232 LYS cc_start: 0.8862 (tppt) cc_final: 0.8545 (tppt) outliers start: 47 outliers final: 32 residues processed: 213 average time/residue: 0.2753 time to fit residues: 79.2053 Evaluate side-chains 208 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 123 VAL 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 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 19 LEU 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 208 GLU 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: 3.9990 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3564 r_free = 0.3564 target = 0.100411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.070467 restraints weight = 20762.291| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.93 r_work: 0.2843 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8916 Z= 0.163 Angle : 0.725 10.746 12106 Z= 0.367 Chirality : 0.046 0.150 1374 Planarity : 0.004 0.047 1540 Dihedral : 7.422 70.131 1257 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.82 % Favored : 95.09 % Rotamer: Outliers : 5.36 % Allowed : 27.90 % 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: 0.18 (0.26), residues: 1120 helix: 1.57 (0.27), residues: 372 sheet: 0.14 (0.31), residues: 276 loop : -1.06 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 164 HIS 0.008 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 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 445) hydrogen bonds : angle 4.77493 ( 1260) SS BOND : bond 0.00496 ( 5) SS BOND : angle 1.81615 ( 10) covalent geometry : bond 0.00374 ( 8911) covalent geometry : angle 0.72378 (12096) *********************** 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 221 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8870 (m) cc_final: 0.8414 (m) REVERT: A 109 MET cc_start: 0.9006 (tmm) cc_final: 0.8352 (tmm) REVERT: A 112 GLN cc_start: 0.8559 (tp40) cc_final: 0.8200 (tp40) REVERT: A 138 LYS cc_start: 0.9416 (mtmm) cc_final: 0.9107 (mtmm) REVERT: A 181 SER cc_start: 0.9180 (m) cc_final: 0.8794 (p) REVERT: A 182 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7301 (pt) REVERT: A 238 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9055 (tp) REVERT: B 97 SER cc_start: 0.9190 (OUTLIER) cc_final: 0.8841 (p) REVERT: B 145 TYR cc_start: 0.9232 (p90) cc_final: 0.8873 (p90) REVERT: B 228 ASP cc_start: 0.8373 (m-30) cc_final: 0.7778 (m-30) REVERT: C 308 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.8866 (mt-10) REVERT: C 317 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8048 (ttmt) REVERT: G 27 ARG cc_start: 0.8368 (tpp80) cc_final: 0.7562 (tpp80) REVERT: S 39 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7652 (tp40) REVERT: S 87 ARG cc_start: 0.7783 (mpp80) cc_final: 0.7053 (mpp80) REVERT: S 89 GLU cc_start: 0.9055 (pm20) cc_final: 0.8847 (pm20) REVERT: S 168 ARG cc_start: 0.9063 (mtm-85) cc_final: 0.8839 (mtm-85) REVERT: S 206 ARG cc_start: 0.8946 (tpp80) cc_final: 0.8346 (tpp80) REVERT: S 208 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8174 (pm20) REVERT: S 211 ASP cc_start: 0.9208 (m-30) cc_final: 0.8898 (m-30) REVERT: S 219 GLN cc_start: 0.9402 (pp30) cc_final: 0.9128 (pp30) REVERT: S 232 LYS cc_start: 0.8888 (tppt) cc_final: 0.8559 (tppt) outliers start: 49 outliers final: 33 residues processed: 212 average time/residue: 0.2332 time to fit residues: 65.7470 Evaluate side-chains 208 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 123 VAL 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 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 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 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 19 LEU 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 208 GLU Chi-restraints excluded: chain S residue 221 LEU 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: 5.9990 chunk 71 optimal weight: 0.0980 chunk 83 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.098983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.068975 restraints weight = 20665.233| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.96 r_work: 0.2804 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8916 Z= 0.237 Angle : 0.786 11.348 12106 Z= 0.396 Chirality : 0.048 0.306 1374 Planarity : 0.004 0.047 1540 Dihedral : 7.488 72.442 1257 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.82 % Favored : 95.09 % Rotamer: Outliers : 4.81 % Allowed : 28.88 % Favored : 66.30 % 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: 0.12 (0.26), residues: 1120 helix: 1.50 (0.27), residues: 372 sheet: 0.09 (0.32), residues: 271 loop : -1.06 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP S 164 HIS 0.008 0.001 HIS A 161 PHE 0.028 0.002 PHE C 274 TYR 0.018 0.002 TYR S 223 ARG 0.007 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 445) hydrogen bonds : angle 4.92001 ( 1260) SS BOND : bond 0.00464 ( 5) SS BOND : angle 1.79190 ( 10) covalent geometry : bond 0.00547 ( 8911) covalent geometry : angle 0.78465 (12096) *********************** 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 208 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8911 (m) cc_final: 0.8480 (m) REVERT: A 112 GLN cc_start: 0.8560 (tp40) cc_final: 0.8229 (tp40) REVERT: A 138 LYS cc_start: 0.9411 (mtmm) cc_final: 0.9127 (mtmm) REVERT: A 181 SER cc_start: 0.9141 (m) cc_final: 0.8740 (p) REVERT: A 182 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7404 (pt) REVERT: A 238 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9063 (tp) REVERT: B 97 SER cc_start: 0.9215 (OUTLIER) cc_final: 0.8873 (p) REVERT: B 145 TYR cc_start: 0.9252 (p90) cc_final: 0.8815 (p90) REVERT: B 228 ASP cc_start: 0.8390 (m-30) cc_final: 0.7745 (m-30) REVERT: B 262 MET cc_start: 0.8573 (tpt) cc_final: 0.8324 (tpt) REVERT: B 297 TRP cc_start: 0.9198 (m100) cc_final: 0.8856 (m100) REVERT: C 308 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8886 (mt-10) REVERT: C 317 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8120 (ttmt) REVERT: G 27 ARG cc_start: 0.8399 (tpp80) cc_final: 0.7800 (tpp80) REVERT: S 39 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7534 (tp40) REVERT: S 168 ARG cc_start: 0.9048 (mtm-85) cc_final: 0.8830 (mtm-85) REVERT: S 206 ARG cc_start: 0.8992 (tpp80) cc_final: 0.8394 (tpp80) REVERT: S 208 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: S 211 ASP cc_start: 0.9210 (m-30) cc_final: 0.8878 (m-30) REVERT: S 219 GLN cc_start: 0.9430 (pp30) cc_final: 0.9058 (pp30) REVERT: S 232 LYS cc_start: 0.8975 (tppt) cc_final: 0.8692 (tppt) outliers start: 44 outliers final: 36 residues processed: 200 average time/residue: 0.2426 time to fit residues: 64.3820 Evaluate side-chains 202 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 123 VAL 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 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 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 22 ASN 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 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 19 LEU 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 208 GLU Chi-restraints excluded: chain S residue 221 LEU 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: 0.8980 chunk 21 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.101738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.072033 restraints weight = 20577.782| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.92 r_work: 0.2872 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8916 Z= 0.142 Angle : 0.771 12.739 12106 Z= 0.384 Chirality : 0.046 0.310 1374 Planarity : 0.004 0.046 1540 Dihedral : 7.448 71.847 1257 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 4.38 % Allowed : 29.21 % Favored : 66.41 % 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: 1.54 (0.27), residues: 373 sheet: 0.12 (0.31), residues: 275 loop : -0.98 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 164 HIS 0.008 0.001 HIS A 259 PHE 0.010 0.001 PHE A 197 TYR 0.016 0.001 TYR S 223 ARG 0.008 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 445) hydrogen bonds : angle 4.84997 ( 1260) SS BOND : bond 0.00330 ( 5) SS BOND : angle 1.47489 ( 10) covalent geometry : bond 0.00323 ( 8911) covalent geometry : angle 0.76988 (12096) ********************** 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 220 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8893 (m) cc_final: 0.8453 (m) REVERT: A 138 LYS cc_start: 0.9384 (mtmm) cc_final: 0.9090 (mtmm) REVERT: A 181 SER cc_start: 0.9111 (m) cc_final: 0.8637 (p) REVERT: A 182 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.6943 (pt) REVERT: A 238 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8988 (tp) REVERT: B 97 SER cc_start: 0.9162 (OUTLIER) cc_final: 0.8797 (p) REVERT: B 145 TYR cc_start: 0.9218 (p90) cc_final: 0.8909 (p90) REVERT: B 186 ASP cc_start: 0.8193 (m-30) cc_final: 0.7770 (m-30) REVERT: B 228 ASP cc_start: 0.8264 (m-30) cc_final: 0.7657 (m-30) REVERT: B 262 MET cc_start: 0.8646 (tpt) cc_final: 0.8424 (tpt) REVERT: B 297 TRP cc_start: 0.9062 (m100) cc_final: 0.8801 (m100) REVERT: C 308 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.8830 (mt-10) REVERT: C 313 ARG cc_start: 0.8998 (mpp80) cc_final: 0.8542 (mtm-85) REVERT: C 317 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7879 (ttmt) REVERT: G 38 MET cc_start: 0.9049 (pmm) cc_final: 0.8849 (pmm) REVERT: S 39 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7473 (tp40) REVERT: S 168 ARG cc_start: 0.9021 (mtm-85) cc_final: 0.8803 (mtm-85) REVERT: S 206 ARG cc_start: 0.8985 (tpp80) cc_final: 0.8396 (tpp80) REVERT: S 208 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8173 (pm20) REVERT: S 211 ASP cc_start: 0.9181 (m-30) cc_final: 0.8890 (m-30) REVERT: S 219 GLN cc_start: 0.9403 (pp30) cc_final: 0.9089 (pp30) REVERT: S 232 LYS cc_start: 0.8933 (tppt) cc_final: 0.8655 (tppt) outliers start: 40 outliers final: 29 residues processed: 211 average time/residue: 0.2444 time to fit residues: 68.6734 Evaluate side-chains 202 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 182 ILE Chi-restraints excluded: chain A residue 198 PHE 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 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 314 LYS 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 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 180 MET Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 221 LEU 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: 0.4980 chunk 82 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.100687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.070844 restraints weight = 20592.039| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.92 r_work: 0.2846 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8916 Z= 0.182 Angle : 0.781 11.885 12106 Z= 0.390 Chirality : 0.047 0.309 1374 Planarity : 0.004 0.047 1540 Dihedral : 7.418 72.608 1257 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 4.38 % Allowed : 29.87 % Favored : 65.75 % 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: 0.19 (0.26), residues: 1120 helix: 1.52 (0.27), residues: 372 sheet: 0.05 (0.31), residues: 276 loop : -0.92 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP S 164 HIS 0.008 0.001 HIS A 259 PHE 0.029 0.001 PHE C 274 TYR 0.016 0.001 TYR C 302 ARG 0.006 0.001 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 445) hydrogen bonds : angle 4.88570 ( 1260) SS BOND : bond 0.00371 ( 5) SS BOND : angle 1.37066 ( 10) covalent geometry : bond 0.00424 ( 8911) covalent geometry : angle 0.78018 (12096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5237.86 seconds wall clock time: 91 minutes 44.80 seconds (5504.80 seconds total)