Starting phenix.real_space_refine on Thu Feb 13 22:38:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xx3_38744/02_2025/8xx3_38744.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xx3_38744/02_2025/8xx3_38744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xx3_38744/02_2025/8xx3_38744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xx3_38744/02_2025/8xx3_38744.map" model { file = "/net/cci-nas-00/data/ceres_data/8xx3_38744/02_2025/8xx3_38744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xx3_38744/02_2025/8xx3_38744.cif" } resolution = 3.38 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= 1.000 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 66 5.16 5 C 6014 2.51 5 N 1638 2.21 5 O 1770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9488 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 336 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 452 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2207 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 288} Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 83 Chain: "A" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1711 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "S" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Time building chain proxies: 5.40, per 1000 atoms: 0.57 Number of scatterers: 9488 At special positions: 0 Unit cell: (88.1875, 121.388, 152.512, 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 66 16.00 O 1770 8.00 N 1638 7.00 C 6014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 35 " distance=2.03 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=2.04 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: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 16 sheets defined 35.7% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'E' and resid 19 through 21 No H-bonds generated for 'chain 'E' and resid 19 through 21' Processing helix chain 'E' and resid 56 through 69 removed outlier: 3.915A pdb=" N GLN E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 67 Processing helix chain 'R' and resid 44 through 76 removed outlier: 4.005A pdb=" N LYS R 48 " --> pdb=" O LEU R 44 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 111 Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 116 through 149 Processing helix chain 'R' and resid 154 through 160 removed outlier: 3.735A pdb=" N GLN R 157 " --> pdb=" O THR R 154 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 177 Processing helix chain 'R' and resid 177 through 183 removed outlier: 3.583A pdb=" N LEU R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 Processing helix chain 'R' and resid 212 through 218 removed outlier: 3.560A pdb=" N GLN R 216 " --> pdb=" O ARG R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 240 removed outlier: 3.788A pdb=" N LYS R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 279 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 285 through 304 Processing helix chain 'R' and resid 304 through 315 removed outlier: 4.389A pdb=" N CYS R 308 " --> pdb=" O ILE R 304 " (cutoff:3.500A) Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 329 removed outlier: 3.596A pdb=" N ARG R 322 " --> pdb=" O GLY R 318 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU R 329 " --> pdb=" O LEU R 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.787A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.113A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.706A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.609A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.646A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.014A 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 208 through 212 removed outlier: 3.809A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 49 through 52 removed outlier: 4.137A pdb=" N VAL E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 184 through 187 Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 188 removed outlier: 9.585A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.401A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.963A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 103 removed outlier: 4.210A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 153 removed outlier: 4.600A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.567A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.406A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.395A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.721A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.511A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.167A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.167A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1323 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: 3.05 Time building geometry restraints manager: 2.76 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: 3070 1.34 - 1.46: 2062 1.46 - 1.58: 4451 1.58 - 1.70: 0 1.70 - 1.83: 91 Bond restraints: 9674 Sorted by residual: bond pdb=" N GLY E 17 " pdb=" CA GLY E 17 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.25e+00 bond pdb=" N GLN D 60 " pdb=" CA GLN D 60 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.59e+00 bond pdb=" N LYS D 65 " pdb=" CA LYS D 65 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.30e-02 5.92e+03 4.66e+00 bond pdb=" CA ALA R 273 " pdb=" CB ALA R 273 " ideal model delta sigma weight residual 1.530 1.497 0.034 1.69e-02 3.50e+03 3.95e+00 bond pdb=" N THR R 279 " pdb=" CA THR R 279 " ideal model delta sigma weight residual 1.455 1.480 -0.024 1.25e-02 6.40e+03 3.82e+00 ... (remaining 9669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 12934 1.69 - 3.38: 167 3.38 - 5.07: 36 5.07 - 6.76: 2 6.76 - 8.45: 3 Bond angle restraints: 13142 Sorted by residual: angle pdb=" N VAL D 59 " pdb=" CA VAL D 59 " pdb=" C VAL D 59 " ideal model delta sigma weight residual 110.23 103.06 7.17 1.04e+00 9.25e-01 4.75e+01 angle pdb=" N LYS D 65 " pdb=" CA LYS D 65 " pdb=" C LYS D 65 " ideal model delta sigma weight residual 112.23 103.78 8.45 1.26e+00 6.30e-01 4.50e+01 angle pdb=" N LEU R 272 " pdb=" CA LEU R 272 " pdb=" C LEU R 272 " ideal model delta sigma weight residual 111.03 105.46 5.57 1.11e+00 8.12e-01 2.52e+01 angle pdb=" C THR B 87 " pdb=" N ASN B 88 " pdb=" CA ASN B 88 " ideal model delta sigma weight residual 122.67 115.36 7.31 1.73e+00 3.34e-01 1.79e+01 angle pdb=" N THR R 279 " pdb=" CA THR R 279 " pdb=" C THR R 279 " ideal model delta sigma weight residual 112.93 108.20 4.73 1.12e+00 7.97e-01 1.78e+01 ... (remaining 13137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 5270 17.31 - 34.62: 425 34.62 - 51.92: 57 51.92 - 69.23: 10 69.23 - 86.54: 5 Dihedral angle restraints: 5767 sinusoidal: 2132 harmonic: 3635 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 140.09 -47.09 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CB CYS R 39 " pdb=" SG CYS R 39 " pdb=" SG CYS R 286 " pdb=" CB CYS R 286 " ideal model delta sinusoidal sigma weight residual 93.00 62.55 30.45 1 1.00e+01 1.00e-02 1.32e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 162.33 17.67 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 5764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1357 0.063 - 0.126: 163 0.126 - 0.188: 8 0.188 - 0.251: 1 0.251 - 0.314: 3 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CA ILE D 66 " pdb=" N ILE D 66 " pdb=" C ILE D 66 " pdb=" CB ILE D 66 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA VAL D 59 " pdb=" N VAL D 59 " pdb=" C VAL D 59 " pdb=" CB VAL D 59 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA LYS D 65 " pdb=" N LYS D 65 " pdb=" C LYS D 65 " pdb=" CB LYS D 65 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 1529 not shown) Planarity restraints: 1675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO G 55 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO B 236 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 310 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO R 311 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO R 311 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 311 " 0.019 5.00e-02 4.00e+02 ... (remaining 1672 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1496 2.76 - 3.30: 8999 3.30 - 3.83: 15238 3.83 - 4.37: 17651 4.37 - 4.90: 31675 Nonbonded interactions: 75059 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR B 165 " pdb=" O PHE B 180 " model vdw 2.258 3.040 nonbonded pdb=" O PHE S 29 " pdb=" NH2 ARG S 72 " model vdw 2.262 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR A 291 " pdb=" O PRO A 294 " model vdw 2.316 3.040 ... (remaining 75054 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: 0.740 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: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.700 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.003 0.044 9674 Z= 0.182 Angle : 0.530 8.448 13142 Z= 0.331 Chirality : 0.044 0.314 1532 Planarity : 0.003 0.040 1675 Dihedral : 12.555 86.538 3396 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.68 (0.25), residues: 1237 helix: 1.88 (0.27), residues: 405 sheet: 0.04 (0.28), residues: 341 loop : -0.38 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS R 242 PHE 0.014 0.001 PHE B 234 TYR 0.016 0.001 TYR S 178 ARG 0.004 0.000 ARG R 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 27 ASN cc_start: 0.7650 (t0) cc_final: 0.6811 (p0) REVERT: D 56 SER cc_start: 0.8160 (t) cc_final: 0.7892 (p) REVERT: R 41 PRO cc_start: 0.7351 (Cg_endo) cc_final: 0.6927 (Cg_exo) REVERT: R 89 ASN cc_start: 0.8547 (m-40) cc_final: 0.8149 (m110) REVERT: R 145 TYR cc_start: 0.8507 (t80) cc_final: 0.8178 (t80) REVERT: R 203 ASN cc_start: 0.6818 (t0) cc_final: 0.6309 (m-40) REVERT: A 231 TYR cc_start: 0.7313 (m-10) cc_final: 0.6926 (m-80) REVERT: A 298 GLU cc_start: 0.8210 (mp0) cc_final: 0.7864 (pp20) REVERT: A 334 VAL cc_start: 0.8950 (t) cc_final: 0.8614 (t) REVERT: B 211 TRP cc_start: 0.6826 (m-10) cc_final: 0.6496 (m-10) REVERT: B 325 MET cc_start: 0.7604 (tpp) cc_final: 0.7188 (tpp) REVERT: G 19 LEU cc_start: 0.9284 (mt) cc_final: 0.9079 (mt) REVERT: G 30 VAL cc_start: 0.8792 (m) cc_final: 0.8587 (p) REVERT: S 151 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7939 (mttp) REVERT: S 208 GLU cc_start: 0.8363 (tt0) cc_final: 0.6760 (pt0) REVERT: S 211 ASP cc_start: 0.5966 (m-30) cc_final: 0.5700 (m-30) outliers start: 1 outliers final: 0 residues processed: 335 average time/residue: 0.2710 time to fit residues: 118.2486 Evaluate side-chains 187 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 GLN D 34 HIS R 89 ASN R 319 GLN A 256 ASN B 6 GLN B 35 ASN B 75 GLN B 88 ASN B 156 GLN B 176 GLN B 220 GLN G 18 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.110569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.086440 restraints weight = 22614.475| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.28 r_work: 0.3158 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 9674 Z= 0.281 Angle : 0.639 14.092 13142 Z= 0.340 Chirality : 0.044 0.217 1532 Planarity : 0.004 0.038 1675 Dihedral : 4.068 28.805 1345 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.71 % Allowed : 11.42 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.90 (0.24), residues: 1237 helix: 2.19 (0.26), residues: 417 sheet: -0.00 (0.27), residues: 345 loop : -0.29 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 207 HIS 0.005 0.001 HIS B 142 PHE 0.013 0.002 PHE S 165 TYR 0.025 0.002 TYR S 178 ARG 0.004 0.001 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 SER cc_start: 0.8008 (t) cc_final: 0.7633 (p) REVERT: R 245 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7645 (mp10) REVERT: A 21 LYS cc_start: 0.9040 (tmtt) cc_final: 0.8508 (mttm) REVERT: A 243 ARG cc_start: 0.8734 (ttm-80) cc_final: 0.8505 (ttm-80) REVERT: S 82 GLN cc_start: 0.8242 (tp40) cc_final: 0.8032 (tp40) outliers start: 27 outliers final: 18 residues processed: 205 average time/residue: 0.2580 time to fit residues: 70.1102 Evaluate side-chains 186 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 290 ASN Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 21 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN D 34 HIS R 150 HIS ** R 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 230 ASN G 11 GLN S 130 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.107065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082591 restraints weight = 22506.539| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.34 r_work: 0.3053 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9674 Z= 0.380 Angle : 0.674 15.146 13142 Z= 0.359 Chirality : 0.046 0.234 1532 Planarity : 0.004 0.040 1675 Dihedral : 4.442 30.971 1345 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.41 % Allowed : 14.63 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.68 (0.24), residues: 1237 helix: 2.15 (0.25), residues: 410 sheet: -0.12 (0.27), residues: 344 loop : -0.54 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 47 HIS 0.005 0.001 HIS B 311 PHE 0.016 0.002 PHE R 59 TYR 0.027 0.002 TYR S 178 ARG 0.005 0.001 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 SER cc_start: 0.8083 (t) cc_final: 0.7631 (p) REVERT: R 145 TYR cc_start: 0.8722 (t80) cc_final: 0.8442 (t80) REVERT: R 198 GLU cc_start: 0.8633 (mp0) cc_final: 0.8390 (mm-30) REVERT: A 21 LYS cc_start: 0.9067 (tmtt) cc_final: 0.8466 (mttm) REVERT: B 215 GLU cc_start: 0.8878 (mp0) cc_final: 0.8568 (mp0) REVERT: B 258 ASP cc_start: 0.7746 (t0) cc_final: 0.7258 (t0) REVERT: G 13 ARG cc_start: 0.8708 (mtt-85) cc_final: 0.8473 (mtt-85) outliers start: 34 outliers final: 24 residues processed: 199 average time/residue: 0.2693 time to fit residues: 70.9522 Evaluate side-chains 186 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 0.2980 chunk 27 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN D 34 HIS R 89 ASN R 268 ASN G 11 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.108604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.082352 restraints weight = 22481.044| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.85 r_work: 0.3121 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9674 Z= 0.212 Angle : 0.607 16.352 13142 Z= 0.321 Chirality : 0.044 0.219 1532 Planarity : 0.004 0.037 1675 Dihedral : 4.166 27.581 1345 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.71 % Allowed : 16.33 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.71 (0.24), residues: 1237 helix: 2.24 (0.25), residues: 411 sheet: -0.04 (0.27), residues: 339 loop : -0.65 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.002 0.001 HIS S 35 PHE 0.011 0.001 PHE R 59 TYR 0.021 0.001 TYR S 178 ARG 0.007 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 SER cc_start: 0.8306 (t) cc_final: 0.7940 (p) REVERT: A 21 LYS cc_start: 0.9029 (tmtt) cc_final: 0.8462 (mttm) REVERT: A 318 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: B 258 ASP cc_start: 0.7689 (t0) cc_final: 0.7228 (t0) outliers start: 27 outliers final: 17 residues processed: 200 average time/residue: 0.2459 time to fit residues: 66.2946 Evaluate side-chains 184 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 37 optimal weight: 7.9990 chunk 7 optimal weight: 0.0270 chunk 65 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 22 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 0.0870 chunk 78 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN D 34 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.109463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083529 restraints weight = 22299.692| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.84 r_work: 0.3149 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9674 Z= 0.180 Angle : 0.626 15.970 13142 Z= 0.323 Chirality : 0.044 0.327 1532 Planarity : 0.003 0.037 1675 Dihedral : 4.076 22.985 1345 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.01 % Allowed : 18.04 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.75 (0.24), residues: 1237 helix: 2.25 (0.26), residues: 411 sheet: 0.02 (0.27), residues: 331 loop : -0.62 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE R 59 TYR 0.020 0.001 TYR S 178 ARG 0.006 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 SER cc_start: 0.8373 (t) cc_final: 0.8013 (p) REVERT: A 21 LYS cc_start: 0.9046 (tmtt) cc_final: 0.8440 (mttm) REVERT: A 318 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.7020 (tm-30) REVERT: B 258 ASP cc_start: 0.7785 (t0) cc_final: 0.7338 (t0) outliers start: 30 outliers final: 19 residues processed: 190 average time/residue: 0.2478 time to fit residues: 63.4078 Evaluate side-chains 185 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN D 34 HIS S 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.106262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.079734 restraints weight = 22443.068| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.86 r_work: 0.3061 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9674 Z= 0.405 Angle : 0.723 16.555 13142 Z= 0.381 Chirality : 0.047 0.312 1532 Planarity : 0.004 0.037 1675 Dihedral : 4.507 23.732 1345 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.51 % Allowed : 18.84 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1237 helix: 1.99 (0.25), residues: 412 sheet: -0.04 (0.27), residues: 338 loop : -0.83 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP S 47 HIS 0.005 0.001 HIS B 311 PHE 0.013 0.002 PHE S 165 TYR 0.028 0.002 TYR S 178 ARG 0.005 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 SER cc_start: 0.8380 (t) cc_final: 0.8023 (p) REVERT: R 145 TYR cc_start: 0.8831 (t80) cc_final: 0.8517 (t80) REVERT: A 55 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6715 (mt) REVERT: A 318 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7151 (tm-30) REVERT: B 215 GLU cc_start: 0.8666 (mp0) cc_final: 0.8394 (mp0) REVERT: B 322 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8642 (m-30) outliers start: 35 outliers final: 25 residues processed: 183 average time/residue: 0.2577 time to fit residues: 63.4443 Evaluate side-chains 183 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 133 SER Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 3 optimal weight: 0.2980 chunk 114 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.109290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.082883 restraints weight = 22597.926| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.91 r_work: 0.3130 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9674 Z= 0.178 Angle : 0.649 13.934 13142 Z= 0.334 Chirality : 0.044 0.320 1532 Planarity : 0.004 0.036 1675 Dihedral : 4.179 18.974 1345 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.61 % Allowed : 20.04 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.62 (0.24), residues: 1237 helix: 2.12 (0.25), residues: 411 sheet: -0.01 (0.27), residues: 329 loop : -0.71 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS D 19 PHE 0.010 0.001 PHE R 59 TYR 0.018 0.001 TYR S 178 ARG 0.010 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 SER cc_start: 0.8350 (t) cc_final: 0.7982 (p) REVERT: R 113 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8533 (pt) REVERT: R 145 TYR cc_start: 0.8731 (t80) cc_final: 0.8325 (t80) REVERT: A 55 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6684 (mt) REVERT: A 318 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7082 (tm-30) outliers start: 26 outliers final: 18 residues processed: 181 average time/residue: 0.2682 time to fit residues: 66.0525 Evaluate side-chains 174 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 320 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 92 optimal weight: 5.9990 chunk 112 optimal weight: 30.0000 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 9 optimal weight: 30.0000 chunk 91 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.107272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.080697 restraints weight = 22745.215| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.89 r_work: 0.3082 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9674 Z= 0.294 Angle : 0.676 13.151 13142 Z= 0.353 Chirality : 0.045 0.308 1532 Planarity : 0.004 0.037 1675 Dihedral : 4.315 20.733 1345 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.01 % Allowed : 19.74 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1237 helix: 2.04 (0.25), residues: 410 sheet: 0.03 (0.27), residues: 331 loop : -0.86 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE B 199 TYR 0.024 0.001 TYR S 178 ARG 0.006 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 SER cc_start: 0.8403 (t) cc_final: 0.8044 (p) REVERT: R 113 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8611 (pt) REVERT: R 145 TYR cc_start: 0.8785 (t80) cc_final: 0.8401 (t80) REVERT: A 55 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6740 (mt) REVERT: A 318 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7111 (tm-30) outliers start: 30 outliers final: 20 residues processed: 178 average time/residue: 0.2443 time to fit residues: 58.5980 Evaluate side-chains 174 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 320 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 63 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 86 optimal weight: 0.1980 chunk 54 optimal weight: 0.0370 chunk 30 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.109253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.082840 restraints weight = 22649.598| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.91 r_work: 0.3130 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9674 Z= 0.177 Angle : 0.656 12.839 13142 Z= 0.338 Chirality : 0.044 0.302 1532 Planarity : 0.003 0.036 1675 Dihedral : 4.095 18.027 1345 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.71 % Allowed : 20.24 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1237 helix: 2.13 (0.25), residues: 411 sheet: 0.03 (0.28), residues: 327 loop : -0.80 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE R 59 TYR 0.017 0.001 TYR S 178 ARG 0.006 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 SER cc_start: 0.8411 (t) cc_final: 0.8054 (p) REVERT: R 113 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8598 (pt) REVERT: R 243 MET cc_start: 0.7873 (ptp) cc_final: 0.7570 (ptp) REVERT: A 55 ILE cc_start: 0.7185 (OUTLIER) cc_final: 0.6784 (mt) REVERT: A 318 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7078 (tm-30) outliers start: 27 outliers final: 20 residues processed: 183 average time/residue: 0.2462 time to fit residues: 60.9330 Evaluate side-chains 181 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 218 PHE Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 89 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 100 optimal weight: 0.0030 chunk 99 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.107805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.081161 restraints weight = 22720.052| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.93 r_work: 0.3094 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9674 Z= 0.260 Angle : 0.689 13.249 13142 Z= 0.360 Chirality : 0.045 0.317 1532 Planarity : 0.004 0.037 1675 Dihedral : 4.189 19.139 1345 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.40 % Allowed : 20.44 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1237 helix: 2.09 (0.25), residues: 411 sheet: 0.03 (0.28), residues: 333 loop : -0.83 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE B 199 TYR 0.024 0.001 TYR S 178 ARG 0.006 0.001 ARG A 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 SER cc_start: 0.8468 (t) cc_final: 0.8121 (p) REVERT: R 113 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8609 (pt) REVERT: R 145 TYR cc_start: 0.8779 (t80) cc_final: 0.8362 (t80) REVERT: A 55 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6715 (mt) REVERT: A 318 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7088 (tm-30) REVERT: A 349 ARG cc_start: 0.8440 (mtp85) cc_final: 0.8150 (mtp85) REVERT: B 217 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7531 (ptt) REVERT: S 113 GLN cc_start: 0.8593 (tp-100) cc_final: 0.8225 (mm110) outliers start: 24 outliers final: 20 residues processed: 172 average time/residue: 0.2466 time to fit residues: 57.0609 Evaluate side-chains 177 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 218 PHE Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 88 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 114 optimal weight: 0.0170 chunk 15 optimal weight: 20.0000 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.108600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.084244 restraints weight = 22396.259| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.96 r_work: 0.3133 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9674 Z= 0.196 Angle : 0.675 13.023 13142 Z= 0.350 Chirality : 0.045 0.335 1532 Planarity : 0.003 0.037 1675 Dihedral : 4.045 17.831 1345 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.71 % Allowed : 20.54 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.65 (0.24), residues: 1237 helix: 2.15 (0.26), residues: 411 sheet: 0.02 (0.28), residues: 329 loop : -0.71 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE R 59 TYR 0.019 0.001 TYR S 178 ARG 0.007 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4667.47 seconds wall clock time: 83 minutes 51.49 seconds (5031.49 seconds total)