Starting phenix.real_space_refine on Sat Aug 23 02:01:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yyw_39681/08_2025/8yyw_39681.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yyw_39681/08_2025/8yyw_39681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yyw_39681/08_2025/8yyw_39681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yyw_39681/08_2025/8yyw_39681.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yyw_39681/08_2025/8yyw_39681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yyw_39681/08_2025/8yyw_39681.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.002 sd= 0.124 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 69 5.16 5 C 5761 2.51 5 N 1530 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9068 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2404 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 10, 'TRANS': 289} Chain: "F" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1817 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {'AKG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.63, per 1000 atoms: 0.18 Number of scatterers: 9068 At special positions: 0 Unit cell: (88.4, 122.4, 129.2, 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 69 16.00 O 1708 8.00 N 1530 7.00 C 5761 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 229 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 106 " - pdb=" SG CYS E 183 " 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: 0.68 Conformation dependent library (CDL) restraints added in 211.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 37.8% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.514A pdb=" N PHE B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 56 removed outlier: 4.103A pdb=" N GLY B 56 " --> pdb=" O SER B 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.808A pdb=" N ASP B 90 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'C' and resid 3 through 25 removed outlier: 3.552A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 8 through 12 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.531A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 35 removed outlier: 3.705A pdb=" N LYS E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 61 Proline residue: E 49 - end of helix Processing helix chain 'E' and resid 68 through 85 removed outlier: 3.771A pdb=" N SER E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 95 removed outlier: 3.924A pdb=" N LEU E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 137 removed outlier: 3.620A pdb=" N LYS E 107 " --> pdb=" O ASP E 103 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS E 114 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER E 119 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE E 121 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU E 122 " --> pdb=" O TYR E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 171 removed outlier: 4.371A pdb=" N ALA E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL E 151 " --> pdb=" O THR E 147 " (cutoff:3.500A) Proline residue: E 167 - end of helix Processing helix chain 'E' and resid 176 through 180 Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.873A pdb=" N SER E 189 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 207 removed outlier: 3.639A pdb=" N ILE E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 225 removed outlier: 3.612A pdb=" N ILE E 222 " --> pdb=" O TYR E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 270 removed outlier: 3.728A pdb=" N ILE E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU E 245 " --> pdb=" O ARG E 241 " (cutoff:3.500A) Proline residue: E 256 - end of helix removed outlier: 3.971A pdb=" N LEU E 269 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU E 270 " --> pdb=" O GLU E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 289 through 303 removed outlier: 3.792A pdb=" N LEU E 299 " --> pdb=" O THR E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 322 removed outlier: 3.558A pdb=" N THR E 316 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 31 removed outlier: 3.530A pdb=" N LYS F 10 " --> pdb=" O SER F 6 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA F 11 " --> pdb=" O ALA F 7 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 52 Processing helix chain 'F' and resid 207 through 216 removed outlier: 3.570A pdb=" N TRP F 211 " --> pdb=" O ARG F 208 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE F 212 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N HIS F 213 " --> pdb=" O LYS F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 255 Processing helix chain 'F' and resid 270 through 281 removed outlier: 3.896A pdb=" N PHE F 274 " --> pdb=" O LYS F 270 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU F 276 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS F 280 " --> pdb=" O GLU F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 309 Processing helix chain 'F' and resid 329 through 347 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.241A pdb=" N GLY B 10 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N CYS B 96 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY B 114 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR B 94 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR B 116 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA B 92 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N MET B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TYR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.513A pdb=" N THR B 243 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR B 227 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 174 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR B 190 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP B 176 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.190A pdb=" N ARG C 46 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN C 340 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.943A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 104 through 105 removed outlier: 6.300A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.602A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN C 175 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 191 through 192 removed outlier: 6.526A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.677A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.723A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 174 through 175 Processing sheet with id=AB4, first strand: chain 'F' and resid 185 through 189 removed outlier: 6.329A pdb=" N ILE F 221 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N PHE F 267 " --> pdb=" O ILE F 221 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE F 223 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASN F 269 " --> pdb=" O PHE F 223 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL F 225 " --> pdb=" O ASN F 269 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1173 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: 1.06 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1476 1.32 - 1.44: 2549 1.44 - 1.57: 5132 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 9253 Sorted by residual: bond pdb=" C ARG E 288 " pdb=" O ARG E 288 " ideal model delta sigma weight residual 1.243 1.193 0.050 9.50e-03 1.11e+04 2.80e+01 bond pdb=" C1 AKG E 601 " pdb=" C2 AKG E 601 " ideal model delta sigma weight residual 1.559 1.455 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C1 AKG E 602 " pdb=" C2 AKG E 602 " ideal model delta sigma weight residual 1.559 1.464 0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C ARG E 288 " pdb=" N PRO E 289 " ideal model delta sigma weight residual 1.337 1.383 -0.046 1.06e-02 8.90e+03 1.90e+01 bond pdb=" C ILE E 29 " pdb=" N PRO E 30 " ideal model delta sigma weight residual 1.336 1.369 -0.033 1.20e-02 6.94e+03 7.46e+00 ... (remaining 9248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 12154 1.54 - 3.08: 307 3.08 - 4.62: 54 4.62 - 6.15: 11 6.15 - 7.69: 8 Bond angle restraints: 12534 Sorted by residual: angle pdb=" N ARG E 288 " pdb=" CA ARG E 288 " pdb=" C ARG E 288 " ideal model delta sigma weight residual 113.57 120.03 -6.46 1.38e+00 5.25e-01 2.19e+01 angle pdb=" N LYS F 349 " pdb=" CA LYS F 349 " pdb=" C LYS F 349 " ideal model delta sigma weight residual 114.04 108.96 5.08 1.24e+00 6.50e-01 1.68e+01 angle pdb=" C SER E 287 " pdb=" N ARG E 288 " pdb=" CA ARG E 288 " ideal model delta sigma weight residual 120.06 124.04 -3.98 1.19e+00 7.06e-01 1.12e+01 angle pdb=" N ILE C 33 " pdb=" CA ILE C 33 " pdb=" C ILE C 33 " ideal model delta sigma weight residual 111.67 109.04 2.63 9.50e-01 1.11e+00 7.67e+00 angle pdb=" N ILE F 285 " pdb=" CA ILE F 285 " pdb=" C ILE F 285 " ideal model delta sigma weight residual 106.21 109.00 -2.79 1.07e+00 8.73e-01 6.78e+00 ... (remaining 12529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 4640 16.93 - 33.87: 629 33.87 - 50.80: 200 50.80 - 67.74: 29 67.74 - 84.67: 10 Dihedral angle restraints: 5508 sinusoidal: 2147 harmonic: 3361 Sorted by residual: dihedral pdb=" CA ILE F 285 " pdb=" C ILE F 285 " pdb=" N CYS F 286 " pdb=" CA CYS F 286 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CB CYS E 24 " pdb=" SG CYS E 24 " pdb=" SG CYS E 274 " pdb=" CB CYS E 274 " ideal model delta sinusoidal sigma weight residual -86.00 -46.90 -39.10 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CA GLU B 234 " pdb=" C GLU B 234 " pdb=" N TYR B 235 " pdb=" CA TYR B 235 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1057 0.045 - 0.090: 292 0.090 - 0.135: 80 0.135 - 0.179: 5 0.179 - 0.224: 1 Chirality restraints: 1435 Sorted by residual: chirality pdb=" CA ARG E 288 " pdb=" N ARG E 288 " pdb=" C ARG E 288 " pdb=" CB ARG E 288 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA TYR B 235 " pdb=" N TYR B 235 " pdb=" C TYR B 235 " pdb=" CB TYR B 235 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.42e-01 chirality pdb=" CA ILE B 189 " pdb=" N ILE B 189 " pdb=" C ILE B 189 " pdb=" CB ILE B 189 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 1432 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 288 " -0.052 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO E 289 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 289 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 289 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 74 " 0.050 5.00e-02 4.00e+02 7.49e-02 8.97e+00 pdb=" N PRO B 75 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 235 " -0.025 2.00e-02 2.50e+03 1.50e-02 4.51e+00 pdb=" CG TYR B 235 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 235 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 235 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 235 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 235 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 235 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 235 " -0.007 2.00e-02 2.50e+03 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 784 2.74 - 3.28: 8401 3.28 - 3.82: 14196 3.82 - 4.36: 16925 4.36 - 4.90: 31410 Nonbonded interactions: 71716 Sorted by model distance: nonbonded pdb=" O ARG C 314 " pdb=" OG SER C 331 " model vdw 2.201 3.040 nonbonded pdb=" O MET C 101 " pdb=" OG1 THR C 102 " model vdw 2.206 3.040 nonbonded pdb=" O PHE B 32 " pdb=" NH2 ARG B 72 " model vdw 2.234 3.120 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR F 290 " pdb=" OE2 GLU F 298 " model vdw 2.243 3.040 ... (remaining 71711 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: 2.690 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.980 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 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 : 0.004 0.104 9257 Z= 0.183 Angle : 0.617 7.693 12542 Z= 0.337 Chirality : 0.044 0.224 1435 Planarity : 0.005 0.080 1582 Dihedral : 17.194 84.669 3324 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.50 % Allowed : 30.71 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.26), residues: 1139 helix: 2.08 (0.28), residues: 384 sheet: 0.20 (0.32), residues: 270 loop : -1.65 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 87 TYR 0.034 0.001 TYR B 235 PHE 0.017 0.001 PHE C 234 TRP 0.020 0.002 TRP C 332 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9253) covalent geometry : angle 0.61648 (12534) SS BOND : bond 0.00235 ( 4) SS BOND : angle 1.09281 ( 8) hydrogen bonds : bond 0.14507 ( 417) hydrogen bonds : angle 5.71393 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.289 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 106 average time/residue: 0.1203 time to fit residues: 16.9158 Evaluate side-chains 97 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain F residue 283 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 GLN E 281 HIS F 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108341 restraints weight = 10263.995| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.74 r_work: 0.2956 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9257 Z= 0.197 Angle : 0.614 9.030 12542 Z= 0.328 Chirality : 0.045 0.262 1435 Planarity : 0.005 0.054 1582 Dihedral : 4.979 44.004 1261 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.39 % Allowed : 29.41 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.26), residues: 1139 helix: 1.95 (0.28), residues: 394 sheet: 0.42 (0.32), residues: 269 loop : -1.72 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 87 TYR 0.033 0.002 TYR B 235 PHE 0.012 0.001 PHE C 151 TRP 0.018 0.002 TRP C 82 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 9253) covalent geometry : angle 0.61358 (12534) SS BOND : bond 0.00405 ( 4) SS BOND : angle 1.32050 ( 8) hydrogen bonds : bond 0.05061 ( 417) hydrogen bonds : angle 4.64738 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.7040 (t80) REVERT: F 240 MET cc_start: 0.5647 (OUTLIER) cc_final: 0.5355 (ttm) outliers start: 34 outliers final: 18 residues processed: 134 average time/residue: 0.1109 time to fit residues: 19.7014 Evaluate side-chains 121 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 149 CYS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 295 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 103 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 91 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN B 194 ASN C 17 GLN C 119 ASN E 281 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.145945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107046 restraints weight = 10292.530| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.10 r_work: 0.2865 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9257 Z= 0.108 Angle : 0.516 8.444 12542 Z= 0.276 Chirality : 0.042 0.182 1435 Planarity : 0.004 0.053 1582 Dihedral : 4.424 41.473 1255 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.09 % Allowed : 29.01 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.26), residues: 1139 helix: 2.15 (0.28), residues: 391 sheet: 0.81 (0.32), residues: 265 loop : -1.78 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 87 TYR 0.021 0.001 TYR B 235 PHE 0.010 0.001 PHE C 241 TRP 0.018 0.001 TRP C 82 HIS 0.003 0.000 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9253) covalent geometry : angle 0.51569 (12534) SS BOND : bond 0.00205 ( 4) SS BOND : angle 0.79726 ( 8) hydrogen bonds : bond 0.03813 ( 417) hydrogen bonds : angle 4.28114 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6719 (t80) REVERT: C 255 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8338 (mp) REVERT: F 240 MET cc_start: 0.5892 (OUTLIER) cc_final: 0.5391 (ttm) outliers start: 31 outliers final: 16 residues processed: 134 average time/residue: 0.0864 time to fit residues: 16.2395 Evaluate side-chains 116 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 240 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 13 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 95 optimal weight: 0.0470 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 93 optimal weight: 0.0870 chunk 77 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN E 281 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105683 restraints weight = 10401.400| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.04 r_work: 0.2827 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9257 Z= 0.124 Angle : 0.523 8.058 12542 Z= 0.279 Chirality : 0.042 0.196 1435 Planarity : 0.004 0.055 1582 Dihedral : 4.424 43.497 1255 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.49 % Allowed : 28.81 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.26), residues: 1139 helix: 2.20 (0.28), residues: 392 sheet: 0.82 (0.32), residues: 268 loop : -1.78 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 87 TYR 0.022 0.001 TYR B 235 PHE 0.012 0.001 PHE C 199 TRP 0.017 0.001 TRP C 82 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9253) covalent geometry : angle 0.52284 (12534) SS BOND : bond 0.00409 ( 4) SS BOND : angle 0.97417 ( 8) hydrogen bonds : bond 0.03944 ( 417) hydrogen bonds : angle 4.19529 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6725 (t80) REVERT: C 175 GLN cc_start: 0.8375 (pt0) cc_final: 0.7404 (mt0) REVERT: F 240 MET cc_start: 0.6106 (OUTLIER) cc_final: 0.5836 (ttm) REVERT: F 276 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6543 (mp0) outliers start: 35 outliers final: 21 residues processed: 138 average time/residue: 0.0881 time to fit residues: 16.6876 Evaluate side-chains 125 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 295 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 109 optimal weight: 0.0570 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN E 281 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109162 restraints weight = 10282.565| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.95 r_work: 0.2972 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9257 Z= 0.095 Angle : 0.484 7.977 12542 Z= 0.258 Chirality : 0.041 0.160 1435 Planarity : 0.004 0.053 1582 Dihedral : 4.253 43.712 1255 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.49 % Allowed : 27.62 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.26), residues: 1139 helix: 2.29 (0.27), residues: 392 sheet: 0.93 (0.32), residues: 273 loop : -1.71 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 134 TYR 0.018 0.001 TYR B 235 PHE 0.011 0.001 PHE C 199 TRP 0.017 0.001 TRP C 82 HIS 0.002 0.000 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 9253) covalent geometry : angle 0.48417 (12534) SS BOND : bond 0.00244 ( 4) SS BOND : angle 0.66538 ( 8) hydrogen bonds : bond 0.03311 ( 417) hydrogen bonds : angle 4.01498 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 235 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.6485 (t80) REVERT: C 175 GLN cc_start: 0.8360 (pt0) cc_final: 0.7415 (mt0) REVERT: C 234 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8596 (m-80) REVERT: C 255 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8240 (mp) REVERT: F 276 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6603 (mp0) outliers start: 45 outliers final: 24 residues processed: 147 average time/residue: 0.0997 time to fit residues: 20.1449 Evaluate side-chains 138 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 295 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 89 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN E 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.097313 restraints weight = 10480.133| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.06 r_work: 0.2741 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 9257 Z= 0.340 Angle : 0.726 11.387 12542 Z= 0.382 Chirality : 0.050 0.287 1435 Planarity : 0.005 0.061 1582 Dihedral : 5.047 41.878 1255 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.89 % Allowed : 28.41 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.26), residues: 1139 helix: 1.79 (0.27), residues: 394 sheet: 0.48 (0.32), residues: 276 loop : -1.84 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 150 TYR 0.036 0.002 TYR B 235 PHE 0.020 0.002 PHE C 199 TRP 0.019 0.002 TRP C 82 HIS 0.006 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00861 ( 9253) covalent geometry : angle 0.72409 (12534) SS BOND : bond 0.00510 ( 4) SS BOND : angle 2.00163 ( 8) hydrogen bonds : bond 0.06060 ( 417) hydrogen bonds : angle 4.59277 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.7126 (t80) REVERT: F 276 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6478 (mp0) outliers start: 39 outliers final: 26 residues processed: 128 average time/residue: 0.1009 time to fit residues: 17.7359 Evaluate side-chains 124 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 310 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103736 restraints weight = 10331.126| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.05 r_work: 0.2955 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9257 Z= 0.127 Angle : 0.541 6.855 12542 Z= 0.288 Chirality : 0.043 0.198 1435 Planarity : 0.004 0.052 1582 Dihedral : 4.621 40.122 1255 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.99 % Allowed : 29.31 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.26), residues: 1139 helix: 2.05 (0.28), residues: 392 sheet: 0.87 (0.32), residues: 269 loop : -1.89 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 134 TYR 0.023 0.001 TYR B 235 PHE 0.013 0.001 PHE C 199 TRP 0.018 0.001 TRP C 82 HIS 0.005 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9253) covalent geometry : angle 0.54088 (12534) SS BOND : bond 0.00306 ( 4) SS BOND : angle 1.03536 ( 8) hydrogen bonds : bond 0.04119 ( 417) hydrogen bonds : angle 4.25650 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6877 (t80) REVERT: C 175 GLN cc_start: 0.8387 (pt0) cc_final: 0.7436 (mt0) REVERT: C 255 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8482 (mp) REVERT: F 276 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6616 (mp0) outliers start: 30 outliers final: 25 residues processed: 124 average time/residue: 0.1021 time to fit residues: 17.5089 Evaluate side-chains 125 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 310 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN E 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.139642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.100239 restraints weight = 10443.086| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.05 r_work: 0.2769 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9257 Z= 0.214 Angle : 0.616 8.329 12542 Z= 0.327 Chirality : 0.045 0.249 1435 Planarity : 0.004 0.056 1582 Dihedral : 4.809 41.066 1255 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.89 % Allowed : 28.81 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.26), residues: 1139 helix: 1.88 (0.28), residues: 397 sheet: 0.72 (0.32), residues: 271 loop : -1.83 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 150 TYR 0.031 0.002 TYR B 235 PHE 0.016 0.002 PHE C 199 TRP 0.018 0.002 TRP C 82 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 9253) covalent geometry : angle 0.61505 (12534) SS BOND : bond 0.00411 ( 4) SS BOND : angle 1.44075 ( 8) hydrogen bonds : bond 0.04995 ( 417) hydrogen bonds : angle 4.37588 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6861 (t80) REVERT: E 176 ASN cc_start: 0.6268 (OUTLIER) cc_final: 0.5964 (t0) REVERT: F 276 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6568 (mp0) outliers start: 39 outliers final: 29 residues processed: 132 average time/residue: 0.1041 time to fit residues: 18.8720 Evaluate side-chains 129 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 33 MET Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 310 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 107 optimal weight: 0.0870 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 62 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN E 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.146360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107403 restraints weight = 10285.222| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.02 r_work: 0.3004 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9257 Z= 0.102 Angle : 0.515 8.769 12542 Z= 0.275 Chirality : 0.042 0.157 1435 Planarity : 0.004 0.048 1582 Dihedral : 4.465 40.948 1255 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.29 % Allowed : 29.41 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.26), residues: 1139 helix: 2.15 (0.27), residues: 392 sheet: 0.99 (0.32), residues: 271 loop : -1.82 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 177 TYR 0.020 0.001 TYR E 92 PHE 0.010 0.001 PHE C 199 TRP 0.019 0.001 TRP C 82 HIS 0.004 0.000 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9253) covalent geometry : angle 0.51466 (12534) SS BOND : bond 0.00292 ( 4) SS BOND : angle 0.71624 ( 8) hydrogen bonds : bond 0.03571 ( 417) hydrogen bonds : angle 4.09864 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.6565 (t80) REVERT: C 175 GLN cc_start: 0.8338 (pt0) cc_final: 0.7376 (mt0) REVERT: C 234 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8671 (m-80) REVERT: E 176 ASN cc_start: 0.6663 (OUTLIER) cc_final: 0.6399 (t0) REVERT: F 276 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6679 (mp0) outliers start: 33 outliers final: 21 residues processed: 132 average time/residue: 0.1064 time to fit residues: 19.1903 Evaluate side-chains 127 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 276 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 25 optimal weight: 0.0050 chunk 9 optimal weight: 0.0040 chunk 89 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 overall best weight: 0.7408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.105943 restraints weight = 10261.829| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.02 r_work: 0.2934 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9257 Z= 0.119 Angle : 0.532 7.477 12542 Z= 0.283 Chirality : 0.042 0.187 1435 Planarity : 0.004 0.052 1582 Dihedral : 4.450 41.973 1255 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.19 % Allowed : 30.61 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.26), residues: 1139 helix: 2.24 (0.27), residues: 392 sheet: 0.95 (0.32), residues: 273 loop : -1.77 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 208 TYR 0.021 0.001 TYR B 235 PHE 0.013 0.001 PHE B 80 TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9253) covalent geometry : angle 0.53136 (12534) SS BOND : bond 0.00297 ( 4) SS BOND : angle 0.92805 ( 8) hydrogen bonds : bond 0.03817 ( 417) hydrogen bonds : angle 4.09567 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7214 (OUTLIER) cc_final: 0.6732 (t80) REVERT: C 45 MET cc_start: 0.9097 (mtt) cc_final: 0.8893 (mtt) REVERT: C 175 GLN cc_start: 0.8328 (pt0) cc_final: 0.7365 (mt0) REVERT: C 234 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8750 (m-80) REVERT: F 276 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6675 (mp0) outliers start: 22 outliers final: 17 residues processed: 119 average time/residue: 0.1084 time to fit residues: 17.6495 Evaluate side-chains 117 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 276 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.143488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104433 restraints weight = 10180.434| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.01 r_work: 0.2858 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9257 Z= 0.138 Angle : 0.549 7.188 12542 Z= 0.292 Chirality : 0.043 0.203 1435 Planarity : 0.004 0.050 1582 Dihedral : 4.537 43.318 1255 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.59 % Allowed : 30.11 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.26), residues: 1139 helix: 2.21 (0.27), residues: 393 sheet: 1.00 (0.32), residues: 268 loop : -1.79 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 208 TYR 0.024 0.001 TYR B 235 PHE 0.012 0.001 PHE C 199 TRP 0.020 0.001 TRP C 82 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9253) covalent geometry : angle 0.54797 (12534) SS BOND : bond 0.00347 ( 4) SS BOND : angle 1.23100 ( 8) hydrogen bonds : bond 0.04068 ( 417) hydrogen bonds : angle 4.15373 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2276.94 seconds wall clock time: 39 minutes 49.69 seconds (2389.69 seconds total)