Starting phenix.real_space_refine on Mon May 12 14:47:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yyw_39681/05_2025/8yyw_39681.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yyw_39681/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yyw_39681/05_2025/8yyw_39681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yyw_39681/05_2025/8yyw_39681.map" model { file = "/net/cci-nas-00/data/ceres_data/8yyw_39681/05_2025/8yyw_39681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yyw_39681/05_2025/8yyw_39681.cif" } resolution = 3.16 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= -0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.39, per 1000 atoms: 0.59 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: 1.99 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.04 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: 2.48 Time building geometry restraints manager: 2.35 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.710 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- 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 : 7.65 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 (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: 0.16 (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 TRP 0.020 0.002 TRP C 332 HIS 0.003 0.001 HIS B 35 PHE 0.017 0.001 PHE C 234 TYR 0.034 0.001 TYR B 235 ARG 0.005 0.000 ARG B 87 Details of bonding type rmsd hydrogen bonds : bond 0.14507 ( 417) hydrogen bonds : angle 5.71393 ( 1173) SS BOND : bond 0.00235 ( 4) SS BOND : angle 1.09281 ( 8) covalent geometry : bond 0.00365 ( 9253) covalent geometry : angle 0.61648 (12534) *********************** 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 : 1.052 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 106 average time/residue: 0.2566 time to fit residues: 36.6473 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 : 0.900 ------------------------------------------------------------------------------- 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 95 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.142373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106635 restraints weight = 10267.684| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.74 r_work: 0.2753 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 9257 Z= 0.261 Angle : 0.674 9.660 12542 Z= 0.359 Chirality : 0.048 0.293 1435 Planarity : 0.005 0.054 1582 Dihedral : 5.174 43.370 1261 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.79 % Allowed : 28.81 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1139 helix: 1.87 (0.28), residues: 392 sheet: 0.35 (0.32), residues: 271 loop : -1.78 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 82 HIS 0.005 0.001 HIS B 35 PHE 0.013 0.002 PHE C 199 TYR 0.039 0.002 TYR B 235 ARG 0.003 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.05661 ( 417) hydrogen bonds : angle 4.76462 ( 1173) SS BOND : bond 0.00473 ( 4) SS BOND : angle 1.54591 ( 8) covalent geometry : bond 0.00653 ( 9253) covalent geometry : angle 0.67356 (12534) *********************** 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: 38 poor density : 100 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.7222 (t80) REVERT: F 240 MET cc_start: 0.5611 (OUTLIER) cc_final: 0.5298 (ttm) outliers start: 38 outliers final: 19 residues processed: 133 average time/residue: 0.2460 time to fit residues: 43.3009 Evaluate side-chains 118 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 252 VAL 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 Chi-restraints excluded: chain F residue 310 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 chunk 108 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN C 119 ASN E 281 HIS E 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111864 restraints weight = 10295.378| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.79 r_work: 0.2969 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9257 Z= 0.116 Angle : 0.530 8.236 12542 Z= 0.285 Chirality : 0.042 0.190 1435 Planarity : 0.004 0.054 1582 Dihedral : 4.557 41.305 1255 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.29 % Allowed : 29.81 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.26 (0.26), residues: 1139 helix: 2.06 (0.28), residues: 391 sheet: 0.71 (0.32), residues: 267 loop : -1.85 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.010 0.001 PHE C 241 TYR 0.021 0.001 TYR B 235 ARG 0.003 0.000 ARG B 87 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 417) hydrogen bonds : angle 4.36937 ( 1173) SS BOND : bond 0.00226 ( 4) SS BOND : angle 0.79820 ( 8) covalent geometry : bond 0.00263 ( 9253) covalent geometry : angle 0.52999 (12534) *********************** 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 140 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.6700 (t80) REVERT: C 195 ASP cc_start: 0.8156 (p0) cc_final: 0.7851 (p0) REVERT: C 255 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8449 (mp) REVERT: F 240 MET cc_start: 0.5843 (OUTLIER) cc_final: 0.5408 (ttm) outliers start: 33 outliers final: 17 residues processed: 134 average time/residue: 0.2087 time to fit residues: 38.7958 Evaluate side-chains 118 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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 139 MET Chi-restraints excluded: chain E residue 149 CYS Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 299 LEU 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 102 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.143417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.104168 restraints weight = 10293.874| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.99 r_work: 0.2667 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9257 Z= 0.230 Angle : 0.628 8.912 12542 Z= 0.334 Chirality : 0.046 0.260 1435 Planarity : 0.005 0.056 1582 Dihedral : 4.819 38.697 1255 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.49 % Allowed : 28.81 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.15 (0.26), residues: 1139 helix: 1.89 (0.28), residues: 395 sheet: 0.55 (0.32), residues: 271 loop : -1.82 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.005 0.001 HIS B 35 PHE 0.016 0.002 PHE C 199 TYR 0.033 0.002 TYR B 235 ARG 0.003 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.05214 ( 417) hydrogen bonds : angle 4.51713 ( 1173) SS BOND : bond 0.00408 ( 4) SS BOND : angle 1.46918 ( 8) covalent geometry : bond 0.00577 ( 9253) covalent geometry : angle 0.62666 (12534) *********************** 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 147 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.6905 (t80) REVERT: C 195 ASP cc_start: 0.8010 (p0) cc_final: 0.7645 (p0) REVERT: C 197 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7506 (mtm-85) REVERT: F 240 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5580 (ttm) REVERT: F 276 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6565 (mp0) outliers start: 45 outliers final: 26 residues processed: 139 average time/residue: 0.2396 time to fit residues: 45.8618 Evaluate side-chains 133 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 197 ARG 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 149 CYS Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 320 LYS 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 262 THR 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 25 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.143818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104582 restraints weight = 10303.195| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.08 r_work: 0.2837 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1169 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= 0.122 Angle : 0.528 7.705 12542 Z= 0.282 Chirality : 0.043 0.194 1435 Planarity : 0.004 0.050 1582 Dihedral : 4.592 44.123 1255 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.29 % Allowed : 29.41 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.26), residues: 1139 helix: 2.07 (0.28), residues: 392 sheet: 0.78 (0.32), residues: 267 loop : -1.81 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS B 35 PHE 0.012 0.001 PHE C 199 TYR 0.022 0.001 TYR B 235 ARG 0.002 0.000 ARG B 87 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 417) hydrogen bonds : angle 4.28380 ( 1173) SS BOND : bond 0.00257 ( 4) SS BOND : angle 0.93179 ( 8) covalent geometry : bond 0.00282 ( 9253) covalent geometry : angle 0.52769 (12534) *********************** 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 151 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6758 (t80) REVERT: C 175 GLN cc_start: 0.8334 (pt0) cc_final: 0.7407 (mt0) REVERT: C 195 ASP cc_start: 0.8019 (p0) cc_final: 0.7684 (p0) REVERT: C 197 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7514 (mtm-85) REVERT: C 234 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8663 (m-80) REVERT: F 240 MET cc_start: 0.6438 (OUTLIER) cc_final: 0.6083 (ttm) REVERT: F 275 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: F 276 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6583 (mp0) outliers start: 43 outliers final: 27 residues processed: 143 average time/residue: 0.2133 time to fit residues: 42.3830 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 : 0.923 ------------------------------------------------------------------------------- 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 147 SER 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 197 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 81 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 171 LEU Chi-restraints excluded: chain E residue 224 THR 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 275 GLU 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 38 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.141439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102035 restraints weight = 10260.649| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.03 r_work: 0.2771 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9257 Z= 0.164 Angle : 0.563 7.311 12542 Z= 0.300 Chirality : 0.044 0.222 1435 Planarity : 0.004 0.056 1582 Dihedral : 4.645 41.281 1255 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.08 % Allowed : 28.41 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1139 helix: 2.09 (0.28), residues: 390 sheet: 0.61 (0.32), residues: 272 loop : -1.81 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.004 0.001 HIS B 35 PHE 0.014 0.001 PHE C 199 TYR 0.027 0.002 TYR B 235 ARG 0.002 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 417) hydrogen bonds : angle 4.30764 ( 1173) SS BOND : bond 0.00333 ( 4) SS BOND : angle 1.10894 ( 8) covalent geometry : bond 0.00401 ( 9253) covalent geometry : angle 0.56226 (12534) *********************** 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 157 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 106 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: B 163 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.8012 (ttmt) REVERT: B 235 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6848 (t80) REVERT: C 195 ASP cc_start: 0.7966 (p0) cc_final: 0.7636 (p0) REVERT: C 197 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7523 (mtm-85) REVERT: F 240 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6238 (ttm) REVERT: F 275 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7557 (tp30) REVERT: F 276 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6563 (mp0) outliers start: 51 outliers final: 33 residues processed: 149 average time/residue: 0.2226 time to fit residues: 45.0017 Evaluate side-chains 141 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 LYS 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 147 SER 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 197 ARG Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 81 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 171 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 320 LYS 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 275 GLU 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 5 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.140791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.101440 restraints weight = 10444.083| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.10 r_work: 0.2780 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9257 Z= 0.183 Angle : 0.590 7.586 12542 Z= 0.315 Chirality : 0.045 0.238 1435 Planarity : 0.004 0.053 1582 Dihedral : 4.750 42.285 1255 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.18 % Allowed : 28.02 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1139 helix: 1.99 (0.28), residues: 394 sheet: 0.78 (0.32), residues: 273 loop : -1.86 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 82 HIS 0.004 0.001 HIS B 35 PHE 0.015 0.001 PHE C 199 TYR 0.030 0.002 TYR B 235 ARG 0.003 0.000 ARG F 205 Details of bonding type rmsd hydrogen bonds : bond 0.04734 ( 417) hydrogen bonds : angle 4.35002 ( 1173) SS BOND : bond 0.00375 ( 4) SS BOND : angle 1.36943 ( 8) covalent geometry : bond 0.00451 ( 9253) covalent geometry : angle 0.58901 (12534) *********************** 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 154 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 102 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.6925 (t80) REVERT: C 175 GLN cc_start: 0.8376 (pt0) cc_final: 0.7454 (mt0) REVERT: C 195 ASP cc_start: 0.8004 (p0) cc_final: 0.7704 (p0) REVERT: C 197 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7535 (mtm-85) REVERT: C 234 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8659 (m-80) REVERT: E 176 ASN cc_start: 0.6365 (OUTLIER) cc_final: 0.6130 (t0) REVERT: F 240 MET cc_start: 0.6794 (OUTLIER) cc_final: 0.6425 (ttm) REVERT: F 275 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7620 (tp30) REVERT: F 276 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6646 (mp0) outliers start: 52 outliers final: 37 residues processed: 145 average time/residue: 0.2155 time to fit residues: 42.9374 Evaluate side-chains 146 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 70 ILE 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 147 SER 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 197 ARG Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 81 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 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 224 THR 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 E residue 320 LYS 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 262 THR Chi-restraints excluded: chain F residue 275 GLU 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 65 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.141668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.102367 restraints weight = 10524.559| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.11 r_work: 0.2817 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9257 Z= 0.158 Angle : 0.568 8.089 12542 Z= 0.304 Chirality : 0.044 0.218 1435 Planarity : 0.004 0.054 1582 Dihedral : 4.696 43.318 1255 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.79 % Allowed : 28.22 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 1139 helix: 2.02 (0.28), residues: 394 sheet: 0.83 (0.32), residues: 273 loop : -1.83 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 82 HIS 0.004 0.001 HIS B 35 PHE 0.014 0.001 PHE C 199 TYR 0.026 0.002 TYR B 235 ARG 0.003 0.000 ARG F 205 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 417) hydrogen bonds : angle 4.29047 ( 1173) SS BOND : bond 0.00350 ( 4) SS BOND : angle 1.18439 ( 8) covalent geometry : bond 0.00384 ( 9253) covalent geometry : angle 0.56758 (12534) *********************** 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 151 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 103 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6897 (t80) REVERT: C 45 MET cc_start: 0.9184 (mtt) cc_final: 0.8952 (mtt) REVERT: C 195 ASP cc_start: 0.8076 (p0) cc_final: 0.7793 (p0) REVERT: C 197 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7576 (mtm-85) REVERT: C 234 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8744 (m-80) REVERT: E 176 ASN cc_start: 0.6638 (OUTLIER) cc_final: 0.6354 (t0) REVERT: F 240 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6581 (ttm) REVERT: F 275 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7616 (tp30) REVERT: F 276 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6713 (mp0) outliers start: 48 outliers final: 35 residues processed: 143 average time/residue: 0.2222 time to fit residues: 43.9550 Evaluate side-chains 140 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 70 ILE 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 147 SER 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 197 ARG Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 81 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 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 224 THR 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 3 CYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 206 SER Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 275 GLU 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 61 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.140015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100716 restraints weight = 10352.161| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.09 r_work: 0.2849 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9257 Z= 0.206 Angle : 0.609 8.456 12542 Z= 0.326 Chirality : 0.045 0.249 1435 Planarity : 0.004 0.054 1582 Dihedral : 4.816 43.109 1255 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.38 % Allowed : 27.52 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1139 helix: 1.96 (0.28), residues: 394 sheet: 0.67 (0.32), residues: 276 loop : -1.78 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 82 HIS 0.005 0.001 HIS B 35 PHE 0.015 0.002 PHE C 199 TYR 0.031 0.002 TYR B 235 ARG 0.003 0.000 ARG F 205 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 417) hydrogen bonds : angle 4.37532 ( 1173) SS BOND : bond 0.00403 ( 4) SS BOND : angle 1.40331 ( 8) covalent geometry : bond 0.00512 ( 9253) covalent geometry : angle 0.60863 (12534) *********************** 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 157 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 103 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.6987 (t80) REVERT: C 45 MET cc_start: 0.9231 (mtt) cc_final: 0.9004 (mtt) REVERT: C 195 ASP cc_start: 0.8052 (p0) cc_final: 0.7768 (p0) REVERT: C 197 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7562 (mtm-85) REVERT: C 234 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8656 (m-80) REVERT: E 127 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8017 (t80) REVERT: E 205 THR cc_start: 0.8813 (m) cc_final: 0.8584 (m) REVERT: F 53 MET cc_start: 0.3627 (OUTLIER) cc_final: 0.2691 (tpt) REVERT: F 240 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.6620 (ttm) REVERT: F 275 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7616 (tp30) REVERT: F 276 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6699 (mp0) outliers start: 54 outliers final: 40 residues processed: 147 average time/residue: 0.2053 time to fit residues: 42.0033 Evaluate side-chains 146 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 98 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 70 ILE 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 197 ARG Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 149 CYS 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 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 272 ILE Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 206 SER Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 275 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 30 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.142397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103179 restraints weight = 10425.888| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.11 r_work: 0.2832 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1341 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= 0.143 Angle : 0.556 8.251 12542 Z= 0.297 Chirality : 0.043 0.209 1435 Planarity : 0.004 0.052 1582 Dihedral : 4.670 43.851 1255 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.59 % Allowed : 28.32 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1139 helix: 2.00 (0.28), residues: 396 sheet: 0.92 (0.32), residues: 274 loop : -1.83 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.004 0.001 HIS E 281 PHE 0.013 0.001 PHE C 199 TYR 0.025 0.001 TYR B 235 ARG 0.003 0.000 ARG F 205 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 417) hydrogen bonds : angle 4.24618 ( 1173) SS BOND : bond 0.00337 ( 4) SS BOND : angle 1.08182 ( 8) covalent geometry : bond 0.00341 ( 9253) covalent geometry : angle 0.55521 (12534) ********************** 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 148 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 102 time to evaluate : 0.926 Fit side-chains REVERT: B 235 TYR cc_start: 0.7326 (OUTLIER) cc_final: 0.6800 (t80) REVERT: C 45 MET cc_start: 0.9192 (mtt) cc_final: 0.8960 (mtt) REVERT: C 195 ASP cc_start: 0.8039 (p0) cc_final: 0.7697 (p0) REVERT: C 197 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7501 (mtm-85) REVERT: C 234 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8706 (m-80) REVERT: F 53 MET cc_start: 0.3733 (OUTLIER) cc_final: 0.2983 (tpt) REVERT: F 234 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6827 (pt) REVERT: F 240 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6395 (ttm) REVERT: F 275 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7612 (tp30) REVERT: F 276 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6741 (mp0) outliers start: 46 outliers final: 36 residues processed: 139 average time/residue: 0.2178 time to fit residues: 41.7695 Evaluate side-chains 142 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 98 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 70 ILE 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 197 ARG Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 149 CYS 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 224 THR Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 206 SER Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 275 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.138150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.098380 restraints weight = 10464.982| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.00 r_work: 0.2758 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 9257 Z= 0.275 Angle : 0.667 9.861 12542 Z= 0.355 Chirality : 0.048 0.274 1435 Planarity : 0.005 0.057 1582 Dihedral : 5.030 45.252 1255 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.59 % Allowed : 28.32 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1139 helix: 1.85 (0.28), residues: 394 sheet: 0.60 (0.32), residues: 276 loop : -1.85 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 82 HIS 0.006 0.001 HIS B 35 PHE 0.017 0.002 PHE C 199 TYR 0.035 0.002 TYR B 235 ARG 0.004 0.000 ARG F 205 Details of bonding type rmsd hydrogen bonds : bond 0.05575 ( 417) hydrogen bonds : angle 4.49038 ( 1173) SS BOND : bond 0.00484 ( 4) SS BOND : angle 1.58046 ( 8) covalent geometry : bond 0.00693 ( 9253) covalent geometry : angle 0.66634 (12534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4471.10 seconds wall clock time: 78 minutes 18.47 seconds (4698.47 seconds total)