Starting phenix.real_space_refine on Wed Apr 30 01:24:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yyw_39681/04_2025/8yyw_39681.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yyw_39681/04_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_39681/04_2025/8yyw_39681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yyw_39681/04_2025/8yyw_39681.map" model { file = "/net/cci-nas-00/data/ceres_data/8yyw_39681/04_2025/8yyw_39681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yyw_39681/04_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.98, per 1000 atoms: 0.66 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: 2.46 Conformation dependent library (CDL) restraints added in 1.1 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: 1.30 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: 2.86 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1476 1.32 - 1.44: 2549 1.44 - 1.57: 5132 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 9253 Sorted by residual: bond pdb=" C ARG E 288 " pdb=" O ARG E 288 " ideal model delta sigma weight residual 1.243 1.193 0.050 9.50e-03 1.11e+04 2.80e+01 bond pdb=" C1 AKG E 601 " pdb=" C2 AKG E 601 " ideal model delta sigma weight residual 1.559 1.455 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C1 AKG E 602 " pdb=" C2 AKG E 602 " ideal model delta sigma weight residual 1.559 1.464 0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C ARG E 288 " pdb=" N PRO E 289 " ideal model delta sigma weight residual 1.337 1.383 -0.046 1.06e-02 8.90e+03 1.90e+01 bond pdb=" C ILE E 29 " pdb=" N PRO E 30 " ideal model delta sigma weight residual 1.336 1.369 -0.033 1.20e-02 6.94e+03 7.46e+00 ... (remaining 9248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 12154 1.54 - 3.08: 307 3.08 - 4.62: 54 4.62 - 6.15: 11 6.15 - 7.69: 8 Bond angle restraints: 12534 Sorted by residual: angle pdb=" N ARG E 288 " pdb=" CA ARG E 288 " pdb=" C ARG E 288 " ideal model delta sigma weight residual 113.57 120.03 -6.46 1.38e+00 5.25e-01 2.19e+01 angle pdb=" N LYS F 349 " pdb=" CA LYS F 349 " pdb=" C LYS F 349 " ideal model delta sigma weight residual 114.04 108.96 5.08 1.24e+00 6.50e-01 1.68e+01 angle pdb=" C SER E 287 " pdb=" N ARG E 288 " pdb=" CA ARG E 288 " ideal model delta sigma weight residual 120.06 124.04 -3.98 1.19e+00 7.06e-01 1.12e+01 angle pdb=" N ILE C 33 " pdb=" CA ILE C 33 " pdb=" C ILE C 33 " ideal model delta sigma weight residual 111.67 109.04 2.63 9.50e-01 1.11e+00 7.67e+00 angle pdb=" N ILE F 285 " pdb=" CA ILE F 285 " pdb=" C ILE F 285 " ideal model delta sigma weight residual 106.21 109.00 -2.79 1.07e+00 8.73e-01 6.78e+00 ... (remaining 12529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 4640 16.93 - 33.87: 629 33.87 - 50.80: 200 50.80 - 67.74: 29 67.74 - 84.67: 10 Dihedral angle restraints: 5508 sinusoidal: 2147 harmonic: 3361 Sorted by residual: dihedral pdb=" CA ILE F 285 " pdb=" C ILE F 285 " pdb=" N CYS F 286 " pdb=" CA CYS F 286 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CB CYS E 24 " pdb=" SG CYS E 24 " pdb=" SG CYS E 274 " pdb=" CB CYS E 274 " ideal model delta sinusoidal sigma weight residual -86.00 -46.90 -39.10 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CA GLU B 234 " pdb=" C GLU B 234 " pdb=" N TYR B 235 " pdb=" CA TYR B 235 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1057 0.045 - 0.090: 292 0.090 - 0.135: 80 0.135 - 0.179: 5 0.179 - 0.224: 1 Chirality restraints: 1435 Sorted by residual: chirality pdb=" CA ARG E 288 " pdb=" N ARG E 288 " pdb=" C ARG E 288 " pdb=" CB ARG E 288 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA TYR B 235 " pdb=" N TYR B 235 " pdb=" C TYR B 235 " pdb=" CB TYR B 235 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.42e-01 chirality pdb=" CA ILE B 189 " pdb=" N ILE B 189 " pdb=" C ILE B 189 " pdb=" CB ILE B 189 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 1432 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 288 " -0.052 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO E 289 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 289 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 289 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 74 " 0.050 5.00e-02 4.00e+02 7.49e-02 8.97e+00 pdb=" N PRO B 75 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 235 " -0.025 2.00e-02 2.50e+03 1.50e-02 4.51e+00 pdb=" CG TYR B 235 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 235 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 235 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 235 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 235 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 235 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 235 " -0.007 2.00e-02 2.50e+03 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 784 2.74 - 3.28: 8401 3.28 - 3.82: 14196 3.82 - 4.36: 16925 4.36 - 4.90: 31410 Nonbonded interactions: 71716 Sorted by model distance: nonbonded pdb=" O ARG C 314 " pdb=" OG SER C 331 " model vdw 2.201 3.040 nonbonded pdb=" O MET C 101 " pdb=" OG1 THR C 102 " model vdw 2.206 3.040 nonbonded pdb=" O PHE B 32 " pdb=" NH2 ARG B 72 " model vdw 2.234 3.120 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR F 290 " pdb=" OE2 GLU F 298 " model vdw 2.243 3.040 ... (remaining 71711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.570 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.320 ------------------------------------------------------------------------------- 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 : 0.960 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 106 average time/residue: 0.2575 time to fit residues: 36.5930 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 : 1.098 ------------------------------------------------------------------------------- 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: 3.65 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 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 : 0.939 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.7221 (t80) REVERT: F 240 MET cc_start: 0.5612 (OUTLIER) cc_final: 0.5301 (ttm) outliers start: 38 outliers final: 19 residues processed: 133 average time/residue: 0.2467 time to fit residues: 43.4579 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 : 0.977 ------------------------------------------------------------------------------- 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: 0.6980 chunk 76 optimal weight: 0.4980 chunk 108 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.148160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109200 restraints weight = 10335.826| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.95 r_work: 0.2986 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9257 Z= 0.120 Angle : 0.535 8.274 12542 Z= 0.287 Chirality : 0.043 0.195 1435 Planarity : 0.004 0.054 1582 Dihedral : 4.588 41.211 1255 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.19 % Allowed : 30.11 % 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: 0.24 (0.26), residues: 1139 helix: 2.05 (0.28), residues: 391 sheet: 0.69 (0.31), residues: 267 loop : -1.86 (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 B 35 PHE 0.010 0.001 PHE C 241 TYR 0.022 0.001 TYR B 235 ARG 0.003 0.000 ARG B 87 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 417) hydrogen bonds : angle 4.39008 ( 1173) SS BOND : bond 0.00256 ( 4) SS BOND : angle 0.84268 ( 8) covalent geometry : bond 0.00273 ( 9253) covalent geometry : angle 0.53439 (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 137 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6811 (t80) REVERT: C 195 ASP cc_start: 0.8218 (p0) cc_final: 0.7984 (p0) REVERT: C 255 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8483 (mp) REVERT: F 240 MET cc_start: 0.5851 (OUTLIER) cc_final: 0.5410 (ttm) outliers start: 32 outliers final: 16 residues processed: 131 average time/residue: 0.2216 time to fit residues: 40.1252 Evaluate side-chains 122 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 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 187 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 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: 10.0000 chunk 40 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 101 optimal weight: 0.0270 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.141838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102662 restraints weight = 10312.431| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.08 r_work: 0.2929 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1100 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 : 0.563 7.947 12542 Z= 0.300 Chirality : 0.044 0.223 1435 Planarity : 0.004 0.055 1582 Dihedral : 4.594 38.335 1255 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.99 % Allowed : 29.41 % Favored : 66.60 % 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: 2.08 (0.28), residues: 391 sheet: 0.73 (0.31), residues: 267 loop : -1.89 (0.27), residues: 481 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 0.013 0.001 PHE C 199 TYR 0.027 0.001 TYR B 235 ARG 0.002 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.04488 ( 417) hydrogen bonds : angle 4.35572 ( 1173) SS BOND : bond 0.00318 ( 4) SS BOND : angle 1.15874 ( 8) covalent geometry : bond 0.00383 ( 9253) covalent geometry : angle 0.56251 (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: 40 poor density : 107 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6999 (t80) REVERT: C 195 ASP cc_start: 0.8138 (p0) cc_final: 0.7812 (p0) REVERT: C 197 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7660 (mtm-85) REVERT: F 240 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5954 (ttm) REVERT: F 276 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6590 (mp0) outliers start: 40 outliers final: 24 residues processed: 139 average time/residue: 0.2226 time to fit residues: 42.4832 Evaluate side-chains 136 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 149 CYS Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 187 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 201 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 295 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.141178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101726 restraints weight = 10335.926| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.07 r_work: 0.2762 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9257 Z= 0.171 Angle : 0.571 7.625 12542 Z= 0.304 Chirality : 0.044 0.231 1435 Planarity : 0.004 0.053 1582 Dihedral : 4.718 44.864 1255 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 5.08 % Allowed : 28.51 % Favored : 66.40 % 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: 0.25 (0.26), residues: 1139 helix: 2.06 (0.28), residues: 392 sheet: 0.75 (0.32), residues: 266 loop : -1.90 (0.26), residues: 481 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 0.029 0.002 TYR B 235 ARG 0.002 0.000 ARG F 205 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 417) hydrogen bonds : angle 4.34618 ( 1173) SS BOND : bond 0.00350 ( 4) SS BOND : angle 1.23734 ( 8) covalent geometry : bond 0.00418 ( 9253) covalent geometry : angle 0.57029 (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 157 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 106 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: B 235 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6809 (t80) REVERT: C 195 ASP cc_start: 0.8013 (p0) cc_final: 0.7683 (p0) REVERT: C 197 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7556 (mtm-85) REVERT: F 240 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.6050 (ttm) REVERT: F 275 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7572 (tp30) REVERT: F 276 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6590 (mp0) outliers start: 51 outliers final: 31 residues processed: 149 average time/residue: 0.2349 time to fit residues: 47.7068 Evaluate side-chains 142 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 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 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 147 THR 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 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 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: 2.9990 chunk 78 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.141347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102049 restraints weight = 10267.332| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.03 r_work: 0.2820 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9257 Z= 0.165 Angle : 0.573 7.297 12542 Z= 0.306 Chirality : 0.044 0.224 1435 Planarity : 0.004 0.054 1582 Dihedral : 4.701 42.442 1255 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.08 % Allowed : 28.22 % 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: 0.27 (0.26), residues: 1139 helix: 2.06 (0.28), residues: 392 sheet: 0.78 (0.32), residues: 266 loop : -1.90 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 82 HIS 0.004 0.001 HIS B 35 PHE 0.014 0.001 PHE C 199 TYR 0.027 0.001 TYR B 235 ARG 0.002 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 417) hydrogen bonds : angle 4.31023 ( 1173) SS BOND : bond 0.00346 ( 4) SS BOND : angle 1.12425 ( 8) covalent geometry : bond 0.00403 ( 9253) covalent geometry : angle 0.57276 (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 : 0.954 Fit side-chains revert: symmetry clash REVERT: B 163 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.8025 (ttmt) REVERT: B 235 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.6859 (t80) REVERT: C 195 ASP cc_start: 0.8029 (p0) cc_final: 0.7684 (p0) REVERT: C 197 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7563 (mtm-85) REVERT: C 234 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.8663 (m-80) REVERT: F 240 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.6246 (ttm) REVERT: F 275 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7584 (tp30) REVERT: F 276 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6583 (mp0) outliers start: 51 outliers final: 33 residues processed: 148 average time/residue: 0.2362 time to fit residues: 48.5280 Evaluate side-chains 148 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 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 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 147 THR 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 272 ILE 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 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 275 GLU Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 295 THR 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: 0.0870 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.142080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102587 restraints weight = 10431.927| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.08 r_work: 0.2829 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9257 Z= 0.152 Angle : 0.553 6.852 12542 Z= 0.295 Chirality : 0.043 0.215 1435 Planarity : 0.004 0.053 1582 Dihedral : 4.664 42.570 1255 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.08 % Allowed : 28.02 % 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: 0.32 (0.26), residues: 1139 helix: 2.09 (0.28), residues: 392 sheet: 0.85 (0.32), residues: 267 loop : -1.88 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 82 HIS 0.004 0.001 HIS B 35 PHE 0.013 0.001 PHE C 199 TYR 0.025 0.002 TYR B 235 ARG 0.002 0.000 ARG F 205 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 417) hydrogen bonds : angle 4.26448 ( 1173) SS BOND : bond 0.00319 ( 4) SS BOND : angle 1.20617 ( 8) covalent geometry : bond 0.00367 ( 9253) covalent geometry : angle 0.55271 (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 156 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 105 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: B 163 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7977 (ttmt) REVERT: B 235 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6835 (t80) REVERT: C 45 MET cc_start: 0.9177 (mtt) cc_final: 0.8939 (mtt) REVERT: C 175 GLN cc_start: 0.8342 (pt0) cc_final: 0.7421 (mt0) REVERT: C 195 ASP cc_start: 0.8013 (p0) cc_final: 0.7681 (p0) REVERT: C 197 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7525 (mtm-85) REVERT: C 234 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8635 (m-80) REVERT: F 240 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6398 (ttm) REVERT: F 275 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7534 (tp30) REVERT: F 276 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6600 (mp0) outliers start: 51 outliers final: 36 residues processed: 148 average time/residue: 0.2408 time to fit residues: 48.6402 Evaluate side-chains 148 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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 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 147 THR 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 187 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 306 SER 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 275 GLU Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 295 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.137545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.099016 restraints weight = 10626.401| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.01 r_work: 0.2715 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 9257 Z= 0.292 Angle : 0.677 10.326 12542 Z= 0.359 Chirality : 0.048 0.284 1435 Planarity : 0.005 0.058 1582 Dihedral : 5.066 44.068 1255 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.58 % Allowed : 27.52 % 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: 0.04 (0.26), residues: 1139 helix: 1.82 (0.28), residues: 393 sheet: 0.46 (0.32), residues: 269 loop : -1.86 (0.27), residues: 477 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 0.037 0.002 TYR B 235 ARG 0.004 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.05771 ( 417) hydrogen bonds : angle 4.55643 ( 1173) SS BOND : bond 0.00474 ( 4) SS BOND : angle 1.65742 ( 8) covalent geometry : bond 0.00734 ( 9253) covalent geometry : angle 0.67570 (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 161 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 105 time to evaluate : 0.952 Fit side-chains REVERT: B 163 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8093 (ttmt) REVERT: B 235 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.7130 (t80) REVERT: C 45 MET cc_start: 0.9279 (mtt) cc_final: 0.9075 (mtt) REVERT: C 197 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7578 (mtm-85) REVERT: C 234 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8657 (m-80) REVERT: E 127 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8071 (t80) REVERT: E 205 THR cc_start: 0.8867 (m) cc_final: 0.8556 (m) REVERT: F 240 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6609 (ttm) REVERT: F 275 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7610 (tp30) REVERT: F 276 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6672 (mp0) outliers start: 56 outliers final: 37 residues processed: 151 average time/residue: 0.2246 time to fit residues: 46.2840 Evaluate side-chains 146 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 101 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 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 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 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 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 166 ILE Chi-restraints excluded: chain E residue 168 MET 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 272 ILE Chi-restraints excluded: chain E residue 293 LEU 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 206 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 61 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.143535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103732 restraints weight = 10275.970| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.11 r_work: 0.2849 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1332 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= 0.129 Angle : 0.554 13.488 12542 Z= 0.291 Chirality : 0.043 0.195 1435 Planarity : 0.004 0.052 1582 Dihedral : 4.707 45.271 1255 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.39 % Allowed : 28.61 % 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: 0.29 (0.26), residues: 1139 helix: 2.02 (0.28), residues: 392 sheet: 0.87 (0.32), residues: 269 loop : -1.89 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS B 35 PHE 0.012 0.001 PHE C 151 TYR 0.021 0.001 TYR B 235 ARG 0.003 0.000 ARG F 208 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 417) hydrogen bonds : angle 4.23488 ( 1173) SS BOND : bond 0.00320 ( 4) SS BOND : angle 0.99599 ( 8) covalent geometry : bond 0.00300 ( 9253) covalent geometry : angle 0.55325 (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 149 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 1.086 Fit side-chains REVERT: B 235 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6737 (t80) REVERT: C 45 MET cc_start: 0.9145 (mtt) cc_final: 0.8935 (mtt) REVERT: C 175 GLN cc_start: 0.8346 (pt0) cc_final: 0.7318 (mt0) REVERT: C 197 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7632 (mtm-85) REVERT: C 234 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8623 (m-80) REVERT: C 255 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8339 (mp) REVERT: E 205 THR cc_start: 0.8799 (m) cc_final: 0.8534 (m) REVERT: F 240 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6774 (ttm) REVERT: F 275 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7593 (tp30) REVERT: F 276 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6707 (mp0) outliers start: 44 outliers final: 33 residues processed: 140 average time/residue: 0.2183 time to fit residues: 42.3164 Evaluate side-chains 143 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 103 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 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 255 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS 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 306 SER Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 201 VAL 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: 1.9990 chunk 83 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 chunk 12 optimal weight: 5.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN C 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105414 restraints weight = 10361.904| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.12 r_work: 0.2913 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1381 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= 0.117 Angle : 0.539 13.011 12542 Z= 0.283 Chirality : 0.042 0.186 1435 Planarity : 0.004 0.053 1582 Dihedral : 4.528 43.777 1255 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.89 % Allowed : 29.01 % 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: 0.45 (0.26), residues: 1139 helix: 2.16 (0.28), residues: 392 sheet: 0.98 (0.32), residues: 266 loop : -1.80 (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 E 281 PHE 0.012 0.001 PHE C 151 TYR 0.021 0.001 TYR B 235 ARG 0.003 0.000 ARG F 208 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 417) hydrogen bonds : angle 4.10526 ( 1173) SS BOND : bond 0.00311 ( 4) SS BOND : angle 0.91819 ( 8) covalent geometry : bond 0.00270 ( 9253) covalent geometry : angle 0.53819 (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 144 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 1.224 Fit side-chains REVERT: B 235 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6755 (t80) REVERT: C 45 MET cc_start: 0.9128 (mtt) cc_final: 0.8912 (mtt) REVERT: C 175 GLN cc_start: 0.8374 (pt0) cc_final: 0.7367 (mt0) REVERT: C 197 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7616 (mtm-85) REVERT: C 234 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8754 (m-80) REVERT: C 255 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8305 (mp) REVERT: C 258 ASP cc_start: 0.8516 (t0) cc_final: 0.8222 (t0) REVERT: E 205 THR cc_start: 0.8800 (m) cc_final: 0.8557 (m) REVERT: F 276 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6666 (mp0) outliers start: 39 outliers final: 29 residues processed: 135 average time/residue: 0.2615 time to fit residues: 49.1238 Evaluate side-chains 133 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 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 255 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS 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 187 THR Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 310 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.144224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105079 restraints weight = 10322.374| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.02 r_work: 0.2927 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9257 Z= 0.120 Angle : 0.538 12.890 12542 Z= 0.282 Chirality : 0.042 0.188 1435 Planarity : 0.004 0.052 1582 Dihedral : 4.534 45.591 1255 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.29 % Allowed : 29.51 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.46 (0.26), residues: 1139 helix: 2.15 (0.28), residues: 393 sheet: 0.95 (0.32), residues: 268 loop : -1.78 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 82 HIS 0.003 0.001 HIS B 35 PHE 0.012 0.001 PHE C 151 TYR 0.021 0.001 TYR B 235 ARG 0.003 0.000 ARG F 208 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 417) hydrogen bonds : angle 4.07761 ( 1173) SS BOND : bond 0.00303 ( 4) SS BOND : angle 0.89541 ( 8) covalent geometry : bond 0.00279 ( 9253) covalent geometry : angle 0.53759 (12534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5375.98 seconds wall clock time: 93 minutes 31.17 seconds (5611.17 seconds total)