Starting phenix.real_space_refine on Wed Sep 17 14:05:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k3f_62014/09_2025/9k3f_62014.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k3f_62014/09_2025/9k3f_62014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k3f_62014/09_2025/9k3f_62014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k3f_62014/09_2025/9k3f_62014.map" model { file = "/net/cci-nas-00/data/ceres_data/9k3f_62014/09_2025/9k3f_62014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k3f_62014/09_2025/9k3f_62014.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 68 5.16 5 C 5558 2.51 5 N 1494 2.21 5 O 1623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8743 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2060 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1908 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2589 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Time building chain proxies: 2.04, per 1000 atoms: 0.23 Number of scatterers: 8743 At special positions: 0 Unit cell: (87.822, 114.597, 136.017, 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 68 16.00 O 1623 8.00 N 1494 7.00 C 5558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 35 " - pdb=" SG CYS R 276 " distance=2.03 Simple disulfide: pdb=" SG CYS R 268 " - pdb=" SG CYS R 274 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 452.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 37.7% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'R' and resid 42 through 65 removed outlier: 3.702A pdb=" N LEU R 46 " --> pdb=" O PRO R 42 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER R 47 " --> pdb=" O GLU R 43 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL R 64 " --> pdb=" O ILE R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 103 removed outlier: 3.576A pdb=" N CYS R 78 " --> pdb=" O TYR R 74 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR R 95 " --> pdb=" O ASN R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 148 removed outlier: 4.845A pdb=" N ASN R 118 " --> pdb=" O GLN R 114 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE R 119 " --> pdb=" O HIS R 115 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP R 121 " --> pdb=" O ASP R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 152 removed outlier: 3.691A pdb=" N TYR R 152 " --> pdb=" O ALA R 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 149 through 152' Processing helix chain 'R' and resid 157 through 182 removed outlier: 4.130A pdb=" N PHE R 179 " --> pdb=" O CYS R 175 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE R 180 " --> pdb=" O GLY R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 197 Processing helix chain 'R' and resid 200 through 223 removed outlier: 4.072A pdb=" N TYR R 207 " --> pdb=" O MET R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 266 removed outlier: 4.294A pdb=" N PHE R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) Proline residue: R 257 - end of helix Processing helix chain 'R' and resid 271 through 279 Processing helix chain 'R' and resid 280 through 299 Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 303 through 310 removed outlier: 3.742A pdb=" N PHE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 38 removed outlier: 3.844A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 252 through 264 No H-bonds generated for 'chain 'A' and resid 252 through 264' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.509A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.088A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 4.075A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.303A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.020A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 47 removed outlier: 7.065A pdb=" N THR A 364 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU A 291 " --> pdb=" O THR A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.031A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.684A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.703A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.565A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.596A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.685A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.317A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.607A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.911A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.264A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.607A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2841 1.34 - 1.46: 2192 1.46 - 1.59: 3790 1.59 - 1.71: 0 1.71 - 1.84: 99 Bond restraints: 8922 Sorted by residual: bond pdb=" CA ALA R 223 " pdb=" C ALA R 223 " ideal model delta sigma weight residual 1.531 1.507 0.024 1.12e-02 7.97e+03 4.67e+00 bond pdb=" CB GLN A 384 " pdb=" CG GLN A 384 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.51e+00 bond pdb=" CG1 ILE A 288 " pdb=" CD1 ILE A 288 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.06e+00 bond pdb=" C GLU S 234 " pdb=" N TYR S 235 " ideal model delta sigma weight residual 1.331 1.273 0.058 3.12e-02 1.03e+03 3.43e+00 bond pdb=" CB PRO S 236 " pdb=" CG PRO S 236 " ideal model delta sigma weight residual 1.506 1.435 0.071 3.90e-02 6.57e+02 3.35e+00 ... (remaining 8917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11707 2.00 - 4.01: 341 4.01 - 6.01: 37 6.01 - 8.01: 9 8.01 - 10.02: 5 Bond angle restraints: 12099 Sorted by residual: angle pdb=" N TYR R 182 " pdb=" CA TYR R 182 " pdb=" C TYR R 182 " ideal model delta sigma weight residual 113.20 103.64 9.56 1.21e+00 6.83e-01 6.24e+01 angle pdb=" N ARG B 197 " pdb=" CA ARG B 197 " pdb=" C ARG B 197 " ideal model delta sigma weight residual 114.62 108.54 6.08 1.14e+00 7.69e-01 2.84e+01 angle pdb=" C SER R 183 " pdb=" CA SER R 183 " pdb=" CB SER R 183 " ideal model delta sigma weight residual 115.79 110.70 5.09 1.19e+00 7.06e-01 1.83e+01 angle pdb=" C PRO B 194 " pdb=" N ASP B 195 " pdb=" CA ASP B 195 " ideal model delta sigma weight residual 121.40 127.05 -5.65 1.52e+00 4.33e-01 1.38e+01 angle pdb=" C GLN A 59 " pdb=" N MET A 60 " pdb=" CA MET A 60 " ideal model delta sigma weight residual 121.14 114.76 6.38 1.75e+00 3.27e-01 1.33e+01 ... (remaining 12094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4840 17.94 - 35.87: 397 35.87 - 53.81: 56 53.81 - 71.74: 10 71.74 - 89.68: 8 Dihedral angle restraints: 5311 sinusoidal: 2037 harmonic: 3274 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 151.42 28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA VAL S 64 " pdb=" C VAL S 64 " pdb=" N LYS S 65 " pdb=" CA LYS S 65 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ASP B 246 " pdb=" C ASP B 246 " pdb=" N ASP B 247 " pdb=" CA ASP B 247 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 5308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 878 0.045 - 0.090: 403 0.090 - 0.135: 93 0.135 - 0.179: 12 0.179 - 0.224: 4 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CG LEU S 174 " pdb=" CB LEU S 174 " pdb=" CD1 LEU S 174 " pdb=" CD2 LEU S 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CG LEU A 270 " pdb=" CB LEU A 270 " pdb=" CD1 LEU A 270 " pdb=" CD2 LEU A 270 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CG LEU B 55 " pdb=" CB LEU B 55 " pdb=" CD1 LEU B 55 " pdb=" CD2 LEU B 55 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.06e-01 ... (remaining 1387 not shown) Planarity restraints: 1533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL S 147 " 0.052 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO S 148 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO S 148 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO S 148 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 256 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO R 257 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO R 257 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 257 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO G 49 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.031 5.00e-02 4.00e+02 ... (remaining 1530 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 267 2.69 - 3.24: 8779 3.24 - 3.80: 13830 3.80 - 4.35: 17854 4.35 - 4.90: 30478 Nonbonded interactions: 71208 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.139 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.145 3.040 nonbonded pdb=" OH TYR R 74 " pdb=" OE2 GLU R 305 " model vdw 2.176 3.040 nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR A 40 " model vdw 2.176 3.040 nonbonded pdb=" OG SER A 250 " pdb=" O ASN A 292 " model vdw 2.194 3.040 ... (remaining 71203 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: 0.010 Normalize map: mean=0, sd=1: 1.100 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.460 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 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 : 0.009 0.079 8926 Z= 0.411 Angle : 0.819 10.017 12107 Z= 0.466 Chirality : 0.052 0.224 1390 Planarity : 0.006 0.079 1533 Dihedral : 13.350 89.677 3183 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.21 % Allowed : 0.74 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.25), residues: 1109 helix: 0.60 (0.26), residues: 386 sheet: -0.85 (0.31), residues: 284 loop : -1.36 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 385 TYR 0.019 0.003 TYR B 145 PHE 0.033 0.003 PHE B 234 TRP 0.021 0.002 TRP S 47 HIS 0.009 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00936 ( 8922) covalent geometry : angle 0.81760 (12099) SS BOND : bond 0.00462 ( 4) SS BOND : angle 2.12608 ( 8) hydrogen bonds : bond 0.18605 ( 426) hydrogen bonds : angle 7.65972 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 229 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: R 168 ILE cc_start: 0.7633 (mt) cc_final: 0.7254 (pt) REVERT: A 22 ARG cc_start: 0.8206 (ttt90) cc_final: 0.7973 (ttt90) REVERT: A 274 LYS cc_start: 0.7937 (tttm) cc_final: 0.7546 (mtpp) REVERT: A 295 ASP cc_start: 0.7767 (p0) cc_final: 0.7429 (p0) REVERT: A 299 GLU cc_start: 0.5541 (mp0) cc_final: 0.5098 (mp0) REVERT: A 314 GLU cc_start: 0.7707 (tp30) cc_final: 0.7461 (tp30) REVERT: A 334 VAL cc_start: 0.7824 (t) cc_final: 0.7499 (p) REVERT: B 76 ASP cc_start: 0.6733 (m-30) cc_final: 0.6517 (m-30) REVERT: B 237 ASN cc_start: 0.7291 (t0) cc_final: 0.6773 (t0) REVERT: B 239 ASN cc_start: 0.7466 (m110) cc_final: 0.6976 (m110) REVERT: B 251 ARG cc_start: 0.8064 (mtt90) cc_final: 0.7858 (mtt90) REVERT: B 283 ARG cc_start: 0.7874 (tpt170) cc_final: 0.7623 (tmt170) outliers start: 2 outliers final: 1 residues processed: 230 average time/residue: 0.5685 time to fit residues: 139.2103 Evaluate side-chains 201 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 185 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 110 ASN B 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.159554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.135742 restraints weight = 12214.837| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.20 r_work: 0.3698 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8926 Z= 0.162 Angle : 0.621 8.901 12107 Z= 0.332 Chirality : 0.044 0.230 1390 Planarity : 0.005 0.052 1533 Dihedral : 5.233 26.750 1221 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.58 % Allowed : 13.19 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.26), residues: 1109 helix: 1.42 (0.27), residues: 386 sheet: -0.61 (0.30), residues: 306 loop : -1.07 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 342 TYR 0.016 0.001 TYR R 182 PHE 0.014 0.002 PHE R 76 TRP 0.015 0.002 TRP S 47 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8922) covalent geometry : angle 0.62059 (12099) SS BOND : bond 0.00765 ( 4) SS BOND : angle 1.32421 ( 8) hydrogen bonds : bond 0.04784 ( 426) hydrogen bonds : angle 5.22818 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 285 LEU cc_start: 0.7999 (mt) cc_final: 0.7798 (mt) REVERT: A 16 ASP cc_start: 0.7268 (m-30) cc_final: 0.7057 (m-30) REVERT: A 22 ARG cc_start: 0.8359 (ttt90) cc_final: 0.8120 (ttm170) REVERT: A 28 LYS cc_start: 0.8443 (ttmm) cc_final: 0.8172 (ttmm) REVERT: A 212 PHE cc_start: 0.8300 (p90) cc_final: 0.7999 (p90) REVERT: A 274 LYS cc_start: 0.7867 (tttm) cc_final: 0.7434 (mtpp) REVERT: A 295 ASP cc_start: 0.7719 (p0) cc_final: 0.7397 (p0) REVERT: A 299 GLU cc_start: 0.6147 (mp0) cc_final: 0.5697 (mp0) REVERT: A 314 GLU cc_start: 0.7617 (tp30) cc_final: 0.7385 (tp30) REVERT: A 347 ARG cc_start: 0.7413 (ttm-80) cc_final: 0.7132 (ttm-80) REVERT: A 348 ILE cc_start: 0.8392 (mm) cc_final: 0.8157 (tp) REVERT: B 76 ASP cc_start: 0.7407 (m-30) cc_final: 0.7175 (m-30) REVERT: B 237 ASN cc_start: 0.7741 (t0) cc_final: 0.7282 (t0) REVERT: B 239 ASN cc_start: 0.7894 (m110) cc_final: 0.7382 (m110) REVERT: B 251 ARG cc_start: 0.8490 (mtt90) cc_final: 0.7985 (ttm170) REVERT: B 322 ASP cc_start: 0.7954 (m-30) cc_final: 0.7749 (m-30) REVERT: S 32 PHE cc_start: 0.8449 (m-80) cc_final: 0.7985 (m-80) REVERT: S 72 ARG cc_start: 0.7944 (ptp-170) cc_final: 0.7509 (ptm160) outliers start: 15 outliers final: 7 residues processed: 218 average time/residue: 0.6327 time to fit residues: 146.3568 Evaluate side-chains 205 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 198 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain S residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 83 optimal weight: 20.0000 chunk 72 optimal weight: 0.0980 chunk 31 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.159388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.135405 restraints weight = 12201.399| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.27 r_work: 0.3681 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8926 Z= 0.174 Angle : 0.596 8.661 12107 Z= 0.317 Chirality : 0.043 0.148 1390 Planarity : 0.005 0.045 1533 Dihedral : 4.932 20.439 1221 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.85 % Allowed : 15.40 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.26), residues: 1109 helix: 1.62 (0.27), residues: 387 sheet: -0.56 (0.30), residues: 308 loop : -0.92 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 265 TYR 0.011 0.001 TYR R 182 PHE 0.028 0.002 PHE R 281 TRP 0.013 0.002 TRP S 47 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8922) covalent geometry : angle 0.59473 (12099) SS BOND : bond 0.00577 ( 4) SS BOND : angle 1.32578 ( 8) hydrogen bonds : bond 0.04506 ( 426) hydrogen bonds : angle 4.90932 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7357 (m-30) cc_final: 0.7112 (m-30) REVERT: A 209 GLU cc_start: 0.6344 (tm-30) cc_final: 0.5989 (tm-30) REVERT: A 212 PHE cc_start: 0.8297 (p90) cc_final: 0.8023 (p90) REVERT: A 213 GLN cc_start: 0.7450 (pp30) cc_final: 0.7140 (pp30) REVERT: A 222 PHE cc_start: 0.7936 (m-80) cc_final: 0.7722 (m-80) REVERT: A 266 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8127 (tp) REVERT: A 267 GLN cc_start: 0.7482 (tp-100) cc_final: 0.7232 (tm-30) REVERT: A 295 ASP cc_start: 0.7718 (p0) cc_final: 0.7430 (p0) REVERT: A 299 GLU cc_start: 0.6081 (OUTLIER) cc_final: 0.5691 (mp0) REVERT: A 314 GLU cc_start: 0.7600 (tp30) cc_final: 0.7368 (tp30) REVERT: A 347 ARG cc_start: 0.7449 (ttm-80) cc_final: 0.7178 (ttm-80) REVERT: B 197 ARG cc_start: 0.8004 (tpp-160) cc_final: 0.7783 (mpp-170) REVERT: B 220 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7249 (mm-40) REVERT: B 237 ASN cc_start: 0.7771 (t0) cc_final: 0.7315 (t0) REVERT: B 239 ASN cc_start: 0.7847 (m110) cc_final: 0.7335 (m110) REVERT: B 251 ARG cc_start: 0.8553 (mtt90) cc_final: 0.8348 (mtt90) REVERT: B 258 ASP cc_start: 0.7503 (t0) cc_final: 0.6630 (t0) REVERT: B 263 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8297 (p) REVERT: S 18 ARG cc_start: 0.8532 (ttm170) cc_final: 0.8275 (tpp-160) REVERT: S 32 PHE cc_start: 0.8505 (m-80) cc_final: 0.7876 (m-80) REVERT: S 220 GLU cc_start: 0.8026 (mp0) cc_final: 0.7631 (mp0) outliers start: 27 outliers final: 14 residues processed: 217 average time/residue: 0.6202 time to fit residues: 142.8729 Evaluate side-chains 223 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 19 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: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.159520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.135020 restraints weight = 12201.553| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.27 r_work: 0.3672 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8926 Z= 0.174 Angle : 0.594 10.235 12107 Z= 0.313 Chirality : 0.042 0.149 1390 Planarity : 0.004 0.045 1533 Dihedral : 4.764 19.300 1220 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.64 % Allowed : 16.35 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.26), residues: 1109 helix: 1.65 (0.27), residues: 388 sheet: -0.46 (0.31), residues: 297 loop : -0.80 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 265 TYR 0.009 0.001 TYR R 277 PHE 0.020 0.002 PHE R 258 TRP 0.013 0.002 TRP S 47 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8922) covalent geometry : angle 0.59364 (12099) SS BOND : bond 0.00509 ( 4) SS BOND : angle 1.25432 ( 8) hydrogen bonds : bond 0.04297 ( 426) hydrogen bonds : angle 4.75766 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 289 MET cc_start: 0.7269 (mpp) cc_final: 0.7024 (mmm) REVERT: A 16 ASP cc_start: 0.7380 (m-30) cc_final: 0.7141 (m-30) REVERT: A 213 GLN cc_start: 0.7389 (pp30) cc_final: 0.7104 (pp30) REVERT: A 266 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8066 (tp) REVERT: A 267 GLN cc_start: 0.7479 (tp-100) cc_final: 0.7249 (tm-30) REVERT: A 314 GLU cc_start: 0.7575 (tp30) cc_final: 0.7304 (tp30) REVERT: A 347 ARG cc_start: 0.7354 (ttm-80) cc_final: 0.7113 (ttm-80) REVERT: B 146 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7631 (mt) REVERT: B 220 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: B 237 ASN cc_start: 0.7754 (t0) cc_final: 0.7214 (t0) REVERT: B 239 ASN cc_start: 0.7848 (m110) cc_final: 0.7288 (m110) REVERT: B 249 THR cc_start: 0.7705 (p) cc_final: 0.7451 (t) REVERT: B 251 ARG cc_start: 0.8557 (mtt90) cc_final: 0.8339 (mtt90) REVERT: B 322 ASP cc_start: 0.7966 (m-30) cc_final: 0.7759 (m-30) REVERT: S 32 PHE cc_start: 0.8599 (m-80) cc_final: 0.8000 (m-80) REVERT: S 220 GLU cc_start: 0.8005 (mp0) cc_final: 0.7663 (mp0) outliers start: 25 outliers final: 17 residues processed: 224 average time/residue: 0.6090 time to fit residues: 145.1433 Evaluate side-chains 221 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 195 MET Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain S residue 155 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 62 optimal weight: 0.0870 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 104 optimal weight: 1.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 110 ASN B 125 ASN B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.160314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.135721 restraints weight = 12126.858| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.28 r_work: 0.3689 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8926 Z= 0.140 Angle : 0.573 9.568 12107 Z= 0.300 Chirality : 0.042 0.139 1390 Planarity : 0.004 0.044 1533 Dihedral : 4.558 19.265 1220 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.27 % Allowed : 17.62 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.26), residues: 1109 helix: 1.71 (0.27), residues: 392 sheet: -0.36 (0.30), residues: 303 loop : -0.86 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 265 TYR 0.010 0.001 TYR R 277 PHE 0.015 0.001 PHE R 258 TRP 0.012 0.002 TRP A 277 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8922) covalent geometry : angle 0.57221 (12099) SS BOND : bond 0.00631 ( 4) SS BOND : angle 1.38732 ( 8) hydrogen bonds : bond 0.03937 ( 426) hydrogen bonds : angle 4.62919 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 66 ASN cc_start: 0.7691 (m110) cc_final: 0.7315 (m-40) REVERT: A 16 ASP cc_start: 0.7389 (m-30) cc_final: 0.7156 (m-30) REVERT: A 22 ARG cc_start: 0.8369 (ttt90) cc_final: 0.8143 (ttm170) REVERT: A 28 LYS cc_start: 0.8405 (ttmm) cc_final: 0.8175 (ttmm) REVERT: A 213 GLN cc_start: 0.7320 (pp30) cc_final: 0.7024 (pp30) REVERT: A 240 ASP cc_start: 0.7377 (m-30) cc_final: 0.7138 (m-30) REVERT: A 267 GLN cc_start: 0.7487 (tp-100) cc_final: 0.7234 (tm-30) REVERT: A 314 GLU cc_start: 0.7579 (tp30) cc_final: 0.7289 (tp30) REVERT: A 347 ARG cc_start: 0.7313 (ttm-80) cc_final: 0.7049 (ttm-80) REVERT: B 146 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7652 (mt) REVERT: B 186 ASP cc_start: 0.7447 (m-30) cc_final: 0.7246 (m-30) REVERT: B 237 ASN cc_start: 0.7719 (t0) cc_final: 0.7167 (t0) REVERT: B 239 ASN cc_start: 0.7846 (m110) cc_final: 0.7255 (m110) REVERT: B 249 THR cc_start: 0.7665 (p) cc_final: 0.7415 (t) REVERT: B 262 MET cc_start: 0.7972 (tpt) cc_final: 0.7624 (tpt) REVERT: S 220 GLU cc_start: 0.8029 (mp0) cc_final: 0.7722 (mp0) outliers start: 31 outliers final: 17 residues processed: 226 average time/residue: 0.6198 time to fit residues: 148.4708 Evaluate side-chains 220 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 155 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 83 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 44 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: A 35 GLN B 88 ASN B 110 ASN B 125 ASN B 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.159858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.135329 restraints weight = 12120.968| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.26 r_work: 0.3681 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8926 Z= 0.163 Angle : 0.590 10.624 12107 Z= 0.308 Chirality : 0.042 0.147 1390 Planarity : 0.004 0.042 1533 Dihedral : 4.554 19.376 1220 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.01 % Allowed : 17.72 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.26), residues: 1109 helix: 1.74 (0.27), residues: 392 sheet: -0.39 (0.30), residues: 299 loop : -0.82 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 265 TYR 0.009 0.001 TYR R 277 PHE 0.014 0.001 PHE B 235 TRP 0.013 0.002 TRP A 277 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8922) covalent geometry : angle 0.58982 (12099) SS BOND : bond 0.00574 ( 4) SS BOND : angle 1.24509 ( 8) hydrogen bonds : bond 0.04074 ( 426) hydrogen bonds : angle 4.63723 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 66 ASN cc_start: 0.7757 (m110) cc_final: 0.7340 (m-40) REVERT: R 218 VAL cc_start: 0.7685 (t) cc_final: 0.7478 (t) REVERT: R 289 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6966 (mmm) REVERT: A 16 ASP cc_start: 0.7372 (m-30) cc_final: 0.7124 (m-30) REVERT: A 51 SER cc_start: 0.7776 (p) cc_final: 0.7325 (m) REVERT: A 213 GLN cc_start: 0.7332 (pp30) cc_final: 0.7020 (pp30) REVERT: A 267 GLN cc_start: 0.7493 (tp-100) cc_final: 0.7243 (tm-30) REVERT: A 274 LYS cc_start: 0.7832 (tttm) cc_final: 0.7521 (mtpp) REVERT: A 314 GLU cc_start: 0.7557 (tp30) cc_final: 0.7253 (tp30) REVERT: B 49 ARG cc_start: 0.8321 (mtp85) cc_final: 0.8118 (mtt-85) REVERT: B 146 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7600 (mt) REVERT: B 237 ASN cc_start: 0.7762 (t0) cc_final: 0.7149 (t0) REVERT: B 239 ASN cc_start: 0.7864 (m110) cc_final: 0.7310 (m110) REVERT: B 249 THR cc_start: 0.7662 (p) cc_final: 0.7404 (t) REVERT: B 262 MET cc_start: 0.8098 (tpt) cc_final: 0.7728 (tpt) REVERT: S 67 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7630 (ttm170) REVERT: S 220 GLU cc_start: 0.7970 (mp0) cc_final: 0.7540 (mp0) outliers start: 38 outliers final: 24 residues processed: 227 average time/residue: 0.6297 time to fit residues: 151.6518 Evaluate side-chains 227 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 289 MET Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 0.0870 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 28 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 92 optimal weight: 0.0170 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 88 ASN B 110 ASN B 125 ASN B 132 ASN B 176 GLN B 230 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.162163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.137802 restraints weight = 12220.717| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.28 r_work: 0.3710 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8926 Z= 0.115 Angle : 0.558 11.528 12107 Z= 0.289 Chirality : 0.041 0.132 1390 Planarity : 0.004 0.043 1533 Dihedral : 4.270 19.753 1220 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.90 % Allowed : 19.09 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.26), residues: 1109 helix: 2.02 (0.27), residues: 386 sheet: -0.15 (0.31), residues: 299 loop : -0.86 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 251 TYR 0.009 0.001 TYR R 277 PHE 0.023 0.001 PHE R 258 TRP 0.012 0.001 TRP A 277 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8922) covalent geometry : angle 0.55773 (12099) SS BOND : bond 0.00563 ( 4) SS BOND : angle 1.10023 ( 8) hydrogen bonds : bond 0.03561 ( 426) hydrogen bonds : angle 4.45229 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 66 ASN cc_start: 0.7662 (m110) cc_final: 0.7291 (m-40) REVERT: R 289 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6873 (mmm) REVERT: A 16 ASP cc_start: 0.7341 (m-30) cc_final: 0.7102 (m-30) REVERT: A 28 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8151 (ttmm) REVERT: A 51 SER cc_start: 0.7758 (p) cc_final: 0.7288 (m) REVERT: A 267 GLN cc_start: 0.7457 (tp-100) cc_final: 0.7240 (tm-30) REVERT: A 274 LYS cc_start: 0.7815 (tttm) cc_final: 0.7520 (mtpp) REVERT: A 314 GLU cc_start: 0.7529 (tp30) cc_final: 0.7217 (tp30) REVERT: B 45 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7345 (mmm) REVERT: B 68 ARG cc_start: 0.8517 (ttt180) cc_final: 0.8266 (mtp180) REVERT: B 128 THR cc_start: 0.8768 (p) cc_final: 0.8510 (t) REVERT: B 237 ASN cc_start: 0.7695 (t0) cc_final: 0.7013 (t0) REVERT: B 239 ASN cc_start: 0.7852 (m110) cc_final: 0.7186 (m110) REVERT: B 249 THR cc_start: 0.7489 (p) cc_final: 0.7217 (t) REVERT: B 262 MET cc_start: 0.8086 (tpt) cc_final: 0.7643 (tpt) REVERT: S 68 PHE cc_start: 0.7859 (m-10) cc_final: 0.7442 (m-10) REVERT: S 116 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8677 (p) REVERT: S 220 GLU cc_start: 0.7831 (mp0) cc_final: 0.7576 (mp0) outliers start: 37 outliers final: 21 residues processed: 228 average time/residue: 0.5702 time to fit residues: 138.2139 Evaluate side-chains 226 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 289 MET Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 70 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 110 ASN B 125 ASN B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.161003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.136580 restraints weight = 12154.037| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.27 r_work: 0.3710 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8926 Z= 0.140 Angle : 0.601 14.371 12107 Z= 0.307 Chirality : 0.042 0.138 1390 Planarity : 0.004 0.042 1533 Dihedral : 4.332 19.863 1220 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.69 % Allowed : 20.57 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.26), residues: 1109 helix: 1.98 (0.27), residues: 386 sheet: -0.15 (0.31), residues: 299 loop : -0.88 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 49 TYR 0.008 0.001 TYR R 277 PHE 0.012 0.001 PHE B 235 TRP 0.014 0.001 TRP A 277 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8922) covalent geometry : angle 0.60023 (12099) SS BOND : bond 0.00517 ( 4) SS BOND : angle 1.22224 ( 8) hydrogen bonds : bond 0.03797 ( 426) hydrogen bonds : angle 4.48919 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: R 66 ASN cc_start: 0.7729 (m110) cc_final: 0.7292 (m-40) REVERT: R 218 VAL cc_start: 0.7615 (t) cc_final: 0.7391 (t) REVERT: R 289 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6859 (mmm) REVERT: A 16 ASP cc_start: 0.7394 (m-30) cc_final: 0.7131 (m-30) REVERT: A 28 LYS cc_start: 0.8420 (ttmm) cc_final: 0.8161 (ttmm) REVERT: A 51 SER cc_start: 0.7798 (p) cc_final: 0.7324 (m) REVERT: A 267 GLN cc_start: 0.7478 (tp-100) cc_final: 0.7246 (tm-30) REVERT: A 274 LYS cc_start: 0.7822 (tttm) cc_final: 0.7524 (mtpp) REVERT: A 314 GLU cc_start: 0.7504 (tp30) cc_final: 0.7178 (tp30) REVERT: A 334 VAL cc_start: 0.7731 (t) cc_final: 0.7333 (p) REVERT: B 45 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7345 (mmm) REVERT: B 128 THR cc_start: 0.8785 (p) cc_final: 0.8509 (t) REVERT: B 237 ASN cc_start: 0.7738 (t0) cc_final: 0.7287 (t0) REVERT: B 239 ASN cc_start: 0.7827 (m110) cc_final: 0.7347 (m110) REVERT: B 249 THR cc_start: 0.7537 (p) cc_final: 0.7263 (t) REVERT: B 262 MET cc_start: 0.8095 (tpt) cc_final: 0.7680 (tpt) REVERT: S 68 PHE cc_start: 0.7876 (m-10) cc_final: 0.7447 (m-10) REVERT: S 116 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8676 (p) REVERT: S 220 GLU cc_start: 0.7890 (mp0) cc_final: 0.7572 (mp0) outliers start: 35 outliers final: 21 residues processed: 218 average time/residue: 0.6235 time to fit residues: 144.6312 Evaluate side-chains 221 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 289 MET Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 0.9990 chunk 108 optimal weight: 0.0980 chunk 40 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 105 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 20.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.161305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.136692 restraints weight = 12134.625| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.28 r_work: 0.3712 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8926 Z= 0.139 Angle : 0.607 15.394 12107 Z= 0.307 Chirality : 0.042 0.137 1390 Planarity : 0.004 0.044 1533 Dihedral : 4.309 19.666 1220 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.38 % Allowed : 21.31 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.26), residues: 1109 helix: 2.08 (0.27), residues: 386 sheet: -0.16 (0.31), residues: 301 loop : -0.89 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 49 TYR 0.017 0.001 TYR S 60 PHE 0.023 0.001 PHE R 258 TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8922) covalent geometry : angle 0.60602 (12099) SS BOND : bond 0.00570 ( 4) SS BOND : angle 1.23088 ( 8) hydrogen bonds : bond 0.03762 ( 426) hydrogen bonds : angle 4.47125 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: R 66 ASN cc_start: 0.7747 (m110) cc_final: 0.7316 (m-40) REVERT: R 289 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6912 (mmm) REVERT: A 16 ASP cc_start: 0.7398 (m-30) cc_final: 0.7151 (m-30) REVERT: A 28 LYS cc_start: 0.8408 (ttmm) cc_final: 0.8148 (ttmm) REVERT: A 267 GLN cc_start: 0.7470 (tp-100) cc_final: 0.7237 (tm-30) REVERT: A 274 LYS cc_start: 0.7793 (tttm) cc_final: 0.7504 (mtpp) REVERT: A 314 GLU cc_start: 0.7563 (tp30) cc_final: 0.7234 (tp30) REVERT: A 334 VAL cc_start: 0.7788 (t) cc_final: 0.7519 (p) REVERT: B 45 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7360 (mmm) REVERT: B 68 ARG cc_start: 0.8578 (ttt180) cc_final: 0.8313 (mtp180) REVERT: B 128 THR cc_start: 0.8779 (p) cc_final: 0.8510 (t) REVERT: B 215 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: B 237 ASN cc_start: 0.7736 (t0) cc_final: 0.7129 (t0) REVERT: B 239 ASN cc_start: 0.7840 (m110) cc_final: 0.7250 (m110) REVERT: B 262 MET cc_start: 0.8113 (tpt) cc_final: 0.7606 (tpt) REVERT: B 283 ARG cc_start: 0.8141 (tpt90) cc_final: 0.7716 (tpt90) REVERT: S 68 PHE cc_start: 0.7900 (m-10) cc_final: 0.7489 (m-10) REVERT: S 116 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8692 (p) REVERT: S 220 GLU cc_start: 0.7858 (mp0) cc_final: 0.7579 (mp0) outliers start: 32 outliers final: 20 residues processed: 215 average time/residue: 0.6147 time to fit residues: 140.6173 Evaluate side-chains 214 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 261 HIS Chi-restraints excluded: chain R residue 289 MET Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 21 optimal weight: 0.0370 chunk 96 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 76 optimal weight: 0.0970 chunk 103 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.0370 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 88 ASN B 110 ASN B 125 ASN B 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.163796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.139412 restraints weight = 12163.411| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.29 r_work: 0.3728 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8926 Z= 0.111 Angle : 0.597 15.391 12107 Z= 0.298 Chirality : 0.041 0.143 1390 Planarity : 0.004 0.043 1533 Dihedral : 4.139 19.280 1220 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.32 % Allowed : 22.36 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.26), residues: 1109 helix: 2.15 (0.27), residues: 387 sheet: -0.07 (0.31), residues: 301 loop : -0.85 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 137 TYR 0.013 0.001 TYR S 60 PHE 0.023 0.001 PHE R 258 TRP 0.015 0.002 TRP A 277 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8922) covalent geometry : angle 0.59639 (12099) SS BOND : bond 0.00624 ( 4) SS BOND : angle 1.13428 ( 8) hydrogen bonds : bond 0.03407 ( 426) hydrogen bonds : angle 4.36765 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 66 ASN cc_start: 0.7653 (m110) cc_final: 0.7302 (m-40) REVERT: R 289 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6847 (mmm) REVERT: A 16 ASP cc_start: 0.7363 (m-30) cc_final: 0.7105 (m-30) REVERT: A 28 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8180 (ttmm) REVERT: A 51 SER cc_start: 0.7734 (p) cc_final: 0.7267 (m) REVERT: A 267 GLN cc_start: 0.7457 (tp-100) cc_final: 0.7211 (tp-100) REVERT: A 274 LYS cc_start: 0.7797 (tttm) cc_final: 0.7528 (mtpp) REVERT: A 314 GLU cc_start: 0.7571 (tp30) cc_final: 0.7247 (tp30) REVERT: A 334 VAL cc_start: 0.7755 (t) cc_final: 0.7553 (p) REVERT: B 45 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7371 (mmm) REVERT: B 68 ARG cc_start: 0.8553 (ttt180) cc_final: 0.8303 (mtp180) REVERT: B 128 THR cc_start: 0.8741 (p) cc_final: 0.8492 (t) REVERT: B 215 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: B 228 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7410 (p0) REVERT: B 237 ASN cc_start: 0.7710 (t0) cc_final: 0.7062 (t0) REVERT: B 239 ASN cc_start: 0.7877 (m110) cc_final: 0.7298 (m110) REVERT: B 246 ASP cc_start: 0.7648 (t0) cc_final: 0.7389 (t0) REVERT: B 249 THR cc_start: 0.7456 (p) cc_final: 0.7140 (t) REVERT: B 262 MET cc_start: 0.8078 (tpt) cc_final: 0.7567 (tpt) REVERT: S 68 PHE cc_start: 0.7853 (m-10) cc_final: 0.7439 (m-10) REVERT: S 116 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8691 (p) REVERT: S 158 SER cc_start: 0.8728 (m) cc_final: 0.8474 (t) REVERT: S 220 GLU cc_start: 0.7830 (mp0) cc_final: 0.7573 (mp0) outliers start: 22 outliers final: 15 residues processed: 213 average time/residue: 0.6218 time to fit residues: 140.8442 Evaluate side-chains 214 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 261 HIS Chi-restraints excluded: chain R residue 289 MET Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 0.0870 chunk 29 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 50 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 176 GLN B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.162545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.138162 restraints weight = 12114.213| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.26 r_work: 0.3714 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8926 Z= 0.133 Angle : 0.614 15.631 12107 Z= 0.309 Chirality : 0.042 0.142 1390 Planarity : 0.004 0.043 1533 Dihedral : 4.229 19.447 1220 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.43 % Allowed : 23.10 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.26), residues: 1109 helix: 2.21 (0.27), residues: 386 sheet: -0.13 (0.31), residues: 302 loop : -0.91 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 49 TYR 0.015 0.001 TYR S 60 PHE 0.011 0.001 PHE B 235 TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8922) covalent geometry : angle 0.61291 (12099) SS BOND : bond 0.00746 ( 4) SS BOND : angle 1.31293 ( 8) hydrogen bonds : bond 0.03625 ( 426) hydrogen bonds : angle 4.40533 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4471.50 seconds wall clock time: 76 minutes 55.54 seconds (4615.54 seconds total)