Starting phenix.real_space_refine on Fri Aug 22 23:50:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6i_36005/08_2025/8j6i_36005.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6i_36005/08_2025/8j6i_36005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j6i_36005/08_2025/8j6i_36005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6i_36005/08_2025/8j6i_36005.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6i_36005/08_2025/8j6i_36005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6i_36005/08_2025/8j6i_36005.cif" } resolution = 2.92 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= 0.000 sd= 0.002 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 65 5.16 5 C 5630 2.51 5 N 1501 2.21 5 O 1605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8801 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2322 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1748 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 405 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1737 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'FI7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.86, per 1000 atoms: 0.21 Number of scatterers: 8801 At special positions: 0 Unit cell: (107.12, 110.416, 129.368, 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 65 16.00 O 1605 8.00 N 1501 7.00 C 5630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.04 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 275.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 36.5% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 25 through 55 removed outlier: 3.638A pdb=" N VAL R 29 " --> pdb=" O PHE R 25 " (cutoff:3.500A) Proline residue: R 31 - end of helix removed outlier: 3.843A pdb=" N GLY R 44 " --> pdb=" O PHE R 40 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU R 47 " --> pdb=" O LEU R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 79 removed outlier: 3.575A pdb=" N CYS R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 89 removed outlier: 4.193A pdb=" N LEU R 83 " --> pdb=" O CYS R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 130 Processing helix chain 'R' and resid 140 through 160 removed outlier: 3.577A pdb=" N THR R 155 " --> pdb=" O LEU R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 165 removed outlier: 4.016A pdb=" N LYS R 164 " --> pdb=" O HIS R 161 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS R 165 " --> pdb=" O LEU R 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 161 through 165' Processing helix chain 'R' and resid 187 through 219 removed outlier: 3.897A pdb=" N ALA R 191 " --> pdb=" O GLN R 187 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 4.420A pdb=" N ARG R 218 " --> pdb=" O SER R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 245 removed outlier: 3.772A pdb=" N PHE R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 261 removed outlier: 3.639A pdb=" N ARG R 251 " --> pdb=" O SER R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 280 Processing helix chain 'R' and resid 280 through 295 removed outlier: 4.150A pdb=" N TYR R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.955A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.513A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 5.176A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.722A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.911A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 3 through 26 removed outlier: 4.537A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.520A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.545A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 169 through 170 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.956A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.163A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.929A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.863A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.529A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.417A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.202A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.857A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.542A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.889A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.612A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.656A pdb=" N VAL H 155 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.883A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 226 " --> pdb=" O GLN H 179 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR H 175 " --> pdb=" O MET H 230 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN H 194 " --> pdb=" O TYR H 190 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1182 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: 1.00 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1407 1.31 - 1.44: 2526 1.44 - 1.57: 4967 1.57 - 1.70: 4 1.70 - 1.82: 92 Bond restraints: 8996 Sorted by residual: bond pdb=" C20 FI7 R 401 " pdb=" C21 FI7 R 401 " ideal model delta sigma weight residual 1.355 1.590 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C26 FI7 R 401 " pdb=" C27 FI7 R 401 " ideal model delta sigma weight residual 1.516 1.344 0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" C13 FI7 R 401 " pdb=" N14 FI7 R 401 " ideal model delta sigma weight residual 1.320 1.474 -0.154 2.00e-02 2.50e+03 5.97e+01 bond pdb=" C08 FI7 R 401 " pdb=" C09 FI7 R 401 " ideal model delta sigma weight residual 1.393 1.542 -0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" C08 FI7 R 401 " pdb=" N14 FI7 R 401 " ideal model delta sigma weight residual 1.327 1.469 -0.142 2.00e-02 2.50e+03 5.02e+01 ... (remaining 8991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 12161 3.94 - 7.88: 31 7.88 - 11.83: 2 11.83 - 15.77: 1 15.77 - 19.71: 1 Bond angle restraints: 12196 Sorted by residual: angle pdb=" N TYR R 269 " pdb=" CA TYR R 269 " pdb=" C TYR R 269 " ideal model delta sigma weight residual 111.11 104.72 6.39 1.20e+00 6.94e-01 2.83e+01 angle pdb=" C LEU R 80 " pdb=" N PRO R 81 " pdb=" CD PRO R 81 " ideal model delta sigma weight residual 125.00 105.29 19.71 4.10e+00 5.95e-02 2.31e+01 angle pdb=" C17 FI7 R 401 " pdb=" N19 FI7 R 401 " pdb=" C20 FI7 R 401 " ideal model delta sigma weight residual 130.45 116.24 14.21 3.00e+00 1.11e-01 2.25e+01 angle pdb=" CA PRO R 81 " pdb=" N PRO R 81 " pdb=" CD PRO R 81 " ideal model delta sigma weight residual 112.00 117.45 -5.45 1.40e+00 5.10e-01 1.51e+01 angle pdb=" C ILE R 13 " pdb=" N ASP R 14 " pdb=" CA ASP R 14 " ideal model delta sigma weight residual 123.91 117.63 6.28 1.66e+00 3.63e-01 1.43e+01 ... (remaining 12191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.24: 4882 25.24 - 50.49: 390 50.49 - 75.73: 34 75.73 - 100.97: 4 100.97 - 126.21: 2 Dihedral angle restraints: 5312 sinusoidal: 2037 harmonic: 3275 Sorted by residual: dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual 93.00 132.79 -39.79 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" C25 FI7 R 401 " pdb=" C26 FI7 R 401 " pdb=" C27 FI7 R 401 " pdb=" C28 FI7 R 401 " ideal model delta sinusoidal sigma weight residual 63.14 -63.07 126.21 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C20 FI7 R 401 " pdb=" C27 FI7 R 401 " pdb=" C28 FI7 R 401 " pdb=" C26 FI7 R 401 " ideal model delta sinusoidal sigma weight residual 45.86 -56.98 102.84 1 3.00e+01 1.11e-03 1.30e+01 ... (remaining 5309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1205 0.054 - 0.108: 136 0.108 - 0.163: 38 0.163 - 0.217: 0 0.217 - 0.271: 2 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA TYR R 269 " pdb=" N TYR R 269 " pdb=" C TYR R 269 " pdb=" CB TYR R 269 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ILE R 13 " pdb=" N ILE R 13 " pdb=" C ILE R 13 " pdb=" CB ILE R 13 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA TYR H 235 " pdb=" N TYR H 235 " pdb=" C TYR H 235 " pdb=" CB TYR H 235 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 1378 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 80 " 0.086 5.00e-02 4.00e+02 1.46e-01 3.39e+01 pdb=" N PRO R 81 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO R 81 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO R 81 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.028 5.00e-02 4.00e+02 4.33e-02 2.99e+00 pdb=" N PRO B 236 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 239 " -0.008 2.00e-02 2.50e+03 1.14e-02 2.28e+00 pdb=" CG PHE H 239 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE H 239 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE H 239 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE H 239 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE H 239 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE H 239 " -0.004 2.00e-02 2.50e+03 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 341 2.71 - 3.26: 8845 3.26 - 3.81: 14116 3.81 - 4.35: 17311 4.35 - 4.90: 29677 Nonbonded interactions: 70290 Sorted by model distance: nonbonded pdb=" O ILE R 278 " pdb=" OG SER R 281 " model vdw 2.167 3.040 nonbonded pdb=" O ASP B 66 " pdb=" OG SER B 67 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.248 3.040 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.262 3.120 nonbonded pdb=" O ASP B 247 " pdb=" OD1 ASP B 247 " model vdw 2.264 3.040 ... (remaining 70285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.620 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 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 : 0.006 0.235 8999 Z= 0.310 Angle : 0.626 19.710 12202 Z= 0.313 Chirality : 0.040 0.271 1381 Planarity : 0.005 0.146 1538 Dihedral : 16.601 126.213 3185 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 25.99 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.27), residues: 1113 helix: 2.35 (0.28), residues: 365 sheet: 1.30 (0.34), residues: 252 loop : -0.41 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 128 TYR 0.015 0.001 TYR H 235 PHE 0.023 0.001 PHE H 239 TRP 0.005 0.001 TRP R 93 HIS 0.004 0.000 HIS R 189 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 8996) covalent geometry : angle 0.62579 (12196) SS BOND : bond 0.00420 ( 3) SS BOND : angle 1.00770 ( 6) hydrogen bonds : bond 0.19237 ( 423) hydrogen bonds : angle 6.91957 ( 1182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.266 Fit side-chains REVERT: R 23 ASP cc_start: 0.5249 (t70) cc_final: 0.4522 (t0) REVERT: R 86 ASN cc_start: 0.5355 (t0) cc_final: 0.4945 (m110) REVERT: R 112 GLN cc_start: 0.6961 (tp40) cc_final: 0.6564 (mm-40) REVERT: R 141 ASN cc_start: 0.5635 (m110) cc_final: 0.5373 (m-40) REVERT: R 227 LYS cc_start: 0.5514 (mtmm) cc_final: 0.5206 (mtpt) REVERT: R 285 MET cc_start: 0.6969 (ttp) cc_final: 0.6581 (ttp) REVERT: R 290 ASP cc_start: 0.7039 (m-30) cc_final: 0.6710 (t70) REVERT: A 195 HIS cc_start: 0.7710 (t70) cc_final: 0.7358 (t-170) REVERT: A 197 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7432 (mttt) REVERT: A 198 MET cc_start: 0.8481 (ttm) cc_final: 0.8246 (ttp) REVERT: A 276 GLU cc_start: 0.6616 (mm-30) cc_final: 0.5968 (mt-10) REVERT: A 305 CYS cc_start: 0.7644 (m) cc_final: 0.6602 (t) REVERT: A 321 THR cc_start: 0.8904 (t) cc_final: 0.8517 (m) REVERT: A 330 LYS cc_start: 0.7417 (mttt) cc_final: 0.7047 (tptt) REVERT: A 349 LYS cc_start: 0.7152 (ttmm) cc_final: 0.6352 (tppt) REVERT: B 46 ARG cc_start: 0.7402 (mtp85) cc_final: 0.7057 (mtp-110) REVERT: B 217 MET cc_start: 0.6776 (pmm) cc_final: 0.5839 (pp-130) REVERT: B 220 GLN cc_start: 0.8300 (mp10) cc_final: 0.8063 (mt0) REVERT: B 230 ASN cc_start: 0.7390 (t0) cc_final: 0.7149 (m-40) REVERT: B 295 ASN cc_start: 0.7403 (m-40) cc_final: 0.7037 (m110) REVERT: B 325 MET cc_start: 0.8172 (tpp) cc_final: 0.7875 (mmm) REVERT: H 69 THR cc_start: 0.6352 (t) cc_final: 0.5795 (m) REVERT: H 82 GLN cc_start: 0.7600 (tp40) cc_final: 0.7339 (tp40) REVERT: H 195 LEU cc_start: 0.7729 (mp) cc_final: 0.7501 (mt) REVERT: H 230 MET cc_start: 0.7464 (tpp) cc_final: 0.6981 (mmm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.4110 time to fit residues: 82.1988 Evaluate side-chains 117 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.0370 chunk 106 optimal weight: 7.9990 overall best weight: 1.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 175 GLN B 176 GLN G 18 GLN H 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.191528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128023 restraints weight = 10172.528| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.97 r_work: 0.3308 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8999 Z= 0.207 Angle : 0.706 10.430 12202 Z= 0.364 Chirality : 0.046 0.224 1381 Planarity : 0.005 0.045 1538 Dihedral : 6.212 50.367 1244 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 6.20 % Allowed : 22.78 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.26), residues: 1113 helix: 1.82 (0.27), residues: 371 sheet: 0.76 (0.32), residues: 288 loop : -0.49 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 251 TYR 0.028 0.002 TYR H 235 PHE 0.021 0.002 PHE A 196 TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 8996) covalent geometry : angle 0.70426 (12196) SS BOND : bond 0.01836 ( 3) SS BOND : angle 2.54757 ( 6) hydrogen bonds : bond 0.04501 ( 423) hydrogen bonds : angle 4.84889 ( 1182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 139 time to evaluate : 0.280 Fit side-chains REVERT: R 23 ASP cc_start: 0.5977 (t70) cc_final: 0.5627 (t0) REVERT: R 25 PHE cc_start: 0.6649 (OUTLIER) cc_final: 0.6146 (t80) REVERT: R 94 LYS cc_start: 0.4983 (OUTLIER) cc_final: 0.4503 (mtmm) REVERT: R 112 GLN cc_start: 0.7034 (tp40) cc_final: 0.6825 (mm-40) REVERT: R 214 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8276 (t) REVERT: R 227 LYS cc_start: 0.5687 (mtmm) cc_final: 0.5223 (pttt) REVERT: R 258 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5396 (mt) REVERT: A 18 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7984 (mmm) REVERT: A 33 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: A 197 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8448 (mttm) REVERT: A 207 GLU cc_start: 0.7382 (tt0) cc_final: 0.6914 (mt-10) REVERT: A 255 ASN cc_start: 0.7972 (m-40) cc_final: 0.7748 (m110) REVERT: A 276 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6613 (mt-10) REVERT: A 312 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7949 (mptm) REVERT: A 321 THR cc_start: 0.9106 (t) cc_final: 0.8750 (m) REVERT: A 324 THR cc_start: 0.7728 (p) cc_final: 0.7396 (m) REVERT: A 349 LYS cc_start: 0.7620 (ttmm) cc_final: 0.6865 (tppt) REVERT: B 50 THR cc_start: 0.9081 (t) cc_final: 0.8841 (m) REVERT: B 120 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8217 (mm) REVERT: B 134 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7995 (ptt-90) REVERT: B 325 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8358 (mmm) REVERT: G 21 MET cc_start: 0.4690 (OUTLIER) cc_final: 0.4356 (ptm) REVERT: H 30 SER cc_start: 0.8111 (t) cc_final: 0.7773 (p) REVERT: H 82 GLN cc_start: 0.7782 (tp40) cc_final: 0.7490 (tp40) REVERT: H 195 LEU cc_start: 0.7762 (mp) cc_final: 0.7403 (mt) REVERT: H 230 MET cc_start: 0.7952 (tpp) cc_final: 0.7596 (mmm) REVERT: H 233 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7133 (mt) outliers start: 58 outliers final: 18 residues processed: 177 average time/residue: 0.3602 time to fit residues: 68.8870 Evaluate side-chains 136 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 237 ASN G 24 ASN H 82 GLN H 142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.190445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.127847 restraints weight = 10113.437| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.86 r_work: 0.3319 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8999 Z= 0.149 Angle : 0.585 7.852 12202 Z= 0.304 Chirality : 0.043 0.196 1381 Planarity : 0.004 0.048 1538 Dihedral : 5.566 58.904 1244 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer: Outliers : 4.92 % Allowed : 24.39 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.26), residues: 1113 helix: 1.87 (0.28), residues: 373 sheet: 0.66 (0.32), residues: 290 loop : -0.55 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 129 TYR 0.027 0.001 TYR H 235 PHE 0.014 0.002 PHE R 180 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8996) covalent geometry : angle 0.58345 (12196) SS BOND : bond 0.01064 ( 3) SS BOND : angle 2.11008 ( 6) hydrogen bonds : bond 0.03860 ( 423) hydrogen bonds : angle 4.52681 ( 1182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: R 25 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6167 (t80) REVERT: R 84 MET cc_start: 0.4542 (tpt) cc_final: 0.4329 (tpt) REVERT: R 162 LEU cc_start: 0.5727 (OUTLIER) cc_final: 0.5278 (pp) REVERT: R 227 LYS cc_start: 0.6011 (mtmm) cc_final: 0.5687 (mtpt) REVERT: A 18 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.8019 (mmm) REVERT: A 22 ASN cc_start: 0.8389 (m-40) cc_final: 0.8184 (m-40) REVERT: A 33 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: A 52 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6785 (tp40) REVERT: A 197 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8451 (mttt) REVERT: A 207 GLU cc_start: 0.7435 (tt0) cc_final: 0.6958 (mt-10) REVERT: A 276 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6642 (mt-10) REVERT: A 305 CYS cc_start: 0.8035 (m) cc_final: 0.7336 (t) REVERT: A 321 THR cc_start: 0.9060 (t) cc_final: 0.8805 (m) REVERT: A 349 LYS cc_start: 0.7716 (ttmm) cc_final: 0.6964 (tppt) REVERT: B 23 LYS cc_start: 0.7595 (tppt) cc_final: 0.7254 (tptp) REVERT: B 50 THR cc_start: 0.8971 (t) cc_final: 0.8666 (m) REVERT: B 120 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.7961 (mm) REVERT: B 134 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8025 (ptt-90) REVERT: B 234 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.8841 (m-80) REVERT: B 325 MET cc_start: 0.8500 (tpp) cc_final: 0.8298 (mmt) REVERT: H 30 SER cc_start: 0.8303 (t) cc_final: 0.8028 (p) REVERT: H 82 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7517 (tp40) REVERT: H 195 LEU cc_start: 0.7802 (mp) cc_final: 0.7442 (mt) REVERT: H 230 MET cc_start: 0.7991 (tpp) cc_final: 0.7595 (mmm) REVERT: H 233 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7184 (mt) outliers start: 46 outliers final: 16 residues processed: 146 average time/residue: 0.4434 time to fit residues: 69.3181 Evaluate side-chains 135 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 ASN R 86 ASN R 112 GLN ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 259 GLN H 142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.186077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121804 restraints weight = 10297.094| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.03 r_work: 0.3226 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8999 Z= 0.211 Angle : 0.649 9.682 12202 Z= 0.337 Chirality : 0.045 0.218 1381 Planarity : 0.005 0.050 1538 Dihedral : 5.824 46.315 1244 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.87 % Rotamer: Outliers : 6.84 % Allowed : 22.35 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.64 (0.26), residues: 1113 helix: 1.67 (0.28), residues: 371 sheet: 0.56 (0.31), residues: 288 loop : -0.68 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 218 TYR 0.028 0.002 TYR H 235 PHE 0.019 0.002 PHE A 267 TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 8996) covalent geometry : angle 0.64514 (12196) SS BOND : bond 0.01913 ( 3) SS BOND : angle 3.17562 ( 6) hydrogen bonds : bond 0.04153 ( 423) hydrogen bonds : angle 4.61156 ( 1182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 122 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: R 94 LYS cc_start: 0.4918 (OUTLIER) cc_final: 0.4674 (mtmm) REVERT: R 112 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6603 (tt0) REVERT: R 162 LEU cc_start: 0.5739 (OUTLIER) cc_final: 0.5271 (pp) REVERT: R 227 LYS cc_start: 0.6246 (mtmm) cc_final: 0.6023 (mtmt) REVERT: R 258 LEU cc_start: 0.5907 (OUTLIER) cc_final: 0.5495 (mt) REVERT: A 33 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7361 (tt0) REVERT: A 52 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6957 (tp40) REVERT: A 197 LYS cc_start: 0.8855 (mtmt) cc_final: 0.8507 (mttt) REVERT: A 207 GLU cc_start: 0.7592 (tt0) cc_final: 0.6888 (mt-10) REVERT: A 276 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6844 (mt-10) REVERT: A 305 CYS cc_start: 0.8013 (m) cc_final: 0.7266 (t) REVERT: A 312 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7836 (mptm) REVERT: A 321 THR cc_start: 0.9115 (t) cc_final: 0.8820 (m) REVERT: A 349 LYS cc_start: 0.7722 (ttmm) cc_final: 0.7003 (tppt) REVERT: B 50 THR cc_start: 0.9071 (t) cc_final: 0.8862 (m) REVERT: B 134 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8118 (ptt-90) REVERT: B 234 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.8481 (m-80) REVERT: G 37 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8425 (mp) REVERT: H 30 SER cc_start: 0.8340 (t) cc_final: 0.8055 (p) REVERT: H 82 GLN cc_start: 0.7764 (tp-100) cc_final: 0.7541 (tp40) REVERT: H 195 LEU cc_start: 0.7824 (mp) cc_final: 0.7418 (mt) outliers start: 64 outliers final: 23 residues processed: 168 average time/residue: 0.3708 time to fit residues: 66.9197 Evaluate side-chains 144 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 184 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 0.2980 chunk 109 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 217 GLN A 294 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 237 ASN H 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.188897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.125321 restraints weight = 10207.297| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.93 r_work: 0.3281 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8999 Z= 0.128 Angle : 0.562 6.373 12202 Z= 0.293 Chirality : 0.041 0.190 1381 Planarity : 0.004 0.049 1538 Dihedral : 5.130 38.542 1244 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer: Outliers : 6.10 % Allowed : 22.46 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.26), residues: 1113 helix: 1.78 (0.28), residues: 370 sheet: 0.53 (0.31), residues: 288 loop : -0.63 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.027 0.001 TYR H 235 PHE 0.015 0.001 PHE R 82 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8996) covalent geometry : angle 0.56087 (12196) SS BOND : bond 0.00978 ( 3) SS BOND : angle 1.73777 ( 6) hydrogen bonds : bond 0.03581 ( 423) hydrogen bonds : angle 4.36410 ( 1182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 117 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: R 60 LYS cc_start: 0.5717 (pttt) cc_final: 0.5285 (pttt) REVERT: R 63 ARG cc_start: 0.5941 (mtm180) cc_final: 0.5600 (mtt90) REVERT: R 94 LYS cc_start: 0.4777 (OUTLIER) cc_final: 0.4575 (mtmm) REVERT: R 162 LEU cc_start: 0.5695 (OUTLIER) cc_final: 0.5151 (pp) REVERT: A 33 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7155 (tt0) REVERT: A 197 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8467 (mttm) REVERT: A 207 GLU cc_start: 0.7515 (tt0) cc_final: 0.6840 (mt-10) REVERT: A 276 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6787 (mt-10) REVERT: A 305 CYS cc_start: 0.8031 (m) cc_final: 0.7348 (t) REVERT: A 312 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7762 (mptm) REVERT: A 349 LYS cc_start: 0.7751 (ttmm) cc_final: 0.7006 (tppt) REVERT: B 50 THR cc_start: 0.9022 (t) cc_final: 0.8719 (m) REVERT: B 134 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7975 (ptt-90) REVERT: B 234 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.8457 (m-80) REVERT: H 30 SER cc_start: 0.8327 (t) cc_final: 0.8059 (p) REVERT: H 82 GLN cc_start: 0.7657 (tp-100) cc_final: 0.7410 (tp40) REVERT: H 86 LEU cc_start: 0.7585 (mt) cc_final: 0.7370 (mm) REVERT: H 195 LEU cc_start: 0.7785 (mp) cc_final: 0.7371 (mt) REVERT: H 233 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7269 (mt) outliers start: 57 outliers final: 28 residues processed: 156 average time/residue: 0.4202 time to fit residues: 70.3437 Evaluate side-chains 144 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 230 ILE Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain R residue 300 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 86 optimal weight: 0.0370 chunk 23 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 237 ASN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.190089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127783 restraints weight = 10033.062| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.97 r_work: 0.3274 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8999 Z= 0.148 Angle : 0.570 7.751 12202 Z= 0.297 Chirality : 0.042 0.193 1381 Planarity : 0.004 0.053 1538 Dihedral : 5.192 43.127 1244 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 6.84 % Allowed : 22.46 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.26), residues: 1113 helix: 1.73 (0.28), residues: 369 sheet: 0.55 (0.31), residues: 288 loop : -0.61 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.026 0.001 TYR H 235 PHE 0.012 0.001 PHE A 267 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8996) covalent geometry : angle 0.56791 (12196) SS BOND : bond 0.01332 ( 3) SS BOND : angle 2.14403 ( 6) hydrogen bonds : bond 0.03639 ( 423) hydrogen bonds : angle 4.35717 ( 1182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 117 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: R 60 LYS cc_start: 0.5724 (pttt) cc_final: 0.5127 (pttt) REVERT: R 63 ARG cc_start: 0.5943 (mtm180) cc_final: 0.5596 (mtt180) REVERT: R 64 ILE cc_start: 0.6563 (OUTLIER) cc_final: 0.6325 (mp) REVERT: R 106 MET cc_start: 0.5569 (OUTLIER) cc_final: 0.4537 (ppp) REVERT: R 107 LEU cc_start: 0.5633 (OUTLIER) cc_final: 0.5351 (tt) REVERT: R 162 LEU cc_start: 0.5674 (OUTLIER) cc_final: 0.5140 (pp) REVERT: A 33 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: A 197 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8480 (mttm) REVERT: A 207 GLU cc_start: 0.7602 (tt0) cc_final: 0.6890 (mt-10) REVERT: A 276 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6928 (mt-10) REVERT: A 305 CYS cc_start: 0.8060 (m) cc_final: 0.7326 (t) REVERT: A 312 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7802 (mptm) REVERT: A 314 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.7096 (mttm) REVERT: A 349 LYS cc_start: 0.7831 (ttmm) cc_final: 0.7118 (tppt) REVERT: B 50 THR cc_start: 0.9010 (t) cc_final: 0.8650 (m) REVERT: B 134 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8016 (ptt-90) REVERT: B 234 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: H 30 SER cc_start: 0.8343 (t) cc_final: 0.8085 (p) REVERT: H 82 GLN cc_start: 0.7697 (tp-100) cc_final: 0.7470 (tp40) REVERT: H 195 LEU cc_start: 0.7798 (mp) cc_final: 0.7407 (mt) REVERT: H 233 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7240 (mt) outliers start: 64 outliers final: 34 residues processed: 157 average time/residue: 0.4006 time to fit residues: 67.3897 Evaluate side-chains 161 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain R residue 300 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 294 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.186854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122784 restraints weight = 10060.802| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.03 r_work: 0.3224 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8999 Z= 0.224 Angle : 0.651 10.226 12202 Z= 0.339 Chirality : 0.045 0.229 1381 Planarity : 0.005 0.052 1538 Dihedral : 5.714 41.490 1244 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.31 % Favored : 95.51 % Rotamer: Outliers : 6.84 % Allowed : 23.32 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.26), residues: 1113 helix: 1.57 (0.27), residues: 366 sheet: 0.29 (0.31), residues: 297 loop : -0.49 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 129 TYR 0.031 0.002 TYR H 235 PHE 0.017 0.002 PHE A 267 TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS R 131 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 8996) covalent geometry : angle 0.64796 (12196) SS BOND : bond 0.02009 ( 3) SS BOND : angle 2.88830 ( 6) hydrogen bonds : bond 0.04174 ( 423) hydrogen bonds : angle 4.60447 ( 1182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 114 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: R 162 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.5119 (pp) REVERT: R 189 HIS cc_start: 0.6040 (OUTLIER) cc_final: 0.5833 (p90) REVERT: R 216 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6335 (mtp85) REVERT: R 252 ILE cc_start: 0.7607 (tp) cc_final: 0.7069 (mt) REVERT: A 24 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7414 (ttm110) REVERT: A 33 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: A 197 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8464 (mttt) REVERT: A 305 CYS cc_start: 0.8084 (m) cc_final: 0.7520 (t) REVERT: A 312 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7765 (mptm) REVERT: A 314 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7192 (mttm) REVERT: A 349 LYS cc_start: 0.7861 (ttmm) cc_final: 0.7154 (tppt) REVERT: B 50 THR cc_start: 0.9050 (t) cc_final: 0.8817 (m) REVERT: B 134 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8149 (ptt-90) REVERT: B 234 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: G 37 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8524 (mp) REVERT: H 30 SER cc_start: 0.8362 (t) cc_final: 0.8104 (p) REVERT: H 82 GLN cc_start: 0.7739 (tp-100) cc_final: 0.7497 (tp40) REVERT: H 195 LEU cc_start: 0.7842 (mp) cc_final: 0.7434 (mt) outliers start: 64 outliers final: 36 residues processed: 159 average time/residue: 0.3915 time to fit residues: 66.8620 Evaluate side-chains 149 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 189 HIS Chi-restraints excluded: chain R residue 216 ARG Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain R residue 300 SER Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN G 18 GLN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.187591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126528 restraints weight = 10038.972| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.00 r_work: 0.3228 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8999 Z= 0.189 Angle : 0.613 9.152 12202 Z= 0.319 Chirality : 0.044 0.201 1381 Planarity : 0.004 0.055 1538 Dihedral : 5.613 40.608 1244 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.69 % Rotamer: Outliers : 6.84 % Allowed : 23.96 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.26), residues: 1113 helix: 1.52 (0.27), residues: 367 sheet: 0.24 (0.31), residues: 297 loop : -0.48 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.029 0.002 TYR H 235 PHE 0.013 0.002 PHE B 292 TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 8996) covalent geometry : angle 0.61104 (12196) SS BOND : bond 0.01703 ( 3) SS BOND : angle 2.53177 ( 6) hydrogen bonds : bond 0.03919 ( 423) hydrogen bonds : angle 4.51970 ( 1182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 107 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: R 162 LEU cc_start: 0.5627 (OUTLIER) cc_final: 0.5060 (pp) REVERT: R 189 HIS cc_start: 0.6057 (OUTLIER) cc_final: 0.5843 (p90) REVERT: R 252 ILE cc_start: 0.7610 (tp) cc_final: 0.7059 (mt) REVERT: A 24 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7394 (ttm110) REVERT: A 33 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: A 197 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8467 (mttm) REVERT: A 305 CYS cc_start: 0.8097 (m) cc_final: 0.7521 (t) REVERT: A 312 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7775 (mptm) REVERT: A 314 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7211 (mttm) REVERT: A 349 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7174 (tppt) REVERT: B 50 THR cc_start: 0.9056 (t) cc_final: 0.8826 (m) REVERT: B 134 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8079 (ptt-90) REVERT: B 154 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8524 (t0) REVERT: B 234 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.8292 (m-80) REVERT: H 30 SER cc_start: 0.8295 (t) cc_final: 0.8029 (p) REVERT: H 82 GLN cc_start: 0.7712 (tp-100) cc_final: 0.7458 (tp40) REVERT: H 195 LEU cc_start: 0.7853 (mp) cc_final: 0.7453 (mt) outliers start: 64 outliers final: 34 residues processed: 151 average time/residue: 0.3648 time to fit residues: 59.4170 Evaluate side-chains 148 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 189 HIS Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain R residue 300 SER Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 77 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 88 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 69 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 294 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.191454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.129096 restraints weight = 10073.705| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.99 r_work: 0.3311 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8999 Z= 0.117 Angle : 0.544 7.270 12202 Z= 0.283 Chirality : 0.041 0.167 1381 Planarity : 0.004 0.054 1538 Dihedral : 5.240 39.332 1244 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 4.81 % Allowed : 25.45 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.26), residues: 1113 helix: 1.75 (0.27), residues: 367 sheet: 0.42 (0.31), residues: 290 loop : -0.53 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 129 TYR 0.025 0.001 TYR H 235 PHE 0.019 0.001 PHE R 82 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8996) covalent geometry : angle 0.54258 (12196) SS BOND : bond 0.00973 ( 3) SS BOND : angle 2.11228 ( 6) hydrogen bonds : bond 0.03360 ( 423) hydrogen bonds : angle 4.31535 ( 1182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: R 103 MET cc_start: 0.5359 (ttp) cc_final: 0.4890 (ttt) REVERT: R 189 HIS cc_start: 0.5900 (OUTLIER) cc_final: 0.5638 (p90) REVERT: R 252 ILE cc_start: 0.7565 (tp) cc_final: 0.7035 (mt) REVERT: A 33 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.7036 (tt0) REVERT: A 197 LYS cc_start: 0.8697 (mtmt) cc_final: 0.8416 (mttm) REVERT: A 207 GLU cc_start: 0.7513 (tt0) cc_final: 0.6817 (tt0) REVERT: A 305 CYS cc_start: 0.8144 (m) cc_final: 0.7581 (t) REVERT: A 312 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7648 (mptm) REVERT: A 314 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7225 (mttm) REVERT: A 349 LYS cc_start: 0.7869 (ttmm) cc_final: 0.7150 (tppt) REVERT: B 50 THR cc_start: 0.8995 (t) cc_final: 0.8663 (m) REVERT: B 134 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.8021 (ptt-90) REVERT: B 234 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: H 30 SER cc_start: 0.8272 (t) cc_final: 0.8002 (p) REVERT: H 82 GLN cc_start: 0.7711 (tp-100) cc_final: 0.7462 (tp40) REVERT: H 195 LEU cc_start: 0.7779 (mp) cc_final: 0.7377 (mt) outliers start: 45 outliers final: 23 residues processed: 140 average time/residue: 0.3833 time to fit residues: 57.9353 Evaluate side-chains 136 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 189 HIS Chi-restraints excluded: chain R residue 300 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 28 optimal weight: 0.0040 chunk 3 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 294 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 237 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.186799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123386 restraints weight = 10051.330| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.01 r_work: 0.3229 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 8999 Z= 0.220 Angle : 0.638 9.827 12202 Z= 0.330 Chirality : 0.045 0.204 1381 Planarity : 0.005 0.055 1538 Dihedral : 5.644 39.982 1244 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.13 % Favored : 95.78 % Rotamer: Outliers : 4.49 % Allowed : 26.31 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.26), residues: 1113 helix: 1.59 (0.27), residues: 368 sheet: 0.20 (0.30), residues: 297 loop : -0.49 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 129 TYR 0.029 0.002 TYR H 235 PHE 0.013 0.002 PHE A 189 TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS R 131 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 8996) covalent geometry : angle 0.63437 (12196) SS BOND : bond 0.02123 ( 3) SS BOND : angle 3.21847 ( 6) hydrogen bonds : bond 0.04038 ( 423) hydrogen bonds : angle 4.52452 ( 1182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: R 216 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6411 (mtp85) REVERT: R 252 ILE cc_start: 0.7559 (tp) cc_final: 0.7013 (mt) REVERT: R 269 TYR cc_start: 0.5341 (m-10) cc_final: 0.5089 (m-80) REVERT: A 33 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: A 197 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8452 (mttm) REVERT: A 305 CYS cc_start: 0.8102 (m) cc_final: 0.7553 (t) REVERT: A 312 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7766 (mptm) REVERT: A 314 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7226 (mttm) REVERT: A 349 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7174 (tppt) REVERT: B 50 THR cc_start: 0.9026 (t) cc_final: 0.8801 (m) REVERT: B 134 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8174 (ptt-90) REVERT: B 234 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.8246 (m-80) REVERT: H 30 SER cc_start: 0.8304 (t) cc_final: 0.8051 (p) REVERT: H 82 GLN cc_start: 0.7766 (tp-100) cc_final: 0.7529 (tp40) REVERT: H 195 LEU cc_start: 0.7855 (mp) cc_final: 0.7465 (mt) outliers start: 42 outliers final: 23 residues processed: 133 average time/residue: 0.4069 time to fit residues: 58.0268 Evaluate side-chains 132 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 216 ARG Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 300 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 16 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 294 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.189742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.126918 restraints weight = 10031.470| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.82 r_work: 0.3299 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8999 Z= 0.131 Angle : 0.564 8.064 12202 Z= 0.292 Chirality : 0.042 0.174 1381 Planarity : 0.004 0.055 1538 Dihedral : 5.293 37.608 1244 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer: Outliers : 3.74 % Allowed : 27.38 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.26), residues: 1113 helix: 1.67 (0.27), residues: 369 sheet: 0.26 (0.30), residues: 295 loop : -0.46 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.026 0.001 TYR H 235 PHE 0.020 0.001 PHE R 82 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 189 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8996) covalent geometry : angle 0.56152 (12196) SS BOND : bond 0.01192 ( 3) SS BOND : angle 2.29069 ( 6) hydrogen bonds : bond 0.03498 ( 423) hydrogen bonds : angle 4.36597 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3295.44 seconds wall clock time: 56 minutes 40.33 seconds (3400.33 seconds total)