Starting phenix.real_space_refine on Thu Mar 13 05:12:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6i_36005/03_2025/8j6i_36005.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6i_36005/03_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_36005/03_2025/8j6i_36005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6i_36005/03_2025/8j6i_36005.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6i_36005/03_2025/8j6i_36005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6i_36005/03_2025/8j6i_36005.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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, 'ARG:plan': 1, 'GLU%COO:plan': 1, 'ASP: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, 'ARG:plan': 2, 'ASP: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: 5.63, per 1000 atoms: 0.64 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: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.17 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: 2.54 Time building geometry restraints manager: 2.91 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 24.320 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.590 ------------------------------------------------------------------------------- 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 8996 Z= 0.458 Angle : 0.626 19.710 12196 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.005 0.001 TRP R 93 HIS 0.004 0.000 HIS R 189 PHE 0.023 0.001 PHE H 239 TYR 0.015 0.001 TYR H 235 ARG 0.005 0.000 ARG R 128 *********************** 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 : 0.950 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: 1.1043 time to fit residues: 221.7027 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 : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN A 347 ASN B 32 GLN B 175 GLN B 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.198526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138684 restraints weight = 10217.081| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.04 r_work: 0.3448 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8996 Z= 0.231 Angle : 0.619 8.119 12196 Z= 0.320 Chirality : 0.043 0.199 1381 Planarity : 0.004 0.045 1538 Dihedral : 6.074 71.353 1244 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 4.81 % Allowed : 24.06 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1113 helix: 2.09 (0.27), residues: 369 sheet: 0.96 (0.33), residues: 278 loop : -0.44 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 189 PHE 0.015 0.002 PHE A 196 TYR 0.023 0.001 TYR H 235 ARG 0.005 0.001 ARG B 49 *********************** 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 171 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 25 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.6080 (t80) REVERT: R 94 LYS cc_start: 0.4801 (OUTLIER) cc_final: 0.4356 (mtmm) REVERT: R 112 GLN cc_start: 0.6948 (tp40) cc_final: 0.6606 (mm-40) REVERT: R 227 LYS cc_start: 0.5555 (mtmm) cc_final: 0.5156 (pttt) REVERT: R 238 ILE cc_start: 0.6129 (OUTLIER) cc_final: 0.5522 (mt) REVERT: A 18 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7444 (mmm) REVERT: A 276 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6361 (mt-10) REVERT: A 305 CYS cc_start: 0.8020 (m) cc_final: 0.7050 (t) REVERT: A 321 THR cc_start: 0.9074 (t) cc_final: 0.8736 (m) REVERT: A 349 LYS cc_start: 0.7325 (ttmm) cc_final: 0.6640 (tppt) REVERT: B 50 THR cc_start: 0.8953 (t) cc_final: 0.8593 (m) REVERT: B 134 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7661 (ptt-90) REVERT: B 234 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.8963 (m-80) REVERT: B 251 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7071 (mtm-85) REVERT: B 325 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8301 (mmm) REVERT: H 30 SER cc_start: 0.7950 (t) cc_final: 0.7599 (p) REVERT: H 82 GLN cc_start: 0.7689 (tp40) cc_final: 0.7398 (tp40) REVERT: H 195 LEU cc_start: 0.7698 (mp) cc_final: 0.7395 (mt) REVERT: H 230 MET cc_start: 0.7864 (tpp) cc_final: 0.7423 (mmm) outliers start: 45 outliers final: 15 residues processed: 155 average time/residue: 0.9566 time to fit residues: 161.0291 Evaluate side-chains 128 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 238 ILE 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 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 322 HIS B 176 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN H 82 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 = 0.4171 r_free = 0.4171 target = 0.189027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127976 restraints weight = 10190.192| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.96 r_work: 0.3269 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8996 Z= 0.294 Angle : 0.648 9.976 12196 Z= 0.334 Chirality : 0.044 0.209 1381 Planarity : 0.004 0.045 1538 Dihedral : 5.903 52.991 1244 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 5.56 % Allowed : 24.28 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1113 helix: 1.81 (0.28), residues: 372 sheet: 0.71 (0.32), residues: 288 loop : -0.63 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 195 PHE 0.020 0.002 PHE A 267 TYR 0.029 0.002 TYR H 235 ARG 0.004 0.001 ARG R 218 *********************** 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 182 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 130 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: R 23 ASP cc_start: 0.6396 (OUTLIER) cc_final: 0.6042 (m-30) REVERT: R 25 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.6197 (t80) REVERT: R 84 MET cc_start: 0.4464 (tpt) cc_final: 0.4245 (tpt) REVERT: R 94 LYS cc_start: 0.4851 (OUTLIER) cc_final: 0.4641 (mtmm) REVERT: R 214 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8292 (t) REVERT: R 227 LYS cc_start: 0.6026 (mtmm) cc_final: 0.5424 (pttt) REVERT: R 258 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5425 (mt) REVERT: A 18 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8125 (mmm) REVERT: A 22 ASN cc_start: 0.8412 (m-40) cc_final: 0.8117 (m-40) REVERT: A 197 LYS cc_start: 0.8866 (mtmt) cc_final: 0.8513 (mttt) REVERT: A 247 MET cc_start: 0.8747 (mtp) cc_final: 0.8547 (mtm) REVERT: A 276 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6723 (mt-10) REVERT: A 305 CYS cc_start: 0.8152 (m) cc_final: 0.7247 (t) REVERT: A 309 ASP cc_start: 0.7965 (m-30) cc_final: 0.7761 (m-30) REVERT: A 312 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7925 (mptm) REVERT: A 321 THR cc_start: 0.9104 (t) cc_final: 0.8767 (m) REVERT: A 349 LYS cc_start: 0.7746 (ttmm) cc_final: 0.6953 (tppt) REVERT: B 23 LYS cc_start: 0.7679 (tppt) cc_final: 0.7446 (tptt) REVERT: B 50 THR cc_start: 0.9056 (t) cc_final: 0.8853 (m) REVERT: B 101 MET cc_start: 0.8869 (ptt) cc_final: 0.8668 (ptp) REVERT: B 120 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8072 (mm) REVERT: B 134 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8074 (ptt-90) REVERT: B 234 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.8737 (m-80) REVERT: H 30 SER cc_start: 0.8240 (t) cc_final: 0.7942 (p) REVERT: H 82 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7585 (tp40) REVERT: H 173 TYR cc_start: 0.7761 (m-10) cc_final: 0.7551 (m-80) REVERT: H 195 LEU cc_start: 0.7826 (mp) cc_final: 0.7425 (mt) REVERT: H 230 MET cc_start: 0.7931 (tpp) cc_final: 0.7623 (mmm) outliers start: 52 outliers final: 16 residues processed: 165 average time/residue: 1.0230 time to fit residues: 181.9184 Evaluate side-chains 141 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 23 ASP 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 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 225 VAL Chi-restraints excluded: chain A residue 312 LYS 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 249 THR Chi-restraints excluded: chain B residue 270 ILE 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 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 210 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 112 GLN B 75 GLN B 175 GLN B 237 ASN G 18 GLN H 142 GLN H 171 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.186350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122918 restraints weight = 10122.303| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.98 r_work: 0.3233 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8996 Z= 0.316 Angle : 0.636 9.877 12196 Z= 0.331 Chirality : 0.044 0.212 1381 Planarity : 0.005 0.050 1538 Dihedral : 5.810 52.537 1244 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 6.52 % Allowed : 21.93 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1113 helix: 1.66 (0.28), residues: 373 sheet: 0.48 (0.31), residues: 297 loop : -0.69 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS G 44 PHE 0.018 0.002 PHE H 239 TYR 0.030 0.002 TYR H 235 ARG 0.004 0.001 ARG R 218 *********************** 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 188 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 127 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: R 94 LYS cc_start: 0.4940 (OUTLIER) cc_final: 0.4681 (mtmm) REVERT: R 112 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6738 (tt0) REVERT: R 162 LEU cc_start: 0.5738 (OUTLIER) cc_final: 0.5206 (pp) REVERT: R 214 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8188 (t) REVERT: R 258 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5524 (mt) REVERT: A 22 ASN cc_start: 0.8429 (m-40) cc_final: 0.8147 (m-40) REVERT: A 197 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8456 (mttt) REVERT: A 207 GLU cc_start: 0.7578 (tt0) cc_final: 0.7259 (mt-10) REVERT: A 247 MET cc_start: 0.8789 (mtp) cc_final: 0.8583 (mtm) REVERT: A 276 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6947 (mt-10) REVERT: A 305 CYS cc_start: 0.8162 (m) cc_final: 0.7483 (t) REVERT: A 312 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7790 (mptm) REVERT: A 321 THR cc_start: 0.9097 (t) cc_final: 0.8817 (m) REVERT: A 349 LYS cc_start: 0.7726 (ttmm) cc_final: 0.7006 (tppt) REVERT: B 50 THR cc_start: 0.9061 (t) cc_final: 0.8844 (m) REVERT: B 120 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.7811 (mm) REVERT: B 134 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8088 (ptt-90) REVERT: B 234 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.8461 (m-80) REVERT: G 37 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8410 (mp) REVERT: H 30 SER cc_start: 0.8321 (t) cc_final: 0.8023 (p) REVERT: H 82 GLN cc_start: 0.7775 (tp-100) cc_final: 0.7562 (tp40) REVERT: H 83 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8071 (ptm) REVERT: H 139 VAL cc_start: 0.8129 (m) cc_final: 0.7848 (p) REVERT: H 195 LEU cc_start: 0.7842 (mp) cc_final: 0.7428 (mt) outliers start: 61 outliers final: 21 residues processed: 168 average time/residue: 1.0065 time to fit residues: 182.8798 Evaluate side-chains 149 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 45 ASN 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 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 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 67 SER 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 0.0170 chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 217 GLN B 237 ASN H 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.189116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126483 restraints weight = 10095.973| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.83 r_work: 0.3298 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8996 Z= 0.181 Angle : 0.556 6.678 12196 Z= 0.291 Chirality : 0.041 0.187 1381 Planarity : 0.004 0.050 1538 Dihedral : 5.314 44.122 1244 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 4.60 % Allowed : 24.06 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1113 helix: 1.81 (0.28), residues: 371 sheet: 0.55 (0.31), residues: 291 loop : -0.66 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 189 PHE 0.025 0.001 PHE R 21 TYR 0.027 0.001 TYR H 235 ARG 0.005 0.000 ARG B 129 *********************** 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 168 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.5984 (mtm180) cc_final: 0.5656 (mtt90) REVERT: A 22 ASN cc_start: 0.8468 (m-40) cc_final: 0.8189 (m-40) REVERT: A 197 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8386 (mttt) REVERT: A 207 GLU cc_start: 0.7419 (tt0) cc_final: 0.7100 (mt-10) REVERT: A 247 MET cc_start: 0.8815 (mtp) cc_final: 0.8613 (mtm) REVERT: A 276 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6921 (mt-10) REVERT: A 305 CYS cc_start: 0.8260 (m) cc_final: 0.7546 (t) REVERT: A 312 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7800 (mptm) REVERT: A 349 LYS cc_start: 0.7707 (ttmm) cc_final: 0.6995 (tppt) REVERT: B 50 THR cc_start: 0.9010 (t) cc_final: 0.8695 (m) REVERT: B 120 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.7813 (mm) REVERT: B 134 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.8019 (ptt-90) REVERT: B 170 ASP cc_start: 0.8149 (t0) cc_final: 0.7936 (t70) REVERT: B 234 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8435 (m-80) REVERT: H 30 SER cc_start: 0.8349 (t) cc_final: 0.8052 (p) REVERT: H 82 GLN cc_start: 0.7748 (tp-100) cc_final: 0.7522 (tp40) REVERT: H 83 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8167 (ptm) REVERT: H 139 VAL cc_start: 0.8183 (m) cc_final: 0.7903 (p) REVERT: H 195 LEU cc_start: 0.7809 (mp) cc_final: 0.7404 (mt) outliers start: 43 outliers final: 20 residues processed: 147 average time/residue: 1.1382 time to fit residues: 179.6177 Evaluate side-chains 142 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 ASN Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 230 ILE Chi-restraints excluded: chain R residue 286 ASN 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 33 ILE Chi-restraints excluded: chain B residue 100 VAL 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 249 THR 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 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 83 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 259 GLN G 18 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 = 0.4163 r_free = 0.4163 target = 0.188940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125553 restraints weight = 9930.675| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.93 r_work: 0.3265 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8996 Z= 0.268 Angle : 0.596 8.830 12196 Z= 0.311 Chirality : 0.043 0.203 1381 Planarity : 0.004 0.054 1538 Dihedral : 5.568 44.085 1244 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.95 % Favored : 95.87 % Rotamer: Outliers : 5.35 % Allowed : 23.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1113 helix: 1.70 (0.27), residues: 373 sheet: 0.39 (0.31), residues: 295 loop : -0.66 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 131 PHE 0.016 0.002 PHE A 267 TYR 0.028 0.002 TYR H 235 ARG 0.005 0.001 ARG B 129 *********************** 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 169 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: R 60 LYS cc_start: 0.5655 (pttt) cc_final: 0.5231 (pttm) REVERT: R 162 LEU cc_start: 0.5726 (OUTLIER) cc_final: 0.5145 (pp) REVERT: A 22 ASN cc_start: 0.8436 (m-40) cc_final: 0.8142 (m-40) REVERT: A 197 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8424 (mttt) REVERT: A 207 GLU cc_start: 0.7439 (tt0) cc_final: 0.7080 (mt-10) REVERT: A 247 MET cc_start: 0.8777 (mtp) cc_final: 0.8566 (mtm) REVERT: A 276 GLU cc_start: 0.7248 (mm-30) cc_final: 0.7018 (mt-10) REVERT: A 305 CYS cc_start: 0.8209 (m) cc_final: 0.7525 (t) REVERT: A 312 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7733 (mptm) REVERT: A 313 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7067 (mtt90) REVERT: A 349 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7130 (tppt) REVERT: B 50 THR cc_start: 0.9050 (t) cc_final: 0.8810 (m) REVERT: B 120 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.7889 (mm) REVERT: B 134 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8096 (ptt-90) REVERT: B 234 PHE cc_start: 0.9399 (OUTLIER) cc_final: 0.8359 (m-80) REVERT: H 30 SER cc_start: 0.8372 (t) cc_final: 0.8087 (p) REVERT: H 82 GLN cc_start: 0.7796 (tp-100) cc_final: 0.7561 (tp40) REVERT: H 83 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8160 (ptm) REVERT: H 195 LEU cc_start: 0.7807 (mp) cc_final: 0.7404 (mt) outliers start: 50 outliers final: 24 residues processed: 150 average time/residue: 1.0441 time to fit residues: 169.2627 Evaluate side-chains 143 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL 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 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 196 THR 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 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS 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 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 142 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.0000 chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 overall best weight: 0.8788 ------------------------------------------------------------------------------- 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 141 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN H 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.190586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.129163 restraints weight = 10087.239| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.01 r_work: 0.3279 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8996 Z= 0.195 Angle : 0.550 6.769 12196 Z= 0.287 Chirality : 0.042 0.184 1381 Planarity : 0.004 0.054 1538 Dihedral : 5.270 40.568 1244 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.50 % Favored : 96.32 % Rotamer: Outliers : 5.24 % Allowed : 24.60 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1113 helix: 1.73 (0.27), residues: 374 sheet: 0.47 (0.31), residues: 293 loop : -0.62 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.017 0.001 PHE R 82 TYR 0.026 0.001 TYR H 235 ARG 0.007 0.000 ARG B 129 *********************** 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 170 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: R 60 LYS cc_start: 0.5594 (pttt) cc_final: 0.4977 (pttm) REVERT: R 64 ILE cc_start: 0.6570 (OUTLIER) cc_final: 0.6324 (mp) REVERT: R 103 MET cc_start: 0.5503 (ttp) cc_final: 0.5033 (ttt) REVERT: R 162 LEU cc_start: 0.5678 (OUTLIER) cc_final: 0.5091 (pp) REVERT: R 189 HIS cc_start: 0.5771 (OUTLIER) cc_final: 0.5559 (p90) REVERT: R 252 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.6973 (mt) REVERT: A 197 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8404 (mttt) REVERT: A 207 GLU cc_start: 0.7291 (tt0) cc_final: 0.6957 (mt-10) REVERT: A 276 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6996 (mt-10) REVERT: A 305 CYS cc_start: 0.8167 (m) cc_final: 0.7547 (t) REVERT: A 312 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7743 (mptm) REVERT: A 314 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7155 (mttm) REVERT: A 349 LYS cc_start: 0.7793 (ttmm) cc_final: 0.7079 (tppt) REVERT: B 50 THR cc_start: 0.9025 (t) cc_final: 0.8679 (m) REVERT: B 120 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.7810 (mm) REVERT: B 134 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8030 (ptt-90) REVERT: B 234 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.8239 (m-80) REVERT: H 30 SER cc_start: 0.8334 (t) cc_final: 0.8053 (p) REVERT: H 82 GLN cc_start: 0.7735 (tp-100) cc_final: 0.7522 (tp40) REVERT: H 195 LEU cc_start: 0.7787 (mp) cc_final: 0.7485 (mt) outliers start: 49 outliers final: 20 residues processed: 153 average time/residue: 1.0699 time to fit residues: 176.2671 Evaluate side-chains 141 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 160 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 189 HIS Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 286 ASN 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 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 120 ILE 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 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 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 20 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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** A 241 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 239 ASN G 24 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 = 0.4117 r_free = 0.4117 target = 0.184696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120966 restraints weight = 10225.041| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.86 r_work: 0.3211 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 8996 Z= 0.459 Angle : 0.711 11.420 12196 Z= 0.372 Chirality : 0.048 0.248 1381 Planarity : 0.005 0.053 1538 Dihedral : 6.307 54.420 1244 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 5.35 % Allowed : 24.60 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1113 helix: 1.46 (0.27), residues: 366 sheet: 0.16 (0.30), residues: 302 loop : -0.55 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 36 HIS 0.006 0.002 HIS R 131 PHE 0.016 0.002 PHE R 117 TYR 0.032 0.002 TYR H 235 ARG 0.006 0.001 ARG R 218 *********************** 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 160 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 110 time to evaluate : 0.978 Fit side-chains REVERT: R 162 LEU cc_start: 0.5728 (OUTLIER) cc_final: 0.5163 (pp) REVERT: A 22 ASN cc_start: 0.8529 (m-40) cc_final: 0.8282 (m-40) REVERT: A 197 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8430 (mttt) REVERT: A 207 GLU cc_start: 0.7599 (tt0) cc_final: 0.7109 (mt-10) REVERT: A 276 GLU cc_start: 0.7307 (mm-30) cc_final: 0.7086 (mt-10) REVERT: A 305 CYS cc_start: 0.8269 (m) cc_final: 0.7622 (t) REVERT: A 314 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7223 (mttm) REVERT: A 349 LYS cc_start: 0.7899 (ttmm) cc_final: 0.7160 (tppt) REVERT: B 50 THR cc_start: 0.9067 (t) cc_final: 0.8847 (m) REVERT: B 120 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8012 (mm) REVERT: B 129 ARG cc_start: 0.7688 (ptt90) cc_final: 0.7445 (ttt90) REVERT: H 30 SER cc_start: 0.8366 (t) cc_final: 0.8094 (p) REVERT: H 195 LEU cc_start: 0.7876 (mp) cc_final: 0.7479 (mt) outliers start: 50 outliers final: 27 residues processed: 141 average time/residue: 1.1251 time to fit residues: 170.6959 Evaluate side-chains 133 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 ASP 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 162 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 225 VAL 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 67 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 249 THR 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 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 142 GLN 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 17 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 65 optimal weight: 0.0670 chunk 42 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 overall best weight: 1.7324 ------------------------------------------------------------------------------- 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** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN H 82 GLN H 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.186558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123220 restraints weight = 10102.847| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.91 r_work: 0.3240 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8996 Z= 0.290 Angle : 0.615 9.199 12196 Z= 0.321 Chirality : 0.044 0.207 1381 Planarity : 0.004 0.053 1538 Dihedral : 5.834 46.247 1244 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.68 % Favored : 96.14 % Rotamer: Outliers : 4.39 % Allowed : 26.63 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1113 helix: 1.56 (0.27), residues: 366 sheet: 0.19 (0.30), residues: 300 loop : -0.56 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.019 0.002 PHE R 82 TYR 0.029 0.002 TYR H 235 ARG 0.004 0.001 ARG B 129 *********************** 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 150 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: R 64 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.6414 (mp) REVERT: R 103 MET cc_start: 0.5399 (ttp) cc_final: 0.5006 (ttt) REVERT: R 162 LEU cc_start: 0.5674 (OUTLIER) cc_final: 0.5099 (pp) REVERT: R 252 ILE cc_start: 0.7557 (tp) cc_final: 0.7024 (mt) REVERT: A 24 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7370 (ttm110) REVERT: A 197 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8360 (mttt) REVERT: A 207 GLU cc_start: 0.7542 (tt0) cc_final: 0.7052 (mt-10) REVERT: A 276 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7089 (mt-10) REVERT: A 305 CYS cc_start: 0.8257 (m) cc_final: 0.7662 (t) REVERT: A 314 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7332 (mttm) REVERT: A 349 LYS cc_start: 0.7912 (ttmm) cc_final: 0.7163 (tppt) REVERT: B 50 THR cc_start: 0.9054 (t) cc_final: 0.8831 (m) REVERT: B 234 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: G 37 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8507 (mp) REVERT: H 30 SER cc_start: 0.8360 (t) cc_final: 0.8083 (p) REVERT: H 192 MET cc_start: 0.7543 (ptm) cc_final: 0.7069 (pp-130) REVERT: H 195 LEU cc_start: 0.7874 (mp) cc_final: 0.7480 (mt) outliers start: 41 outliers final: 22 residues processed: 139 average time/residue: 1.2209 time to fit residues: 183.4356 Evaluate side-chains 135 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 160 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL 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 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 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 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 184 SER Chi-restraints excluded: chain H residue 230 MET 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 57 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 0.0000 chunk 81 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 75 GLN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.189950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127561 restraints weight = 10118.569| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.04 r_work: 0.3291 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8996 Z= 0.190 Angle : 0.562 9.978 12196 Z= 0.292 Chirality : 0.042 0.173 1381 Planarity : 0.004 0.054 1538 Dihedral : 5.214 37.367 1244 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 3.42 % Allowed : 27.81 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1113 helix: 1.69 (0.27), residues: 367 sheet: 0.26 (0.30), residues: 300 loop : -0.47 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 189 PHE 0.011 0.001 PHE A 189 TYR 0.025 0.001 TYR H 235 ARG 0.007 0.000 ARG B 129 ********************** 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 141 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: R 103 MET cc_start: 0.5285 (ttp) cc_final: 0.4856 (ttt) REVERT: R 252 ILE cc_start: 0.7580 (tp) cc_final: 0.7081 (mt) REVERT: A 24 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7330 (ttm110) REVERT: A 197 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8375 (mttt) REVERT: A 207 GLU cc_start: 0.7339 (tt0) cc_final: 0.6869 (mt-10) REVERT: A 276 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7088 (mt-10) REVERT: A 305 CYS cc_start: 0.8225 (m) cc_final: 0.7657 (t) REVERT: A 314 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7261 (mttm) REVERT: A 349 LYS cc_start: 0.7897 (ttmm) cc_final: 0.7151 (tppt) REVERT: B 50 THR cc_start: 0.9029 (t) cc_final: 0.8704 (m) REVERT: B 234 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: G 37 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8377 (mp) REVERT: H 30 SER cc_start: 0.8320 (t) cc_final: 0.8031 (p) REVERT: H 195 LEU cc_start: 0.7859 (mp) cc_final: 0.7484 (mt) outliers start: 32 outliers final: 17 residues processed: 130 average time/residue: 1.0392 time to fit residues: 145.7564 Evaluate side-chains 129 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS 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 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 85 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.1364 ------------------------------------------------------------------------------- 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** A 294 ASN B 175 GLN B 237 ASN H 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.186244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123351 restraints weight = 10121.317| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.06 r_work: 0.3205 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8996 Z= 0.340 Angle : 0.649 10.720 12196 Z= 0.336 Chirality : 0.045 0.209 1381 Planarity : 0.005 0.053 1538 Dihedral : 5.656 38.454 1244 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 3.74 % Allowed : 27.49 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.26), residues: 1113 helix: 1.63 (0.27), residues: 366 sheet: 0.10 (0.30), residues: 302 loop : -0.51 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS R 189 PHE 0.015 0.002 PHE R 82 TYR 0.030 0.002 TYR H 235 ARG 0.004 0.001 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8516.13 seconds wall clock time: 147 minutes 58.07 seconds (8878.07 seconds total)