Starting phenix.real_space_refine on Mon May 12 02:31:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6i_36005/05_2025/8j6i_36005.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6i_36005/05_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_36005/05_2025/8j6i_36005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6i_36005/05_2025/8j6i_36005.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6i_36005/05_2025/8j6i_36005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6i_36005/05_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-5687/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: 5.30, per 1000 atoms: 0.60 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: 2.32 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: 0.98 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: 2.50 Time building geometry restraints manager: 2.63 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.420 Find NCS groups from input model: 0.080 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:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.235 8999 Z= 0.310 Angle : 0.626 19.710 12202 Z= 0.313 Chirality : 0.040 0.271 1381 Planarity : 0.005 0.146 1538 Dihedral : 16.601 126.213 3185 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 25.99 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.19237 ( 423) hydrogen bonds : angle 6.91957 ( 1182) SS BOND : bond 0.00420 ( 3) SS BOND : angle 1.00770 ( 6) covalent geometry : bond 0.00618 ( 8996) covalent geometry : angle 0.62579 (12196) *********************** 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 : 1.008 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: 1.0584 time to fit residues: 213.0497 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 : 0.986 ------------------------------------------------------------------------------- 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 = 84)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138303 restraints weight = 10217.082| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.11 r_work: 0.3453 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 8999 Z= 0.157 Angle : 0.620 8.119 12202 Z= 0.321 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 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 423) hydrogen bonds : angle 4.84000 ( 1182) SS BOND : bond 0.01189 ( 3) SS BOND : angle 1.78427 ( 6) covalent geometry : bond 0.00349 ( 8996) covalent geometry : angle 0.61857 (12196) *********************** 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 : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 25 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.6078 (t80) REVERT: R 94 LYS cc_start: 0.4806 (OUTLIER) cc_final: 0.4363 (mtmm) REVERT: R 112 GLN cc_start: 0.6924 (tp40) cc_final: 0.6581 (mm-40) REVERT: R 227 LYS cc_start: 0.5540 (mtmm) cc_final: 0.5143 (pttt) REVERT: R 238 ILE cc_start: 0.6105 (OUTLIER) cc_final: 0.5504 (mt) REVERT: A 18 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7421 (mmm) REVERT: A 276 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6350 (mt-10) REVERT: A 305 CYS cc_start: 0.8002 (m) cc_final: 0.7025 (t) REVERT: A 321 THR cc_start: 0.9073 (t) cc_final: 0.8737 (m) REVERT: A 349 LYS cc_start: 0.7322 (ttmm) cc_final: 0.6630 (tppt) REVERT: B 50 THR cc_start: 0.8960 (t) cc_final: 0.8601 (m) REVERT: B 134 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7652 (ptt-90) REVERT: B 234 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.8958 (m-80) REVERT: B 251 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7053 (mtm-85) REVERT: B 325 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8300 (mmm) REVERT: H 30 SER cc_start: 0.7934 (t) cc_final: 0.7582 (p) REVERT: H 82 GLN cc_start: 0.7674 (tp40) cc_final: 0.7383 (tp40) REVERT: H 195 LEU cc_start: 0.7687 (mp) cc_final: 0.7380 (mt) REVERT: H 230 MET cc_start: 0.7850 (tpp) cc_final: 0.7407 (mmm) outliers start: 45 outliers final: 15 residues processed: 155 average time/residue: 0.9361 time to fit residues: 157.4484 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 : 1.001 ------------------------------------------------------------------------------- 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: 10.0000 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.188475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124961 restraints weight = 10196.775| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.87 r_work: 0.3281 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8999 Z= 0.204 Angle : 0.662 10.211 12202 Z= 0.342 Chirality : 0.045 0.226 1381 Planarity : 0.005 0.046 1538 Dihedral : 5.951 53.476 1244 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.87 % Rotamer: Outliers : 5.67 % Allowed : 23.96 % Favored : 70.37 % 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: 0.79 (0.26), residues: 1113 helix: 1.77 (0.28), residues: 373 sheet: 0.71 (0.32), residues: 288 loop : -0.62 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.021 0.002 PHE A 267 TYR 0.030 0.002 TYR H 235 ARG 0.004 0.001 ARG R 218 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 423) hydrogen bonds : angle 4.68088 ( 1182) SS BOND : bond 0.01805 ( 3) SS BOND : angle 2.76541 ( 6) covalent geometry : bond 0.00472 ( 8996) covalent geometry : angle 0.65931 (12196) *********************** 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 184 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 131 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: R 23 ASP cc_start: 0.6391 (OUTLIER) cc_final: 0.6001 (m-30) REVERT: R 25 PHE cc_start: 0.6710 (OUTLIER) cc_final: 0.6185 (t80) REVERT: R 84 MET cc_start: 0.4504 (tpt) cc_final: 0.4271 (tpt) REVERT: R 94 LYS cc_start: 0.4869 (OUTLIER) cc_final: 0.4651 (mtmm) REVERT: R 214 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8288 (t) REVERT: R 227 LYS cc_start: 0.6043 (mtmm) cc_final: 0.5433 (pttt) REVERT: R 258 LEU cc_start: 0.5886 (OUTLIER) cc_final: 0.5441 (mt) REVERT: A 22 ASN cc_start: 0.8433 (m-40) cc_final: 0.8145 (m-40) REVERT: A 197 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8471 (mttt) REVERT: A 276 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6761 (mt-10) REVERT: A 305 CYS cc_start: 0.8143 (m) cc_final: 0.7272 (t) REVERT: A 312 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7943 (mptm) REVERT: A 321 THR cc_start: 0.9102 (t) cc_final: 0.8769 (m) REVERT: A 349 LYS cc_start: 0.7744 (ttmm) cc_final: 0.6960 (tppt) REVERT: B 23 LYS cc_start: 0.7686 (tppt) cc_final: 0.7459 (tptt) REVERT: B 50 THR cc_start: 0.9048 (t) cc_final: 0.8841 (m) REVERT: B 120 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8054 (mm) REVERT: B 134 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8083 (ptt-90) REVERT: H 30 SER cc_start: 0.8250 (t) cc_final: 0.7950 (p) REVERT: H 82 GLN cc_start: 0.7863 (tp-100) cc_final: 0.7593 (tp40) REVERT: H 195 LEU cc_start: 0.7858 (mp) cc_final: 0.7454 (mt) REVERT: H 230 MET cc_start: 0.7916 (tpp) cc_final: 0.7652 (mmm) outliers start: 53 outliers final: 19 residues processed: 168 average time/residue: 1.0064 time to fit residues: 182.2331 Evaluate side-chains 141 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 225 VAL 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 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 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: 6.9990 chunk 91 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 ASN R 86 ASN R 112 GLN B 75 GLN B 175 GLN B 237 ASN B 259 GLN H 142 GLN H 171 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.187649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126276 restraints weight = 10051.963| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.81 r_work: 0.3241 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8999 Z= 0.223 Angle : 0.662 9.911 12202 Z= 0.344 Chirality : 0.045 0.219 1381 Planarity : 0.005 0.050 1538 Dihedral : 5.961 51.689 1244 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 6.10 % Allowed : 22.57 % 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: 0.64 (0.26), residues: 1113 helix: 1.69 (0.27), residues: 366 sheet: 0.43 (0.31), residues: 300 loop : -0.60 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS R 131 PHE 0.020 0.002 PHE A 267 TYR 0.031 0.002 TYR H 235 ARG 0.004 0.001 ARG R 218 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 423) hydrogen bonds : angle 4.63756 ( 1182) SS BOND : bond 0.02322 ( 3) SS BOND : angle 2.92490 ( 6) covalent geometry : bond 0.00525 ( 8996) covalent geometry : angle 0.65862 (12196) *********************** 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 176 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 119 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: R 94 LYS cc_start: 0.4954 (OUTLIER) cc_final: 0.4674 (mtmm) REVERT: R 112 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6909 (tt0) REVERT: R 162 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.5287 (pp) REVERT: R 214 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.8235 (t) REVERT: R 227 LYS cc_start: 0.6256 (mtmm) cc_final: 0.6023 (mtmt) REVERT: R 258 LEU cc_start: 0.5899 (OUTLIER) cc_final: 0.5458 (mt) REVERT: A 22 ASN cc_start: 0.8460 (m-40) cc_final: 0.8148 (m-40) REVERT: A 197 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8507 (mttt) REVERT: A 207 GLU cc_start: 0.7596 (tt0) cc_final: 0.7249 (mt-10) REVERT: A 276 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7078 (mt-10) REVERT: A 305 CYS cc_start: 0.8179 (m) cc_final: 0.7385 (t) REVERT: A 312 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7828 (mptm) REVERT: A 321 THR cc_start: 0.9111 (t) cc_final: 0.8840 (m) REVERT: A 349 LYS cc_start: 0.7806 (ttmm) cc_final: 0.7098 (tppt) REVERT: B 50 THR cc_start: 0.9072 (t) cc_final: 0.8830 (m) REVERT: B 120 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.7835 (mm) REVERT: B 134 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8123 (ptt-90) REVERT: B 234 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.8568 (m-80) REVERT: G 37 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8473 (mp) REVERT: H 30 SER cc_start: 0.8379 (t) cc_final: 0.8069 (p) REVERT: H 195 LEU cc_start: 0.7861 (mp) cc_final: 0.7458 (mt) outliers start: 57 outliers final: 18 residues processed: 160 average time/residue: 1.0325 time to fit residues: 177.6547 Evaluate side-chains 140 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 230 ILE 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 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 317 CYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 52 optimal weight: 0.0770 chunk 85 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 217 GLN B 237 ASN H 82 GLN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.190755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128140 restraints weight = 10003.666| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.93 r_work: 0.3308 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8999 Z= 0.127 Angle : 0.566 6.524 12202 Z= 0.295 Chirality : 0.042 0.198 1381 Planarity : 0.004 0.049 1538 Dihedral : 5.381 42.279 1244 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 5.35 % Allowed : 22.99 % Favored : 71.66 % 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: 0.66 (0.26), residues: 1113 helix: 1.71 (0.28), residues: 374 sheet: 0.50 (0.31), residues: 293 loop : -0.66 (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 H 35 PHE 0.012 0.001 PHE R 180 TYR 0.028 0.001 TYR H 235 ARG 0.006 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 423) hydrogen bonds : angle 4.36920 ( 1182) SS BOND : bond 0.00969 ( 3) SS BOND : angle 2.10908 ( 6) covalent geometry : bond 0.00286 ( 8996) covalent geometry : angle 0.56372 (12196) *********************** 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 175 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.5962 (mtm180) cc_final: 0.5616 (mtt90) REVERT: R 227 LYS cc_start: 0.6216 (mtmm) cc_final: 0.6005 (mtmt) REVERT: A 22 ASN cc_start: 0.8425 (m-40) cc_final: 0.8147 (m-40) REVERT: A 197 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8408 (mttt) REVERT: A 207 GLU cc_start: 0.7444 (tt0) cc_final: 0.7101 (mt-10) REVERT: A 276 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6970 (mt-10) REVERT: A 305 CYS cc_start: 0.8106 (m) cc_final: 0.7346 (t) REVERT: A 312 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7808 (mptm) REVERT: A 349 LYS cc_start: 0.7815 (ttmm) cc_final: 0.7094 (tppt) REVERT: B 50 THR cc_start: 0.9026 (t) cc_final: 0.8678 (m) REVERT: B 120 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7715 (mm) REVERT: B 134 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.8035 (ptt-90) REVERT: B 170 ASP cc_start: 0.8206 (t0) cc_final: 0.7988 (t70) REVERT: B 234 PHE cc_start: 0.9365 (OUTLIER) cc_final: 0.8571 (m-80) REVERT: H 30 SER cc_start: 0.8336 (t) cc_final: 0.8041 (p) REVERT: H 82 GLN cc_start: 0.7821 (tp-100) cc_final: 0.7588 (tp40) REVERT: H 139 VAL cc_start: 0.8226 (m) cc_final: 0.7919 (p) REVERT: H 195 LEU cc_start: 0.7793 (mp) cc_final: 0.7390 (mt) outliers start: 50 outliers final: 20 residues processed: 154 average time/residue: 1.1009 time to fit residues: 181.9466 Evaluate side-chains 140 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 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 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 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 45 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER 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: 1.9990 chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 ASN ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4143 r_free = 0.4143 target = 0.187216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123511 restraints weight = 9956.866| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.90 r_work: 0.3247 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8999 Z= 0.211 Angle : 0.634 9.698 12202 Z= 0.330 Chirality : 0.044 0.218 1381 Planarity : 0.005 0.054 1538 Dihedral : 5.805 46.862 1244 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 5.78 % Allowed : 22.99 % Favored : 71.23 % 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: 1.72 (0.27), residues: 365 sheet: 0.31 (0.31), residues: 301 loop : -0.55 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS R 131 PHE 0.021 0.002 PHE R 21 TYR 0.030 0.002 TYR H 235 ARG 0.005 0.001 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 423) hydrogen bonds : angle 4.54581 ( 1182) SS BOND : bond 0.01958 ( 3) SS BOND : angle 2.79373 ( 6) covalent geometry : bond 0.00499 ( 8996) covalent geometry : angle 0.63116 (12196) *********************** 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 172 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 118 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: R 64 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6356 (mp) REVERT: R 94 LYS cc_start: 0.4957 (OUTLIER) cc_final: 0.4717 (mtmm) REVERT: A 22 ASN cc_start: 0.8442 (m-40) cc_final: 0.8149 (m-40) REVERT: A 197 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8415 (mttt) REVERT: A 207 GLU cc_start: 0.7553 (tt0) cc_final: 0.7079 (mt-10) REVERT: A 276 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7106 (mt-10) REVERT: A 305 CYS cc_start: 0.8186 (m) cc_final: 0.7447 (t) REVERT: A 312 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7734 (mptm) REVERT: A 349 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7130 (tppt) REVERT: B 50 THR cc_start: 0.9069 (t) cc_final: 0.8849 (m) REVERT: B 134 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8148 (ptt-90) REVERT: B 234 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.8475 (m-80) REVERT: G 37 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8488 (mp) REVERT: H 30 SER cc_start: 0.8364 (t) cc_final: 0.8086 (p) REVERT: H 83 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8161 (ptm) REVERT: H 195 LEU cc_start: 0.7848 (mp) cc_final: 0.7466 (mt) outliers start: 54 outliers final: 21 residues processed: 156 average time/residue: 0.9458 time to fit residues: 159.5277 Evaluate side-chains 141 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 94 LYS Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 160 VAL 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 312 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 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 333 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 237 ASN H 82 GLN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.189080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.126168 restraints weight = 10079.337| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.90 r_work: 0.3279 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8999 Z= 0.149 Angle : 0.572 8.408 12202 Z= 0.299 Chirality : 0.042 0.193 1381 Planarity : 0.004 0.053 1538 Dihedral : 5.286 34.963 1244 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.86 % Favored : 95.96 % Rotamer: Outliers : 5.03 % Allowed : 24.39 % Favored : 70.59 % 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: 0.67 (0.26), residues: 1113 helix: 1.72 (0.27), residues: 367 sheet: 0.41 (0.31), residues: 298 loop : -0.54 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.019 0.001 PHE R 21 TYR 0.027 0.001 TYR H 235 ARG 0.006 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 423) hydrogen bonds : angle 4.39710 ( 1182) SS BOND : bond 0.01342 ( 3) SS BOND : angle 1.92915 ( 6) covalent geometry : bond 0.00343 ( 8996) covalent geometry : angle 0.57078 (12196) *********************** 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 164 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 117 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: R 64 ILE cc_start: 0.6634 (OUTLIER) cc_final: 0.6399 (mp) REVERT: R 189 HIS cc_start: 0.5880 (OUTLIER) cc_final: 0.5664 (p90) REVERT: R 285 MET cc_start: 0.6769 (ttp) cc_final: 0.6506 (ttp) REVERT: A 24 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7335 (ttm110) REVERT: A 197 LYS cc_start: 0.8724 (mtmt) cc_final: 0.8370 (mttt) REVERT: A 207 GLU cc_start: 0.7376 (tt0) cc_final: 0.6937 (mt-10) REVERT: A 305 CYS cc_start: 0.8154 (m) cc_final: 0.7594 (t) REVERT: A 312 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7723 (mptm) REVERT: A 314 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7173 (mttm) REVERT: A 349 LYS cc_start: 0.7870 (ttmm) cc_final: 0.7148 (tppt) REVERT: B 50 THR cc_start: 0.9042 (t) cc_final: 0.8714 (m) REVERT: B 134 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8082 (ptt-90) REVERT: B 234 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: G 37 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8482 (mp) REVERT: H 30 SER cc_start: 0.8357 (t) cc_final: 0.8078 (p) REVERT: H 142 GLN cc_start: 0.6085 (OUTLIER) cc_final: 0.5864 (mt0) REVERT: H 195 LEU cc_start: 0.7827 (mp) cc_final: 0.7430 (mt) outliers start: 47 outliers final: 22 residues processed: 150 average time/residue: 1.1628 time to fit residues: 188.0830 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 : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 189 HIS Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 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 G residue 21 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 142 GLN 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: 6.9990 chunk 36 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 H 82 GLN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.185938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123214 restraints weight = 10185.741| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.13 r_work: 0.3205 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 8999 Z= 0.236 Angle : 0.662 10.836 12202 Z= 0.344 Chirality : 0.045 0.222 1381 Planarity : 0.005 0.055 1538 Dihedral : 5.756 37.468 1244 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.15 % Rotamer: Outliers : 5.67 % Allowed : 24.28 % 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: 0.50 (0.26), residues: 1113 helix: 1.57 (0.27), residues: 366 sheet: 0.19 (0.30), residues: 302 loop : -0.52 (0.30), 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 131 PHE 0.016 0.002 PHE B 292 TYR 0.030 0.002 TYR H 235 ARG 0.004 0.001 ARG R 218 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 423) hydrogen bonds : angle 4.63416 ( 1182) SS BOND : bond 0.02160 ( 3) SS BOND : angle 2.95724 ( 6) covalent geometry : bond 0.00559 ( 8996) covalent geometry : angle 0.65911 (12196) *********************** 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 162 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 109 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7400 (ttm110) REVERT: A 197 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8437 (mttt) REVERT: A 207 GLU cc_start: 0.7536 (tt0) cc_final: 0.7088 (mt-10) REVERT: A 305 CYS cc_start: 0.8264 (m) cc_final: 0.7611 (t) REVERT: A 314 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7210 (mttm) REVERT: A 349 LYS cc_start: 0.7913 (ttmm) cc_final: 0.7172 (tppt) REVERT: B 50 THR cc_start: 0.9073 (t) cc_final: 0.8844 (m) REVERT: B 134 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8184 (ptt-90) REVERT: B 234 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: H 30 SER cc_start: 0.8372 (t) cc_final: 0.8108 (p) REVERT: H 195 LEU cc_start: 0.7843 (mp) cc_final: 0.7469 (mt) outliers start: 53 outliers final: 28 residues processed: 145 average time/residue: 1.0508 time to fit residues: 164.3137 Evaluate side-chains 143 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 160 VAL 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 225 VAL Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain 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 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: 9.9990 chunk 87 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.188655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.126649 restraints weight = 10078.781| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.06 r_work: 0.3249 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8999 Z= 0.146 Angle : 0.575 8.563 12202 Z= 0.300 Chirality : 0.042 0.187 1381 Planarity : 0.004 0.054 1538 Dihedral : 5.449 37.344 1244 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 4.17 % Allowed : 26.42 % Favored : 69.41 % 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 : -0.46 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.015 0.001 PHE R 21 TYR 0.027 0.001 TYR H 235 ARG 0.006 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 423) hydrogen bonds : angle 4.43578 ( 1182) SS BOND : bond 0.01321 ( 3) SS BOND : angle 1.92000 ( 6) covalent geometry : bond 0.00335 ( 8996) covalent geometry : angle 0.57402 (12196) *********************** 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 153 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: R 189 HIS cc_start: 0.6015 (OUTLIER) cc_final: 0.5783 (p90) REVERT: R 252 ILE cc_start: 0.7604 (tp) cc_final: 0.7057 (mt) REVERT: R 285 MET cc_start: 0.6779 (ttp) cc_final: 0.6465 (ttp) REVERT: A 24 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7378 (ttm110) REVERT: A 197 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8397 (mttt) REVERT: A 207 GLU cc_start: 0.7399 (tt0) cc_final: 0.6945 (mt-10) REVERT: A 305 CYS cc_start: 0.8243 (m) cc_final: 0.7611 (t) REVERT: A 314 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7233 (mttm) REVERT: A 349 LYS cc_start: 0.7925 (ttmm) cc_final: 0.7185 (tppt) REVERT: B 50 THR cc_start: 0.9050 (t) cc_final: 0.8731 (m) REVERT: B 134 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.8118 (ptt-90) REVERT: B 234 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.8216 (m-80) REVERT: H 30 SER cc_start: 0.8322 (t) cc_final: 0.8042 (p) REVERT: H 195 LEU cc_start: 0.7886 (mp) cc_final: 0.7511 (mt) outliers start: 39 outliers final: 21 residues processed: 143 average time/residue: 1.0400 time to fit residues: 160.0240 Evaluate side-chains 138 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 189 HIS 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 225 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 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 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 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: 0.3980 chunk 37 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 0.0010 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 112 GLN A 241 ASN A 294 ASN B 75 GLN B 175 GLN B 237 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.192094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130132 restraints weight = 10107.045| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.89 r_work: 0.3351 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8999 Z= 0.109 Angle : 0.532 7.989 12202 Z= 0.276 Chirality : 0.041 0.172 1381 Planarity : 0.004 0.056 1538 Dihedral : 5.038 33.840 1244 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 2.67 % Allowed : 27.81 % Favored : 69.52 % 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: 0.79 (0.26), residues: 1113 helix: 1.84 (0.27), residues: 367 sheet: 0.46 (0.31), residues: 287 loop : -0.48 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.002 0.000 HIS R 189 PHE 0.021 0.001 PHE R 82 TYR 0.022 0.001 TYR H 235 ARG 0.008 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 423) hydrogen bonds : angle 4.22470 ( 1182) SS BOND : bond 0.00756 ( 3) SS BOND : angle 1.32189 ( 6) covalent geometry : bond 0.00236 ( 8996) covalent geometry : angle 0.53097 (12196) ********************** 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 142 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.950 Fit side-chains REVERT: R 103 MET cc_start: 0.5335 (ttp) cc_final: 0.4923 (ttt) REVERT: R 189 HIS cc_start: 0.5870 (OUTLIER) cc_final: 0.5624 (p90) REVERT: R 285 MET cc_start: 0.6801 (ttp) cc_final: 0.6493 (ttp) REVERT: A 197 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8351 (mttt) REVERT: A 207 GLU cc_start: 0.7192 (tt0) cc_final: 0.6864 (mt-10) REVERT: A 305 CYS cc_start: 0.8229 (m) cc_final: 0.7602 (t) REVERT: A 314 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7204 (mttm) REVERT: A 349 LYS cc_start: 0.7780 (ttmm) cc_final: 0.7088 (tppt) REVERT: B 50 THR cc_start: 0.8929 (t) cc_final: 0.8601 (m) REVERT: B 134 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7940 (ptt90) REVERT: B 234 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8311 (m-80) REVERT: G 21 MET cc_start: 0.5290 (OUTLIER) cc_final: 0.4450 (mmp) REVERT: H 30 SER cc_start: 0.8311 (t) cc_final: 0.8003 (p) REVERT: H 195 LEU cc_start: 0.7848 (mp) cc_final: 0.7484 (mt) REVERT: H 230 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.8003 (mmm) outliers start: 25 outliers final: 11 residues processed: 133 average time/residue: 1.0973 time to fit residues: 156.8331 Evaluate side-chains 121 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 189 HIS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 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 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 0.0000 chunk 17 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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 141 ASN A 294 ASN B 142 HIS B 237 ASN H 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.191184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.128561 restraints weight = 10088.325| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.90 r_work: 0.3324 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8999 Z= 0.123 Angle : 0.550 7.587 12202 Z= 0.285 Chirality : 0.041 0.168 1381 Planarity : 0.004 0.056 1538 Dihedral : 5.080 33.786 1244 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 2.25 % Allowed : 28.34 % Favored : 69.41 % 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: 367 sheet: 0.58 (0.31), residues: 286 loop : -0.50 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 93 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.001 PHE R 21 TYR 0.024 0.001 TYR R 269 ARG 0.007 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 423) hydrogen bonds : angle 4.24502 ( 1182) SS BOND : bond 0.00993 ( 3) SS BOND : angle 1.57784 ( 6) covalent geometry : bond 0.00276 ( 8996) covalent geometry : angle 0.54853 (12196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8253.32 seconds wall clock time: 142 minutes 19.63 seconds (8539.63 seconds total)