Starting phenix.real_space_refine on Sat Dec 28 13:10:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hqm_34950/12_2024/8hqm_34950.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hqm_34950/12_2024/8hqm_34950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hqm_34950/12_2024/8hqm_34950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hqm_34950/12_2024/8hqm_34950.map" model { file = "/net/cci-nas-00/data/ceres_data/8hqm_34950/12_2024/8hqm_34950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hqm_34950/12_2024/8hqm_34950.cif" } resolution = 2.95 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= 0.005 sd= 0.040 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 64 5.16 5 C 5484 2.51 5 N 1461 2.21 5 O 1609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8618 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2245 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 291} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "H" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1768 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2440 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 6, 'TRANS': 300} Chain breaks: 1 Chain: "A" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1719 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 212} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'140': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.15, per 1000 atoms: 0.60 Number of scatterers: 8618 At special positions: 0 Unit cell: (104, 119.6, 130, 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 64 16.00 O 1609 8.00 N 1461 7.00 C 5484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 186 " 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: 2.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 15 sheets defined 37.3% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'C' and resid 10 through 21 removed outlier: 4.487A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.579A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'R' and resid 38 through 72 Proline residue: R 58 - end of helix removed outlier: 3.976A pdb=" N LEU R 72 " --> pdb=" O LEU R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 87 Processing helix chain 'R' and resid 94 through 102 removed outlier: 3.557A pdb=" N TRP R 98 " --> pdb=" O THR R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 145 Processing helix chain 'R' and resid 146 through 154 removed outlier: 3.914A pdb=" N ARG R 151 " --> pdb=" O ALA R 147 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 180 Proline residue: R 176 - end of helix Processing helix chain 'R' and resid 194 through 208 Processing helix chain 'R' and resid 208 through 228 Processing helix chain 'R' and resid 233 through 272 Proline residue: R 257 - end of helix Processing helix chain 'R' and resid 279 through 312 Proline residue: R 305 - end of helix Processing helix chain 'R' and resid 312 through 331 removed outlier: 3.701A pdb=" N ARG R 316 " --> pdb=" O THR R 312 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 346 removed outlier: 4.211A pdb=" N GLU R 346 " --> pdb=" O ARG R 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.752A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.647A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.557A pdb=" N TYR A 290 " --> pdb=" O TYR A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.623A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 50 removed outlier: 3.508A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.626A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.060A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.501A pdb=" N THR B 159 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 191 removed outlier: 3.820A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 234 removed outlier: 4.091A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY B 244 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 242 " --> pdb=" O CYS B 233 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.755A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.994A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N MET H 83 " --> pdb=" O ARG H 18 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.567A pdb=" N TYR H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG H 98 " --> pdb=" O PHE H 110 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.567A pdb=" N TYR H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR H 94 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 129 through 130 Processing sheet with id=AB4, first strand: chain 'H' and resid 134 through 136 removed outlier: 3.874A pdb=" N GLY H 213 " --> pdb=" O LEU H 233 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE H 177 " --> pdb=" O TRP H 164 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU H 166 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU H 175 " --> pdb=" O LEU H 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 143 through 145 removed outlier: 3.557A pdb=" N ILE H 145 " --> pdb=" O LEU H 202 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER H 192 " --> pdb=" O THR H 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 185 through 191 removed outlier: 5.990A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1188 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: 2.60 Time building geometry restraints manager: 2.83 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: 1394 1.31 - 1.44: 2438 1.44 - 1.57: 4869 1.57 - 1.69: 0 1.69 - 1.82: 89 Bond restraints: 8790 Sorted by residual: bond pdb=" N 140 R 401 " pdb=" C3 140 R 401 " ideal model delta sigma weight residual 1.337 1.450 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" N LYS A 314 " pdb=" CA LYS A 314 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.10e-02 8.26e+03 8.21e+00 bond pdb=" N LEU R 282 " pdb=" CA LEU R 282 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.22e+00 bond pdb=" N PHE R 141 " pdb=" CA PHE R 141 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.20e-02 6.94e+03 6.02e+00 bond pdb=" N LEU B 286 " pdb=" CA LEU B 286 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.22e-02 6.72e+03 5.33e+00 ... (remaining 8785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 11536 2.24 - 4.48: 295 4.48 - 6.72: 46 6.72 - 8.96: 16 8.96 - 11.20: 4 Bond angle restraints: 11897 Sorted by residual: angle pdb=" C GLU R 88 " pdb=" N LEU R 89 " pdb=" CA LEU R 89 " ideal model delta sigma weight residual 121.54 130.10 -8.56 1.91e+00 2.74e-01 2.01e+01 angle pdb=" N VAL R 57 " pdb=" CA VAL R 57 " pdb=" C VAL R 57 " ideal model delta sigma weight residual 108.88 117.77 -8.89 2.16e+00 2.14e-01 1.70e+01 angle pdb=" C TYR H 178 " pdb=" N ARG H 179 " pdb=" CA ARG H 179 " ideal model delta sigma weight residual 122.46 127.80 -5.34 1.41e+00 5.03e-01 1.43e+01 angle pdb=" CB MET R 192 " pdb=" CG MET R 192 " pdb=" SD MET R 192 " ideal model delta sigma weight residual 112.70 123.90 -11.20 3.00e+00 1.11e-01 1.39e+01 angle pdb=" C CYS H 217 " pdb=" N MET H 218 " pdb=" CA MET H 218 " ideal model delta sigma weight residual 121.54 128.43 -6.89 1.91e+00 2.74e-01 1.30e+01 ... (remaining 11892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 4539 17.59 - 35.17: 512 35.17 - 52.76: 129 52.76 - 70.35: 18 70.35 - 87.93: 8 Dihedral angle restraints: 5206 sinusoidal: 2004 harmonic: 3202 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 6.39 86.61 1 1.00e+01 1.00e-02 9.03e+01 dihedral pdb=" CB CYS R 115 " pdb=" SG CYS R 115 " pdb=" SG CYS R 186 " pdb=" CB CYS R 186 " ideal model delta sinusoidal sigma weight residual 93.00 141.58 -48.58 1 1.00e+01 1.00e-02 3.25e+01 dihedral pdb=" CA ASP B 205 " pdb=" C ASP B 205 " pdb=" N ALA B 206 " pdb=" CA ALA B 206 " ideal model delta harmonic sigma weight residual -180.00 -157.68 -22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 5203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 989 0.052 - 0.103: 283 0.103 - 0.155: 77 0.155 - 0.207: 6 0.207 - 0.258: 3 Chirality restraints: 1358 Sorted by residual: chirality pdb=" CB ILE R 245 " pdb=" CA ILE R 245 " pdb=" CG1 ILE R 245 " pdb=" CG2 ILE R 245 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE R 136 " pdb=" CA ILE R 136 " pdb=" CG1 ILE R 136 " pdb=" CG2 ILE R 136 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CG LEU H 4 " pdb=" CB LEU H 4 " pdb=" CD1 LEU H 4 " pdb=" CD2 LEU H 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1355 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 314 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C LYS A 314 " 0.038 2.00e-02 2.50e+03 pdb=" O LYS A 314 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP A 315 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 225 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C LEU H 225 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU H 225 " 0.014 2.00e-02 2.50e+03 pdb=" N THR H 226 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 252 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C LEU R 252 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU R 252 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL R 253 " -0.012 2.00e-02 2.50e+03 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1663 2.77 - 3.30: 8474 3.30 - 3.84: 15030 3.84 - 4.37: 16831 4.37 - 4.90: 28471 Nonbonded interactions: 70469 Sorted by model distance: nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 74 " model vdw 2.241 3.040 nonbonded pdb=" OG SER A 228 " pdb=" O LYS A 270 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.258 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.262 3.040 nonbonded pdb=" O VAL R 142 " pdb=" OG SER R 150 " model vdw 2.276 3.040 ... (remaining 70464 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.180 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:17.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.005 0.113 8790 Z= 0.327 Angle : 0.899 11.196 11897 Z= 0.476 Chirality : 0.052 0.258 1358 Planarity : 0.006 0.044 1495 Dihedral : 16.059 87.934 3133 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.43 % Allowed : 20.71 % Favored : 78.86 % 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: -1.84 (0.24), residues: 1084 helix: -0.55 (0.25), residues: 383 sheet: -1.26 (0.31), residues: 265 loop : -1.65 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 111 HIS 0.006 0.002 HIS R 242 PHE 0.022 0.003 PHE A 189 TYR 0.021 0.002 TYR R 49 ARG 0.006 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 1.139 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 48 average time/residue: 1.6761 time to fit residues: 85.4395 Evaluate side-chains 42 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 282 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN B 293 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN R 70 GLN A 244 HIS A 346 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8790 Z= 0.289 Angle : 0.596 7.008 11897 Z= 0.316 Chirality : 0.041 0.149 1358 Planarity : 0.004 0.043 1495 Dihedral : 5.989 57.444 1215 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.72 % Allowed : 21.35 % Favored : 76.93 % 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: -1.16 (0.25), residues: 1084 helix: 0.31 (0.26), residues: 396 sheet: -1.13 (0.31), residues: 269 loop : -1.44 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS H 35 PHE 0.011 0.001 PHE H 227 TYR 0.014 0.001 TYR R 49 ARG 0.004 0.000 ARG R 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 1.041 Fit side-chains REVERT: H 232 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8624 (mttt) outliers start: 16 outliers final: 2 residues processed: 56 average time/residue: 1.5526 time to fit residues: 93.2024 Evaluate side-chains 42 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 212 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 33 optimal weight: 0.1980 chunk 78 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8790 Z= 0.158 Angle : 0.543 7.329 11897 Z= 0.283 Chirality : 0.040 0.138 1358 Planarity : 0.003 0.041 1495 Dihedral : 5.381 47.709 1213 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.25 % Allowed : 22.10 % Favored : 75.64 % 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: -0.87 (0.25), residues: 1084 helix: 0.71 (0.26), residues: 394 sheet: -0.98 (0.31), residues: 266 loop : -1.45 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 111 HIS 0.003 0.000 HIS H 35 PHE 0.011 0.001 PHE B 253 TYR 0.013 0.001 TYR H 178 ARG 0.004 0.000 ARG R 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 1.166 Fit side-chains REVERT: H 232 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8550 (mttt) outliers start: 21 outliers final: 5 residues processed: 61 average time/residue: 1.3056 time to fit residues: 85.4403 Evaluate side-chains 46 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 212 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 8790 Z= 0.238 Angle : 0.539 7.273 11897 Z= 0.283 Chirality : 0.040 0.154 1358 Planarity : 0.003 0.041 1495 Dihedral : 5.249 41.309 1213 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.79 % Allowed : 22.42 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1084 helix: 0.84 (0.26), residues: 396 sheet: -1.01 (0.31), residues: 270 loop : -1.34 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE B 253 TYR 0.012 0.001 TYR R 49 ARG 0.002 0.000 ARG R 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 1.088 Fit side-chains REVERT: H 93 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7273 (tpp) REVERT: H 218 MET cc_start: 0.7724 (ttp) cc_final: 0.7509 (ttm) REVERT: H 232 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8570 (mttt) outliers start: 26 outliers final: 10 residues processed: 63 average time/residue: 1.1754 time to fit residues: 80.0573 Evaluate side-chains 52 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8790 Z= 0.165 Angle : 0.533 8.096 11897 Z= 0.274 Chirality : 0.039 0.134 1358 Planarity : 0.003 0.041 1495 Dihedral : 5.048 39.373 1213 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.90 % Allowed : 23.28 % Favored : 73.82 % 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 (0.25), residues: 1084 helix: 0.99 (0.26), residues: 396 sheet: -0.91 (0.31), residues: 264 loop : -1.36 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.002 0.000 HIS H 35 PHE 0.010 0.001 PHE B 253 TYR 0.012 0.001 TYR H 178 ARG 0.003 0.000 ARG R 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 42 time to evaluate : 0.994 Fit side-chains REVERT: H 93 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7367 (tpp) REVERT: H 218 MET cc_start: 0.7745 (ttp) cc_final: 0.7470 (ttm) REVERT: H 232 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8526 (mttt) outliers start: 27 outliers final: 8 residues processed: 66 average time/residue: 1.1783 time to fit residues: 84.2538 Evaluate side-chains 51 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 212 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 8.9990 chunk 94 optimal weight: 0.0050 chunk 20 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 104 optimal weight: 0.0870 chunk 86 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 30.0000 overall best weight: 3.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8790 Z= 0.204 Angle : 0.538 8.346 11897 Z= 0.277 Chirality : 0.040 0.136 1358 Planarity : 0.003 0.041 1495 Dihedral : 5.006 39.785 1213 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.47 % Allowed : 23.50 % Favored : 74.03 % 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: -0.60 (0.25), residues: 1084 helix: 1.00 (0.26), residues: 397 sheet: -0.95 (0.31), residues: 270 loop : -1.31 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 111 HIS 0.003 0.000 HIS H 35 PHE 0.013 0.001 PHE H 80 TYR 0.013 0.001 TYR R 49 ARG 0.003 0.000 ARG R 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 1.050 Fit side-chains REVERT: H 93 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7309 (tpp) REVERT: H 218 MET cc_start: 0.7718 (ttp) cc_final: 0.7412 (ttm) REVERT: H 232 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8537 (mttt) outliers start: 23 outliers final: 12 residues processed: 60 average time/residue: 1.2165 time to fit residues: 78.7887 Evaluate side-chains 55 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 212 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8790 Z= 0.213 Angle : 0.544 9.157 11897 Z= 0.279 Chirality : 0.040 0.135 1358 Planarity : 0.003 0.041 1495 Dihedral : 4.987 40.317 1213 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.22 % Allowed : 22.32 % Favored : 74.46 % 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: -0.56 (0.25), residues: 1084 helix: 1.05 (0.26), residues: 397 sheet: -0.86 (0.31), residues: 262 loop : -1.35 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 111 HIS 0.003 0.000 HIS H 35 PHE 0.013 0.001 PHE H 80 TYR 0.012 0.001 TYR R 49 ARG 0.003 0.000 ARG R 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 41 time to evaluate : 1.048 Fit side-chains REVERT: H 218 MET cc_start: 0.7641 (ttp) cc_final: 0.7292 (ttm) REVERT: H 232 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8550 (mttt) outliers start: 30 outliers final: 13 residues processed: 68 average time/residue: 1.2395 time to fit residues: 91.0011 Evaluate side-chains 55 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 282 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8790 Z= 0.255 Angle : 0.563 10.009 11897 Z= 0.288 Chirality : 0.040 0.185 1358 Planarity : 0.003 0.041 1495 Dihedral : 5.053 41.802 1213 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.04 % Allowed : 23.28 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1084 helix: 1.02 (0.26), residues: 394 sheet: -0.94 (0.31), residues: 268 loop : -1.32 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 111 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.001 PHE H 80 TYR 0.013 0.001 TYR R 49 ARG 0.003 0.000 ARG R 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: H 218 MET cc_start: 0.7780 (ttp) cc_final: 0.7459 (ttm) REVERT: H 232 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8576 (mttt) outliers start: 19 outliers final: 14 residues processed: 58 average time/residue: 1.3091 time to fit residues: 81.7213 Evaluate side-chains 57 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 282 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 76 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8790 Z= 0.204 Angle : 0.562 12.033 11897 Z= 0.284 Chirality : 0.040 0.153 1358 Planarity : 0.003 0.042 1495 Dihedral : 4.999 41.533 1213 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.72 % Allowed : 23.82 % Favored : 74.46 % 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: -0.58 (0.25), residues: 1084 helix: 1.04 (0.26), residues: 397 sheet: -0.89 (0.31), residues: 266 loop : -1.36 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.002 0.000 HIS H 35 PHE 0.012 0.001 PHE H 80 TYR 0.012 0.001 TYR R 49 ARG 0.003 0.000 ARG R 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: H 218 MET cc_start: 0.7752 (ttp) cc_final: 0.7498 (ttm) REVERT: H 232 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8543 (mttt) REVERT: R 331 MET cc_start: 0.9161 (mpp) cc_final: 0.8423 (mpp) outliers start: 16 outliers final: 10 residues processed: 56 average time/residue: 1.3365 time to fit residues: 80.4016 Evaluate side-chains 53 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 0.0000 chunk 68 optimal weight: 10.0000 overall best weight: 2.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8790 Z= 0.181 Angle : 0.557 12.461 11897 Z= 0.281 Chirality : 0.040 0.132 1358 Planarity : 0.003 0.042 1495 Dihedral : 4.926 40.437 1213 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.50 % Allowed : 24.14 % Favored : 74.36 % 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: -0.53 (0.25), residues: 1084 helix: 1.11 (0.26), residues: 397 sheet: -0.76 (0.32), residues: 255 loop : -1.43 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 108 HIS 0.002 0.000 HIS H 35 PHE 0.012 0.001 PHE H 80 TYR 0.012 0.001 TYR R 49 ARG 0.003 0.000 ARG R 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.913 Fit side-chains REVERT: H 218 MET cc_start: 0.7704 (ttp) cc_final: 0.7424 (ttm) REVERT: H 232 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8573 (mttt) REVERT: R 331 MET cc_start: 0.9135 (mpp) cc_final: 0.8430 (mpp) outliers start: 14 outliers final: 11 residues processed: 55 average time/residue: 1.3258 time to fit residues: 78.4450 Evaluate side-chains 53 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2315 r_free = 0.2315 target = 0.028952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2121 r_free = 0.2121 target = 0.024733 restraints weight = 89055.481| |-----------------------------------------------------------------------------| r_work (start): 0.2106 rms_B_bonded: 3.03 r_work: 0.2049 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8790 Z= 0.254 Angle : 0.577 12.660 11897 Z= 0.292 Chirality : 0.040 0.135 1358 Planarity : 0.003 0.042 1495 Dihedral : 5.037 42.396 1213 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.39 % Allowed : 24.25 % Favored : 74.36 % 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: -0.58 (0.25), residues: 1084 helix: 1.07 (0.26), residues: 394 sheet: -0.90 (0.31), residues: 263 loop : -1.37 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE H 80 TYR 0.013 0.001 TYR R 49 ARG 0.003 0.000 ARG R 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.19 seconds wall clock time: 42 minutes 3.38 seconds (2523.38 seconds total)