Starting phenix.real_space_refine on Fri Oct 23 01:01:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wnd_66114/10_2026/9wnd_66114_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wnd_66114/10_2026/9wnd_66114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wnd_66114/10_2026/9wnd_66114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wnd_66114/10_2026/9wnd_66114.map" model { file = "/net/cci-nas-00/data/ceres_data/9wnd_66114/10_2026/9wnd_66114_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wnd_66114/10_2026/9wnd_66114_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 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 33 5.16 5 C 4670 2.51 5 N 1246 2.21 5 O 1281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7230 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1734 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain breaks: 2 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 6, 'TYR:plan': 2, 'PHE:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 4, 'HIS:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "B" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1701 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 7, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 582 Unresolved non-hydrogen dihedrals: 376 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 19, 'GLU:plan': 18, 'ASN:plan1': 6, 'ASP:plan': 20, 'PHE:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 289 Chain: "C" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2223 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASP:plan': 23, 'GLN:plan1': 8, 'ARG:plan': 16, 'GLU:plan': 8, 'ASN:plan1': 7, 'HIS:plan': 1, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 232 Chain: "D" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1557 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 6, 'GLU:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 1, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'91Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.14, per 1000 atoms: 0.16 Number of scatterers: 7230 At special positions: 0 Unit cell: (120.12, 91.91, 118.3, 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 33 16.00 O 1281 8.00 N 1246 7.00 C 4670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 252.7 milliseconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 39.9% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 81 through 102 removed outlier: 4.027A pdb=" N ASN A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 127 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 144 through 179 Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 188 through 208 Processing helix chain 'A' and resid 208 through 216 removed outlier: 3.982A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.666A pdb=" N VAL A 221 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 removed outlier: 3.969A pdb=" N SER A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 263 Processing helix chain 'A' and resid 317 through 348 removed outlier: 3.815A pdb=" N MET A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 355 through 382 removed outlier: 4.243A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'B' and resid 10 through 25 Processing helix chain 'B' and resid 29 through 44 Processing helix chain 'B' and resid 45 through 48 removed outlier: 3.990A pdb=" N ASP B 48 " --> pdb=" O ALA B 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 48' Processing helix chain 'B' and resid 86 through 111 Processing helix chain 'B' and resid 173 through 178 removed outlier: 4.209A pdb=" N GLN B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 211 through 215 removed outlier: 4.289A pdb=" N ARG B 215 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 236 Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.576A pdb=" N TYR B 243 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 263 through 282 removed outlier: 3.869A pdb=" N ILE B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 323 removed outlier: 3.529A pdb=" N ARG B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 26 removed outlier: 3.569A pdb=" N ALA C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 36 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.823A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.505A pdb=" N ASP D 90 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'B' and resid 150 through 156 removed outlier: 3.560A pdb=" N PHE B 150 " --> pdb=" O ASP B 165 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ALA B 185 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ARG B 115 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE B 187 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 117 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 189 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE B 186 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE B 222 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE B 188 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASN B 224 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL B 190 " --> pdb=" O ASN B 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.546A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 331 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.587A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.132A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.794A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 189 through 192 removed outlier: 3.893A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY C 202 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.333A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 276 through 277 Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.553A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 155 through 160 Processing sheet with id=AB3, first strand: chain 'D' and resid 194 through 195 removed outlier: 5.637A pdb=" N LEU D 187 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR D 238 " --> pdb=" O GLN D 231 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 194 through 195 removed outlier: 5.637A pdb=" N LEU D 187 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1254 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: 0.61 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2183 1.34 - 1.45: 1288 1.45 - 1.57: 3877 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 7392 Sorted by residual: bond pdb=" CA THR B 314 " pdb=" C THR B 314 " ideal model delta sigma weight residual 1.524 1.462 0.061 1.32e-02 5.74e+03 2.16e+01 bond pdb=" N VAL A 127 " pdb=" CA VAL A 127 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.77e+01 bond pdb=" C GLU C 226 " pdb=" N SER C 227 " ideal model delta sigma weight residual 1.328 1.377 -0.048 1.23e-02 6.61e+03 1.55e+01 bond pdb=" C TRP C 99 " pdb=" N VAL C 100 " ideal model delta sigma weight residual 1.334 1.379 -0.045 1.24e-02 6.50e+03 1.34e+01 bond pdb=" C MET C 325 " pdb=" N ALA C 326 " ideal model delta sigma weight residual 1.331 1.376 -0.045 1.23e-02 6.61e+03 1.34e+01 ... (remaining 7387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 9744 1.73 - 3.46: 372 3.46 - 5.19: 57 5.19 - 6.92: 9 6.92 - 8.66: 1 Bond angle restraints: 10183 Sorted by residual: angle pdb=" C LEU A 126 " pdb=" N VAL A 127 " pdb=" CA VAL A 127 " ideal model delta sigma weight residual 123.16 118.10 5.06 1.06e+00 8.90e-01 2.28e+01 angle pdb=" CA ALA A 90 " pdb=" C ALA A 90 " pdb=" O ALA A 90 " ideal model delta sigma weight residual 120.90 116.16 4.74 1.03e+00 9.43e-01 2.12e+01 angle pdb=" N ILE B 315 " pdb=" CA ILE B 315 " pdb=" C ILE B 315 " ideal model delta sigma weight residual 111.44 105.50 5.94 1.34e+00 5.57e-01 1.96e+01 angle pdb=" C PHE A 244 " pdb=" CA PHE A 244 " pdb=" CB PHE A 244 " ideal model delta sigma weight residual 110.90 117.58 -6.68 1.58e+00 4.01e-01 1.79e+01 angle pdb=" N THR B 314 " pdb=" CA THR B 314 " pdb=" C THR B 314 " ideal model delta sigma weight residual 111.69 106.56 5.13 1.23e+00 6.61e-01 1.74e+01 ... (remaining 10178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 3841 16.07 - 32.13: 245 32.13 - 48.20: 76 48.20 - 64.26: 18 64.26 - 80.33: 4 Dihedral angle restraints: 4184 sinusoidal: 1017 harmonic: 3167 Sorted by residual: dihedral pdb=" CB CYS A 148 " pdb=" SG CYS A 148 " pdb=" SG CYS A 227 " pdb=" CB CYS A 227 " ideal model delta sinusoidal sigma weight residual -86.00 -142.85 56.85 1 1.00e+01 1.00e-02 4.35e+01 dihedral pdb=" CA TRP C 82 " pdb=" C TRP C 82 " pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta harmonic sigma weight residual 180.00 161.92 18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA CYS D 96 " pdb=" C CYS D 96 " pdb=" N VAL D 97 " pdb=" CA VAL D 97 " ideal model delta harmonic sigma weight residual -180.00 -163.85 -16.15 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 4181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 977 0.052 - 0.104: 214 0.104 - 0.156: 36 0.156 - 0.208: 12 0.208 - 0.260: 4 Chirality restraints: 1243 Sorted by residual: chirality pdb=" CB VAL B 311 " pdb=" CA VAL B 311 " pdb=" CG1 VAL B 311 " pdb=" CG2 VAL B 311 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA VAL A 84 " pdb=" N VAL A 84 " pdb=" C VAL A 84 " pdb=" CB VAL A 84 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ILE D 216 " pdb=" N ILE D 216 " pdb=" C ILE D 216 " pdb=" CB ILE D 216 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1240 not shown) Planarity restraints: 1308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 224 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" C VAL D 224 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL D 224 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY D 225 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 135 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.88e+00 pdb=" C ILE A 135 " 0.042 2.00e-02 2.50e+03 pdb=" O ILE A 135 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU A 136 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 142 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C GLN D 142 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN D 142 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA D 143 " 0.014 2.00e-02 2.50e+03 ... (remaining 1305 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 2828 2.88 - 3.39: 6832 3.39 - 3.89: 11966 3.89 - 4.40: 13143 4.40 - 4.90: 22743 Nonbonded interactions: 57512 Sorted by model distance: nonbonded pdb=" O VAL B 311 " pdb=" OG1 THR B 314 " model vdw 2.375 3.040 nonbonded pdb=" N THR B 251 " pdb=" O THR B 251 " model vdw 2.578 2.496 nonbonded pdb=" O ASN C 155 " pdb=" N ILE C 171 " model vdw 2.590 3.120 nonbonded pdb=" N TYR D 102 " pdb=" O TYR D 102 " model vdw 2.591 2.496 nonbonded pdb=" N THR B 314 " pdb=" N ILE B 315 " model vdw 2.593 2.560 ... (remaining 57507 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: 0.540 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.890 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 0.061 7395 Z= 0.361 Angle : 0.736 8.656 10189 Z= 0.480 Chirality : 0.048 0.260 1243 Planarity : 0.005 0.063 1308 Dihedral : 13.144 80.327 2127 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.18 % Allowed : 15.19 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.26), residues: 1076 helix: 1.46 (0.27), residues: 384 sheet: -1.18 (0.31), residues: 250 loop : -0.94 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 150 TYR 0.010 0.001 TYR C 289 PHE 0.019 0.002 PHE B 272 TRP 0.028 0.002 TRP A 336 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.36 ( 7392) covalent geometry : angle 0.73531 / 0.48 (10183) SS BOND : bond 0.00164 / 0.08 ( 3) SS BOND : angle 1.36163 / 0.78 ( 6) hydrogen bonds : bond 0.13477 / 9.97 ( 432) hydrogen bonds : angle 6.27540 / 4.62 ( 1254) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 162 time to evaluate : 0.129 Fit side-chains REVERT: A 330 PHE cc_start: 0.7664 (m-10) cc_final: 0.7356 (m-80) REVERT: A 333 VAL cc_start: 0.8375 (t) cc_final: 0.7947 (m) REVERT: A 361 LEU cc_start: 0.7514 (mt) cc_final: 0.7300 (mt) REVERT: A 380 TYR cc_start: 0.8102 (m-80) cc_final: 0.7828 (m-80) outliers start: 6 outliers final: 3 residues processed: 166 average time/residue: 0.0374 time to fit residues: 8.9589 Evaluate side-chains 159 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain C residue 211 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 106, 38] chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.0070 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.0670 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 0.0010 overall best weight: 0.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 HIS B 303 ASN C 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.133130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.119474 restraints weight = 12168.240| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.94 r_work: 0.3541 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7395 Z= 0.101 Angle : 0.478 5.875 10189 Z= 0.254 Chirality : 0.040 0.133 1243 Planarity : 0.003 0.029 1308 Dihedral : 4.830 51.435 1150 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.55 % Allowed : 17.75 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.26), residues: 1076 helix: 2.12 (0.27), residues: 388 sheet: -1.17 (0.31), residues: 264 loop : -0.72 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 274 TYR 0.014 0.001 TYR D 190 PHE 0.014 0.001 PHE A 243 TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 7392) covalent geometry : angle 0.47765 / 0.25 (10183) SS BOND : bond 0.00118 / 0.06 ( 3) SS BOND : angle 0.79251 / 0.46 ( 6) hydrogen bonds : bond 0.03213 / 2.29 ( 432) hydrogen bonds : angle 4.78940 / 3.59 ( 1254) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.135 Fit side-chains REVERT: A 330 PHE cc_start: 0.7643 (m-10) cc_final: 0.7412 (m-80) REVERT: A 380 TYR cc_start: 0.8230 (m-80) cc_final: 0.7940 (m-80) REVERT: A 387 TYR cc_start: 0.7588 (m-80) cc_final: 0.7132 (m-10) REVERT: D 239 PHE cc_start: 0.7457 (m-80) cc_final: 0.7134 (m-80) outliers start: 18 outliers final: 12 residues processed: 167 average time/residue: 0.0443 time to fit residues: 10.6383 Evaluate side-chains 162 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain D residue 167 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [61, 34, 54, 28, 97, 101, 5, 4, 93, 94, 41] chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 5 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.131374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.117648 restraints weight = 12037.433| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.93 r_work: 0.3516 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7395 Z= 0.131 Angle : 0.491 6.053 10189 Z= 0.261 Chirality : 0.040 0.128 1243 Planarity : 0.003 0.033 1308 Dihedral : 4.647 48.813 1148 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.35 % Allowed : 20.91 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.26), residues: 1076 helix: 2.36 (0.27), residues: 385 sheet: -1.08 (0.31), residues: 261 loop : -0.70 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 191 TYR 0.010 0.001 TYR C 289 PHE 0.016 0.002 PHE A 244 TRP 0.012 0.002 TRP C 211 HIS 0.002 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 7392) covalent geometry : angle 0.49075 / 0.26 (10183) SS BOND : bond 0.00184 / 0.09 ( 3) SS BOND : angle 0.82536 / 0.48 ( 6) hydrogen bonds : bond 0.03346 / 2.40 ( 432) hydrogen bonds : angle 4.59495 / 3.47 ( 1254) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.182 Fit side-chains REVERT: A 380 TYR cc_start: 0.8286 (m-80) cc_final: 0.8041 (m-80) REVERT: D 239 PHE cc_start: 0.7583 (m-80) cc_final: 0.7180 (m-80) outliers start: 17 outliers final: 15 residues processed: 152 average time/residue: 0.0701 time to fit residues: 14.9139 Evaluate side-chains 161 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain D residue 167 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [54, 34, 46, 76, 55, 12, 92, 20, 44, 77, 53] chunk 54 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 0.0970 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 303 ASN B 324 ASN C 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.128004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.114369 restraints weight = 12187.343| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.92 r_work: 0.3469 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7395 Z= 0.245 Angle : 0.578 8.095 10189 Z= 0.313 Chirality : 0.043 0.153 1243 Planarity : 0.004 0.034 1308 Dihedral : 5.364 52.071 1148 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.72 % Allowed : 19.53 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.26), residues: 1076 helix: 2.03 (0.27), residues: 385 sheet: -1.24 (0.30), residues: 261 loop : -0.95 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 191 TYR 0.023 0.002 TYR C 289 PHE 0.021 0.002 PHE C 241 TRP 0.016 0.002 TRP C 169 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.24 ( 7392) covalent geometry : angle 0.57764 / 0.31 (10183) SS BOND : bond 0.00287 / 0.15 ( 3) SS BOND : angle 0.91963 / 0.52 ( 6) hydrogen bonds : bond 0.04097 / 2.94 ( 432) hydrogen bonds : angle 4.97762 / 3.77 ( 1254) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.248 Fit side-chains REVERT: C 87 THR cc_start: 0.8222 (m) cc_final: 0.7995 (m) REVERT: C 163 ASP cc_start: 0.7254 (p0) cc_final: 0.7017 (p0) REVERT: C 325 MET cc_start: 0.7890 (mmm) cc_final: 0.7676 (mmt) REVERT: D 239 PHE cc_start: 0.7736 (m-80) cc_final: 0.7409 (m-80) outliers start: 29 outliers final: 19 residues processed: 164 average time/residue: 0.0667 time to fit residues: 15.5094 Evaluate side-chains 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 167 HIS Chi-restraints excluded: chain D residue 172 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [48, 79, 20, 24, 34, 35, 94, 21, 100, 29, 42] chunk 48 optimal weight: 1.9990 chunk 79 optimal weight: 0.0050 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.130477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116913 restraints weight = 12115.435| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.92 r_work: 0.3507 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7395 Z= 0.133 Angle : 0.491 6.936 10189 Z= 0.264 Chirality : 0.040 0.133 1243 Planarity : 0.004 0.036 1308 Dihedral : 4.730 52.033 1146 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.73 % Allowed : 21.50 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.27), residues: 1076 helix: 2.29 (0.27), residues: 387 sheet: -1.20 (0.30), residues: 263 loop : -0.80 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 191 TYR 0.013 0.001 TYR A 387 PHE 0.019 0.002 PHE B 308 TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7392) covalent geometry : angle 0.49119 / 0.26 (10183) SS BOND : bond 0.00249 / 0.12 ( 3) SS BOND : angle 0.52294 / 0.29 ( 6) hydrogen bonds : bond 0.03323 / 2.37 ( 432) hydrogen bonds : angle 4.63958 / 3.53 ( 1254) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.252 Fit side-chains REVERT: A 87 LEU cc_start: 0.7481 (mt) cc_final: 0.7186 (tp) REVERT: C 325 MET cc_start: 0.7877 (mmm) cc_final: 0.7671 (mmt) REVERT: D 239 PHE cc_start: 0.7625 (m-80) cc_final: 0.7256 (m-80) outliers start: 24 outliers final: 15 residues processed: 161 average time/residue: 0.0707 time to fit residues: 16.0095 Evaluate side-chains 165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain D residue 167 HIS Chi-restraints excluded: chain D residue 172 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [44, 81, 106, 71, 45, 36, 93, 48, 67, 37, 49] chunk 44 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 106 optimal weight: 0.2980 chunk 71 optimal weight: 0.0470 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 93 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.118662 restraints weight = 12180.209| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.93 r_work: 0.3531 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7395 Z= 0.105 Angle : 0.482 6.942 10189 Z= 0.254 Chirality : 0.040 0.136 1243 Planarity : 0.003 0.036 1308 Dihedral : 4.468 51.103 1146 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.94 % Allowed : 23.67 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 1076 helix: 2.53 (0.27), residues: 388 sheet: -1.14 (0.31), residues: 263 loop : -0.74 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 191 TYR 0.015 0.001 TYR A 387 PHE 0.010 0.001 PHE B 308 TRP 0.017 0.001 TRP C 82 HIS 0.001 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 7392) covalent geometry : angle 0.48204 / 0.25 (10183) SS BOND : bond 0.00219 / 0.11 ( 3) SS BOND : angle 0.41311 / 0.23 ( 6) hydrogen bonds : bond 0.03050 / 2.16 ( 432) hydrogen bonds : angle 4.41717 / 3.37 ( 1254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.244 Fit side-chains REVERT: A 87 LEU cc_start: 0.7520 (mt) cc_final: 0.7301 (tp) REVERT: C 79 LEU cc_start: 0.8343 (tp) cc_final: 0.8048 (tt) REVERT: C 163 ASP cc_start: 0.7171 (p0) cc_final: 0.6932 (p0) REVERT: D 239 PHE cc_start: 0.7591 (m-80) cc_final: 0.7175 (m-80) outliers start: 20 outliers final: 16 residues processed: 154 average time/residue: 0.0690 time to fit residues: 15.0375 Evaluate side-chains 160 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain D residue 167 HIS Chi-restraints excluded: chain D residue 172 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [17, 52, 88, 2, 16, 91, 92, 19, 15, 31, 82] chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 ASN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.130355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.116713 restraints weight = 12201.924| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.92 r_work: 0.3505 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7395 Z= 0.153 Angle : 0.507 6.971 10189 Z= 0.270 Chirality : 0.041 0.145 1243 Planarity : 0.004 0.033 1308 Dihedral : 4.735 52.269 1146 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.54 % Allowed : 23.08 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.27), residues: 1076 helix: 2.44 (0.27), residues: 388 sheet: -1.17 (0.30), residues: 263 loop : -0.80 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 274 TYR 0.017 0.002 TYR A 387 PHE 0.025 0.002 PHE B 308 TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 7392) covalent geometry : angle 0.50684 / 0.27 (10183) SS BOND : bond 0.00206 / 0.10 ( 3) SS BOND : angle 0.41942 / 0.22 ( 6) hydrogen bonds : bond 0.03365 / 2.41 ( 432) hydrogen bonds : angle 4.52722 / 3.45 ( 1254) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: C 79 LEU cc_start: 0.8342 (tp) cc_final: 0.8064 (tt) REVERT: D 239 PHE cc_start: 0.7624 (m-80) cc_final: 0.7167 (m-80) outliers start: 23 outliers final: 19 residues processed: 154 average time/residue: 0.0729 time to fit residues: 15.6975 Evaluate side-chains 162 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 167 HIS Chi-restraints excluded: chain D residue 172 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [36, 97, 95, 67, 18, 82, 41, 92, 14, 84, 75] chunk 36 optimal weight: 0.0070 chunk 97 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.130858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.117329 restraints weight = 12249.986| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.91 r_work: 0.3517 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7395 Z= 0.137 Angle : 0.496 6.847 10189 Z= 0.264 Chirality : 0.041 0.130 1243 Planarity : 0.004 0.034 1308 Dihedral : 4.673 51.188 1146 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.14 % Allowed : 24.65 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.27), residues: 1076 helix: 2.45 (0.27), residues: 389 sheet: -1.11 (0.31), residues: 249 loop : -0.78 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 274 TYR 0.017 0.001 TYR A 387 PHE 0.025 0.002 PHE B 308 TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 7392) covalent geometry : angle 0.49604 / 0.26 (10183) SS BOND : bond 0.00224 / 0.11 ( 3) SS BOND : angle 0.39489 / 0.22 ( 6) hydrogen bonds : bond 0.03244 / 2.31 ( 432) hydrogen bonds : angle 4.48300 / 3.42 ( 1254) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.176 Fit side-chains REVERT: C 79 LEU cc_start: 0.8334 (tp) cc_final: 0.8058 (tt) REVERT: C 163 ASP cc_start: 0.7191 (p0) cc_final: 0.6980 (p0) REVERT: D 239 PHE cc_start: 0.7596 (m-80) cc_final: 0.7138 (m-80) outliers start: 21 outliers final: 19 residues processed: 149 average time/residue: 0.0675 time to fit residues: 14.0754 Evaluate side-chains 162 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 167 HIS Chi-restraints excluded: chain D residue 172 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [6, 91, 49, 93, 25, 72, 74, 39, 52, 101, 4] chunk 6 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 72 optimal weight: 0.0870 chunk 74 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.131007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.117524 restraints weight = 12045.445| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.89 r_work: 0.3519 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7395 Z= 0.133 Angle : 0.501 7.614 10189 Z= 0.265 Chirality : 0.040 0.129 1243 Planarity : 0.004 0.033 1308 Dihedral : 4.639 51.329 1146 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.54 % Allowed : 23.87 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 1076 helix: 2.51 (0.27), residues: 389 sheet: -1.11 (0.31), residues: 249 loop : -0.77 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 274 TYR 0.017 0.001 TYR A 387 PHE 0.027 0.002 PHE B 308 TRP 0.014 0.001 TRP C 82 HIS 0.001 0.000 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7392) covalent geometry : angle 0.50062 / 0.27 (10183) SS BOND : bond 0.00227 / 0.11 ( 3) SS BOND : angle 0.35998 / 0.19 ( 6) hydrogen bonds : bond 0.03218 / 2.29 ( 432) hydrogen bonds : angle 4.46792 / 3.41 ( 1254) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: C 79 LEU cc_start: 0.8342 (tp) cc_final: 0.8056 (tt) REVERT: C 163 ASP cc_start: 0.7212 (p0) cc_final: 0.6973 (p0) REVERT: D 239 PHE cc_start: 0.7603 (m-80) cc_final: 0.7180 (m-80) outliers start: 23 outliers final: 21 residues processed: 152 average time/residue: 0.0709 time to fit residues: 15.0563 Evaluate side-chains 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 167 HIS Chi-restraints excluded: chain D residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [41, 10, 63, 101, 46, 80, 36, 68, 28, 89, 9] chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 101 optimal weight: 0.0570 chunk 46 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.130772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.117296 restraints weight = 12159.573| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.90 r_work: 0.3511 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7395 Z= 0.142 Angle : 0.500 6.854 10189 Z= 0.267 Chirality : 0.041 0.130 1243 Planarity : 0.004 0.034 1308 Dihedral : 4.701 51.395 1146 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.54 % Allowed : 24.06 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.27), residues: 1076 helix: 2.49 (0.27), residues: 388 sheet: -1.08 (0.31), residues: 249 loop : -0.78 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 150 TYR 0.016 0.001 TYR A 387 PHE 0.031 0.002 PHE B 308 TRP 0.014 0.001 TRP C 169 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 7392) covalent geometry : angle 0.50016 / 0.27 (10183) SS BOND : bond 0.00221 / 0.11 ( 3) SS BOND : angle 0.38112 / 0.21 ( 6) hydrogen bonds : bond 0.03280 / 2.34 ( 432) hydrogen bonds : angle 4.49248 / 3.43 ( 1254) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: C 79 LEU cc_start: 0.8327 (tp) cc_final: 0.8049 (tt) REVERT: C 325 MET cc_start: 0.7939 (mmm) cc_final: 0.7729 (mmt) REVERT: D 239 PHE cc_start: 0.7615 (m-80) cc_final: 0.7182 (m-80) outliers start: 23 outliers final: 22 residues processed: 152 average time/residue: 0.0730 time to fit residues: 15.6213 Evaluate side-chains 166 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 167 HIS Chi-restraints excluded: chain D residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [96, 84, 100, 44, 4, 70, 97, 35, 94, 98, 61] chunk 96 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 98 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.130146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.116626 restraints weight = 12136.815| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.90 r_work: 0.3501 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7395 Z= 0.161 Angle : 0.524 7.533 10189 Z= 0.279 Chirality : 0.041 0.131 1243 Planarity : 0.004 0.032 1308 Dihedral : 4.847 51.679 1146 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.34 % Allowed : 23.87 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.26), residues: 1076 helix: 2.43 (0.27), residues: 388 sheet: -1.06 (0.31), residues: 247 loop : -0.80 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 150 TYR 0.017 0.002 TYR A 387 PHE 0.030 0.002 PHE B 308 TRP 0.014 0.002 TRP C 169 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 7392) covalent geometry : angle 0.52430 / 0.28 (10183) SS BOND : bond 0.00249 / 0.12 ( 3) SS BOND : angle 0.40951 / 0.21 ( 6) hydrogen bonds : bond 0.03414 / 2.44 ( 432) hydrogen bonds : angle 4.57564 / 3.49 ( 1254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1885.92 seconds wall clock time: 32 minutes 53.95 seconds (1973.95 seconds total)