Starting phenix.real_space_refine on Thu Jul 2 04:45:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f8v_31493/07_2026/7f8v_31493.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f8v_31493/07_2026/7f8v_31493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7f8v_31493/07_2026/7f8v_31493.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f8v_31493/07_2026/7f8v_31493.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f8v_31493/07_2026/7f8v_31493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f8v_31493/07_2026/7f8v_31493.map" model { file = "/net/cci-nas-00/data/ceres_data/7f8v_31493/07_2026/7f8v_31493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f8v_31493/07_2026/7f8v_31493.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 53 5.16 5 C 4224 2.51 5 N 1127 2.21 5 O 1197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6601 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1748 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 1 Chain: "B" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2347 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 300} Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 245 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 4, 'TRANS': 28} Chain: "E" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 133 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PCA:plan-2': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2128 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALA A 236 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 236 " occ=0.00 Time building chain proxies: 1.06, per 1000 atoms: 0.16 Number of scatterers: 6601 At special positions: 0 Unit cell: (110.77, 117.04, 81.51, 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 53 16.00 O 1197 8.00 N 1127 7.00 C 4224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 205 " distance=2.04 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 282.8 milliseconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1592 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 11 sheets defined 43.5% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.607A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.517A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP A 212 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.254A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.583A pdb=" N PHE A 260 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 261' Processing helix chain 'A' and resid 271 through 282 removed outlier: 5.208A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 331 through 352 Processing helix chain 'C' and resid 30 through 45 Processing helix chain 'R' and resid 56 through 81 removed outlier: 4.475A pdb=" N ASN R 72 " --> pdb=" O SER R 68 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 107 Processing helix chain 'R' and resid 107 through 117 removed outlier: 3.612A pdb=" N LEU R 113 " --> pdb=" O PRO R 109 " (cutoff:3.500A) Proline residue: R 114 - end of helix Processing helix chain 'R' and resid 123 through 157 Processing helix chain 'R' and resid 158 through 166 removed outlier: 3.558A pdb=" N ALA R 162 " --> pdb=" O ARG R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 186 Processing helix chain 'R' and resid 187 through 192 Processing helix chain 'R' and resid 211 through 227 Processing helix chain 'R' and resid 227 through 248 Processing helix chain 'R' and resid 327 through 360 removed outlier: 4.132A pdb=" N ARG R 333 " --> pdb=" O LYS R 329 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET R 334 " --> pdb=" O ARG R 330 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL R 339 " --> pdb=" O LEU R 335 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE R 342 " --> pdb=" O ILE R 338 " (cutoff:3.500A) Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 362 through 367 removed outlier: 3.725A pdb=" N ALA R 366 " --> pdb=" O GLY R 362 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU R 367 " --> pdb=" O ALA R 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 362 through 367' Processing helix chain 'R' and resid 369 through 391 removed outlier: 4.091A pdb=" N LEU R 377 " --> pdb=" O SER R 373 " (cutoff:3.500A) Proline residue: R 387 - end of helix removed outlier: 3.678A pdb=" N TYR R 390 " --> pdb=" O ASN R 386 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS R 391 " --> pdb=" O PRO R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 394 through 405 removed outlier: 3.837A pdb=" N ARG R 398 " --> pdb=" O HIS R 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 192 Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 227 removed outlier: 5.613A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 265 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N HIS A 323 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 267 " --> pdb=" O HIS A 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.517A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.894A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 5.898A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.135A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.098A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.995A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 276 Processing sheet with id=AB1, first strand: chain 'B' and resid 295 through 296 removed outlier: 3.677A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 197 through 198 removed outlier: 3.699A pdb=" N VAL R 202 " --> pdb=" O VAL R 198 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 942 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: 0.63 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1238 1.33 - 1.45: 1708 1.45 - 1.57: 3720 1.57 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 6743 Sorted by residual: bond pdb=" N LEU A 284 " pdb=" CA LEU A 284 " ideal model delta sigma weight residual 1.458 1.500 -0.041 1.37e-02 5.33e+03 9.10e+00 bond pdb=" C ALA R 370 " pdb=" N PRO R 371 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.66e+00 bond pdb=" N MET R 134 " pdb=" CA MET R 134 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.17e-02 7.31e+03 6.42e+00 bond pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.34e-02 5.57e+03 3.48e+00 bond pdb=" C TYR R 189 " pdb=" N PRO R 190 " ideal model delta sigma weight residual 1.336 1.352 -0.016 9.80e-03 1.04e+04 2.83e+00 ... (remaining 6738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 8787 1.98 - 3.96: 291 3.96 - 5.95: 57 5.95 - 7.93: 9 7.93 - 9.91: 6 Bond angle restraints: 9150 Sorted by residual: angle pdb=" N PCA E 1 " pdb=" CA PCA E 1 " pdb=" CB PCA E 1 " ideal model delta sigma weight residual 110.50 102.21 8.29 1.70e+00 3.46e-01 2.38e+01 angle pdb=" N PRO E 3 " pdb=" CA PRO E 3 " pdb=" C PRO E 3 " ideal model delta sigma weight residual 112.47 104.67 7.80 2.06e+00 2.36e-01 1.43e+01 angle pdb=" CB MET A 18 " pdb=" CG MET A 18 " pdb=" SD MET A 18 " ideal model delta sigma weight residual 112.70 122.52 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C MET R 134 " pdb=" CA MET R 134 " pdb=" CB MET R 134 " ideal model delta sigma weight residual 110.96 106.03 4.93 1.54e+00 4.22e-01 1.02e+01 angle pdb=" CA MET R 108 " pdb=" CB MET R 108 " pdb=" CG MET R 108 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.14e+00 ... (remaining 9145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3600 17.86 - 35.72: 308 35.72 - 53.58: 61 53.58 - 71.44: 9 71.44 - 89.30: 6 Dihedral angle restraints: 3984 sinusoidal: 1526 harmonic: 2458 Sorted by residual: dihedral pdb=" CB CYS R 127 " pdb=" SG CYS R 127 " pdb=" SG CYS R 205 " pdb=" CB CYS R 205 " ideal model delta sinusoidal sigma weight residual 93.00 175.61 -82.61 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CA CYS R 107 " pdb=" C CYS R 107 " pdb=" N MET R 108 " pdb=" CA MET R 108 " ideal model delta harmonic sigma weight residual -180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA MET R 186 " pdb=" C MET R 186 " pdb=" N VAL R 187 " pdb=" CA VAL R 187 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 3981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 779 0.054 - 0.108: 218 0.108 - 0.161: 52 0.161 - 0.215: 4 0.215 - 0.269: 4 Chirality restraints: 1057 Sorted by residual: chirality pdb=" CA MET R 108 " pdb=" N MET R 108 " pdb=" C MET R 108 " pdb=" CB MET R 108 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA MET R 134 " pdb=" N MET R 134 " pdb=" C MET R 134 " pdb=" CB MET R 134 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB THR R 178 " pdb=" CA THR R 178 " pdb=" OG1 THR R 178 " pdb=" CG2 THR R 178 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1054 not shown) Planarity restraints: 1147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N PCA E 1 " -0.136 2.00e-02 2.50e+03 9.12e-02 1.04e+02 pdb=" CA PCA E 1 " 0.115 2.00e-02 2.50e+03 pdb=" CG PCA E 1 " -0.042 2.00e-02 2.50e+03 pdb=" CD PCA E 1 " -0.024 2.00e-02 2.50e+03 pdb=" OE PCA E 1 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 288 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO A 289 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 52 " 0.044 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO C 53 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " 0.036 5.00e-02 4.00e+02 ... (remaining 1144 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1360 2.78 - 3.31: 6306 3.31 - 3.84: 11190 3.84 - 4.37: 13216 4.37 - 4.90: 22806 Nonbonded interactions: 54878 Sorted by model distance: nonbonded pdb=" O HIS R 364 " pdb=" OG SER R 368 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.290 3.040 nonbonded pdb=" OE1 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.307 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.308 3.040 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.310 3.120 ... (remaining 54873 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.230 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 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 0.068 6744 Z= 0.226 Angle : 0.873 9.912 9152 Z= 0.468 Chirality : 0.054 0.269 1057 Planarity : 0.007 0.091 1147 Dihedral : 14.097 89.299 2389 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.49 (0.26), residues: 832 helix: -0.08 (0.27), residues: 331 sheet: -1.03 (0.41), residues: 131 loop : -1.78 (0.28), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 398 TYR 0.016 0.003 TYR A 231 PHE 0.026 0.002 PHE R 343 TRP 0.036 0.003 TRP B 211 HIS 0.013 0.002 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 ( 6743) covalent geometry : angle 0.87286 / 0.47 ( 9150) SS BOND : bond 0.00541 / 0.28 ( 1) SS BOND : angle 1.94450 / 1.09 ( 2) hydrogen bonds : bond 0.14800 / 10.08 ( 321) hydrogen bonds : angle 7.45076 / 5.05 ( 942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: B 118 ASP cc_start: 0.7171 (t0) cc_final: 0.6889 (t0) REVERT: C 32 LYS cc_start: 0.7713 (mppt) cc_final: 0.7474 (mtmm) REVERT: E 5 LEU cc_start: 0.5831 (pt) cc_final: 0.5492 (tt) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0645 time to fit residues: 10.8156 Evaluate side-chains 100 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 ASN R 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.194577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.168143 restraints weight = 7422.092| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 1.98 r_work: 0.4065 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6744 Z= 0.147 Angle : 0.605 8.659 9152 Z= 0.317 Chirality : 0.043 0.173 1057 Planarity : 0.005 0.050 1147 Dihedral : 4.829 18.275 915 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.26 % Allowed : 8.15 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.86 (0.27), residues: 832 helix: 0.72 (0.28), residues: 332 sheet: -0.88 (0.40), residues: 142 loop : -1.66 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 152 TYR 0.016 0.002 TYR R 238 PHE 0.014 0.002 PHE B 234 TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 6743) covalent geometry : angle 0.60517 / 0.32 ( 9150) SS BOND : bond 0.00299 / 0.16 ( 1) SS BOND : angle 0.36396 / 0.20 ( 2) hydrogen bonds : bond 0.04588 / 3.00 ( 321) hydrogen bonds : angle 5.81851 / 3.95 ( 942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7153 (mmm) cc_final: 0.6913 (mmm) REVERT: A 276 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6812 (pm20) outliers start: 9 outliers final: 8 residues processed: 112 average time/residue: 0.0719 time to fit residues: 11.2941 Evaluate side-chains 104 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 216 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.192923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.166928 restraints weight = 7362.674| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 1.91 r_work: 0.4062 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6744 Z= 0.131 Angle : 0.568 7.850 9152 Z= 0.297 Chirality : 0.042 0.165 1057 Planarity : 0.004 0.043 1147 Dihedral : 4.665 23.885 915 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.53 % Allowed : 10.11 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.70 (0.28), residues: 832 helix: 0.99 (0.29), residues: 331 sheet: -1.01 (0.40), residues: 142 loop : -1.62 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 152 TYR 0.014 0.001 TYR R 238 PHE 0.011 0.001 PHE B 234 TRP 0.015 0.002 TRP R 165 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6743) covalent geometry : angle 0.56806 / 0.30 ( 9150) SS BOND : bond 0.00128 / 0.07 ( 1) SS BOND : angle 0.03788 / 0.02 ( 2) hydrogen bonds : bond 0.04172 / 2.73 ( 321) hydrogen bonds : angle 5.54535 / 3.76 ( 942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7148 (mmm) cc_final: 0.6897 (mmm) REVERT: A 200 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7348 (m-10) REVERT: A 276 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6872 (pm20) REVERT: R 85 LEU cc_start: 0.5863 (mt) cc_final: 0.5647 (mp) outliers start: 18 outliers final: 15 residues processed: 110 average time/residue: 0.0648 time to fit residues: 10.1423 Evaluate side-chains 106 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 108 MET Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 216 GLN Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 393 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 3 optimal weight: 0.8980 chunk 74 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 HIS A 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.191508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.166708 restraints weight = 7447.698| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 1.82 r_work: 0.4041 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6744 Z= 0.131 Angle : 0.565 7.477 9152 Z= 0.293 Chirality : 0.042 0.152 1057 Planarity : 0.004 0.040 1147 Dihedral : 4.629 25.993 915 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.53 % Allowed : 12.92 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.61 (0.28), residues: 832 helix: 1.13 (0.29), residues: 330 sheet: -1.16 (0.40), residues: 142 loop : -1.54 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 396 TYR 0.013 0.001 TYR R 238 PHE 0.014 0.001 PHE R 110 TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6743) covalent geometry : angle 0.56512 / 0.29 ( 9150) SS BOND : bond 0.00103 / 0.05 ( 1) SS BOND : angle 0.19284 / 0.11 ( 2) hydrogen bonds : bond 0.03918 / 2.57 ( 321) hydrogen bonds : angle 5.41100 / 3.67 ( 942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7395 (m-10) REVERT: A 248 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.5785 (mtp) REVERT: A 276 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6897 (pm20) REVERT: B 61 MET cc_start: 0.6859 (ppp) cc_final: 0.6418 (ppp) REVERT: B 270 ILE cc_start: 0.6604 (mm) cc_final: 0.6264 (mt) REVERT: R 246 TYR cc_start: 0.5107 (m-10) cc_final: 0.4896 (m-10) outliers start: 18 outliers final: 13 residues processed: 114 average time/residue: 0.0588 time to fit residues: 9.5161 Evaluate side-chains 108 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 108 MET Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 216 GLN Chi-restraints excluded: chain R residue 222 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 70 optimal weight: 0.3980 chunk 76 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 54 optimal weight: 0.0470 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.192824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.166893 restraints weight = 7549.774| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 1.93 r_work: 0.4067 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 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 0.029 6744 Z= 0.115 Angle : 0.552 10.224 9152 Z= 0.284 Chirality : 0.042 0.159 1057 Planarity : 0.004 0.040 1147 Dihedral : 4.502 26.820 915 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.81 % Allowed : 13.62 % Favored : 83.57 % 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 (0.29), residues: 832 helix: 1.31 (0.29), residues: 331 sheet: -1.03 (0.40), residues: 147 loop : -1.47 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 356 TYR 0.010 0.001 TYR R 238 PHE 0.013 0.001 PHE R 110 TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6743) covalent geometry : angle 0.55251 / 0.28 ( 9150) SS BOND : bond 0.00037 / 0.02 ( 1) SS BOND : angle 0.13215 / 0.07 ( 2) hydrogen bonds : bond 0.03736 / 2.45 ( 321) hydrogen bonds : angle 5.27907 / 3.60 ( 942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7319 (m-10) REVERT: A 248 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.5724 (mtp) REVERT: A 276 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6877 (pm20) REVERT: B 61 MET cc_start: 0.6878 (ppp) cc_final: 0.6427 (ppp) REVERT: B 270 ILE cc_start: 0.6612 (mm) cc_final: 0.6281 (mt) REVERT: R 246 TYR cc_start: 0.4958 (m-10) cc_final: 0.4670 (m-10) REVERT: R 353 ASN cc_start: 0.7225 (m-40) cc_final: 0.6920 (m110) outliers start: 20 outliers final: 13 residues processed: 115 average time/residue: 0.0558 time to fit residues: 9.1560 Evaluate side-chains 112 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 216 GLN Chi-restraints excluded: chain R residue 222 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.4980 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.196284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.167617 restraints weight = 7105.001| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 2.16 r_work: 0.4090 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3919 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6744 Z= 0.131 Angle : 0.572 9.182 9152 Z= 0.293 Chirality : 0.042 0.167 1057 Planarity : 0.004 0.041 1147 Dihedral : 4.580 28.535 915 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.81 % Allowed : 14.75 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.29), residues: 832 helix: 1.30 (0.29), residues: 331 sheet: -1.03 (0.40), residues: 148 loop : -1.57 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 152 TYR 0.010 0.001 TYR R 238 PHE 0.035 0.002 PHE B 292 TRP 0.018 0.002 TRP R 165 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 6743) covalent geometry : angle 0.57218 / 0.29 ( 9150) SS BOND : bond 0.00101 / 0.05 ( 1) SS BOND : angle 0.26306 / 0.15 ( 2) hydrogen bonds : bond 0.03778 / 2.48 ( 321) hydrogen bonds : angle 5.31276 / 3.63 ( 942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7401 (m-10) REVERT: A 248 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.6038 (mtp) REVERT: A 276 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: B 270 ILE cc_start: 0.6347 (mm) cc_final: 0.6072 (mt) REVERT: R 134 MET cc_start: 0.5122 (mmp) cc_final: 0.4905 (mmp) REVERT: R 246 TYR cc_start: 0.4935 (m-10) cc_final: 0.4637 (m-10) REVERT: R 353 ASN cc_start: 0.7204 (m-40) cc_final: 0.6796 (m110) outliers start: 20 outliers final: 15 residues processed: 111 average time/residue: 0.0637 time to fit residues: 10.0877 Evaluate side-chains 114 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 216 GLN Chi-restraints excluded: chain R residue 222 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 60 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 79 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 27 optimal weight: 0.0170 chunk 4 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.197656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.169937 restraints weight = 7041.715| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 2.06 r_work: 0.4107 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3943 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6744 Z= 0.119 Angle : 0.552 8.533 9152 Z= 0.284 Chirality : 0.042 0.185 1057 Planarity : 0.004 0.041 1147 Dihedral : 4.513 30.319 915 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.53 % Allowed : 15.17 % Favored : 82.30 % 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: -0.37 (0.29), residues: 832 helix: 1.38 (0.29), residues: 331 sheet: -1.00 (0.40), residues: 147 loop : -1.49 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.010 0.001 TYR A 231 PHE 0.024 0.002 PHE A 275 TRP 0.017 0.002 TRP R 165 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 6743) covalent geometry : angle 0.55168 / 0.28 ( 9150) SS BOND : bond 0.00072 / 0.04 ( 1) SS BOND : angle 0.18275 / 0.11 ( 2) hydrogen bonds : bond 0.03667 / 2.40 ( 321) hydrogen bonds : angle 5.23233 / 3.58 ( 942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 248 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.5938 (mtp) REVERT: B 61 MET cc_start: 0.6783 (ppp) cc_final: 0.6457 (ppp) REVERT: B 270 ILE cc_start: 0.6398 (mm) cc_final: 0.6122 (mt) REVERT: R 134 MET cc_start: 0.5150 (mmp) cc_final: 0.4917 (mmp) REVERT: R 246 TYR cc_start: 0.4973 (m-10) cc_final: 0.4664 (m-10) outliers start: 18 outliers final: 15 residues processed: 116 average time/residue: 0.0668 time to fit residues: 11.1415 Evaluate side-chains 117 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 56 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 216 GLN Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 331 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 0.0470 chunk 73 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 196 HIS A 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.196506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.168216 restraints weight = 7098.490| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.13 r_work: 0.4093 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3927 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6744 Z= 0.129 Angle : 0.565 8.412 9152 Z= 0.292 Chirality : 0.042 0.187 1057 Planarity : 0.004 0.042 1147 Dihedral : 4.591 31.946 915 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.67 % Allowed : 16.15 % Favored : 81.18 % 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: -0.41 (0.29), residues: 832 helix: 1.33 (0.29), residues: 331 sheet: -0.98 (0.41), residues: 147 loop : -1.51 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 152 TYR 0.013 0.001 TYR A 231 PHE 0.022 0.002 PHE B 292 TRP 0.017 0.002 TRP B 211 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 6743) covalent geometry : angle 0.56528 / 0.29 ( 9150) SS BOND : bond 0.00044 / 0.02 ( 1) SS BOND : angle 0.19746 / 0.11 ( 2) hydrogen bonds : bond 0.03704 / 2.43 ( 321) hydrogen bonds : angle 5.26961 / 3.60 ( 942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: A 248 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.5992 (mtp) REVERT: A 276 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: B 61 MET cc_start: 0.6842 (ppp) cc_final: 0.6440 (ppp) REVERT: B 270 ILE cc_start: 0.6406 (mm) cc_final: 0.6164 (mt) REVERT: R 246 TYR cc_start: 0.5038 (m-10) cc_final: 0.4752 (m-10) outliers start: 19 outliers final: 15 residues processed: 112 average time/residue: 0.0643 time to fit residues: 10.3444 Evaluate side-chains 118 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 216 GLN Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 331 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 0.0270 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.197062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.168690 restraints weight = 7148.168| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.17 r_work: 0.4100 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3932 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6744 Z= 0.126 Angle : 0.573 8.198 9152 Z= 0.295 Chirality : 0.042 0.185 1057 Planarity : 0.004 0.042 1147 Dihedral : 4.591 33.034 915 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.81 % Allowed : 16.71 % Favored : 80.48 % 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 (0.29), residues: 832 helix: 1.33 (0.29), residues: 331 sheet: -1.00 (0.41), residues: 148 loop : -1.48 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 152 TYR 0.010 0.001 TYR A 231 PHE 0.021 0.002 PHE R 65 TRP 0.025 0.002 TRP R 346 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 6743) covalent geometry : angle 0.57269 / 0.30 ( 9150) SS BOND : bond 0.00035 / 0.02 ( 1) SS BOND : angle 0.13864 / 0.08 ( 2) hydrogen bonds : bond 0.03727 / 2.44 ( 321) hydrogen bonds : angle 5.25273 / 3.59 ( 942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: A 248 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6009 (mtp) REVERT: A 276 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: B 61 MET cc_start: 0.6907 (ppp) cc_final: 0.6537 (ppp) REVERT: B 270 ILE cc_start: 0.6410 (mm) cc_final: 0.6151 (mt) REVERT: R 246 TYR cc_start: 0.5038 (m-10) cc_final: 0.4737 (m-10) REVERT: R 353 ASN cc_start: 0.7046 (m-40) cc_final: 0.6690 (m-40) outliers start: 20 outliers final: 17 residues processed: 115 average time/residue: 0.0701 time to fit residues: 11.4091 Evaluate side-chains 122 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 56 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 216 GLN Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 331 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 67 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 0.1980 chunk 81 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 73 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 HIS A 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.198211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.170630 restraints weight = 7081.360| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.08 r_work: 0.4117 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6744 Z= 0.118 Angle : 0.578 8.842 9152 Z= 0.296 Chirality : 0.042 0.188 1057 Planarity : 0.004 0.042 1147 Dihedral : 4.561 34.261 915 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.81 % Allowed : 16.85 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.29), residues: 832 helix: 1.23 (0.29), residues: 337 sheet: -0.98 (0.41), residues: 148 loop : -1.52 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 152 TYR 0.009 0.001 TYR R 132 PHE 0.022 0.002 PHE B 292 TRP 0.027 0.002 TRP R 165 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6743) covalent geometry : angle 0.57780 / 0.30 ( 9150) SS BOND : bond 0.00034 / 0.02 ( 1) SS BOND : angle 0.06366 / 0.04 ( 2) hydrogen bonds : bond 0.03622 / 2.36 ( 321) hydrogen bonds : angle 5.25417 / 3.62 ( 942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.7296 (m-10) REVERT: A 248 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.5997 (mtp) REVERT: A 276 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6965 (pm20) REVERT: A 332 ASN cc_start: 0.5497 (OUTLIER) cc_final: 0.5031 (m-40) REVERT: B 61 MET cc_start: 0.6849 (ppp) cc_final: 0.6531 (ppp) REVERT: B 270 ILE cc_start: 0.6014 (mm) cc_final: 0.5809 (mt) REVERT: B 312 ASP cc_start: 0.6451 (OUTLIER) cc_final: 0.6240 (m-30) REVERT: R 246 TYR cc_start: 0.5175 (m-10) cc_final: 0.4888 (m-10) outliers start: 20 outliers final: 15 residues processed: 114 average time/residue: 0.0651 time to fit residues: 10.6400 Evaluate side-chains 124 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 216 GLN Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 331 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 71 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 24 optimal weight: 0.0670 chunk 58 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 HIS ** A 332 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 = 0.4517 r_free = 0.4517 target = 0.197484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.169380 restraints weight = 7102.638| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 2.13 r_work: 0.4103 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6744 Z= 0.127 Angle : 0.589 8.468 9152 Z= 0.303 Chirality : 0.043 0.200 1057 Planarity : 0.004 0.042 1147 Dihedral : 4.618 35.343 915 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.67 % Allowed : 17.13 % Favored : 80.20 % 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: -0.49 (0.29), residues: 832 helix: 1.19 (0.29), residues: 337 sheet: -0.98 (0.41), residues: 148 loop : -1.55 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 152 TYR 0.010 0.001 TYR A 231 PHE 0.018 0.002 PHE R 65 TRP 0.022 0.002 TRP R 165 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 6743) covalent geometry : angle 0.58941 / 0.30 ( 9150) SS BOND : bond 0.00068 / 0.04 ( 1) SS BOND : angle 0.16208 / 0.10 ( 2) hydrogen bonds : bond 0.03749 / 2.48 ( 321) hydrogen bonds : angle 5.29904 / 3.65 ( 942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1997.89 seconds wall clock time: 34 minutes 59.43 seconds (2099.43 seconds total)