Starting phenix.real_space_refine on Thu Jul 2 16:11:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p02_13141/07_2026/7p02_13141.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p02_13141/07_2026/7p02_13141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7p02_13141/07_2026/7p02_13141.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p02_13141/07_2026/7p02_13141.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p02_13141/07_2026/7p02_13141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p02_13141/07_2026/7p02_13141.map" model { file = "/net/cci-nas-00/data/ceres_data/7p02_13141/07_2026/7p02_13141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p02_13141/07_2026/7p02_13141.cif" } resolution = 2.87 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= -0.001 sd= 0.048 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 63 5.16 5 C 5805 2.51 5 N 1542 2.21 5 O 1652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 9062 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2559 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 396 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "A" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1870 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2347 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Chain: "P" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 76 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.15, per 1000 atoms: 0.24 Number of scatterers: 9062 At special positions: 0 Unit cell: (88.536, 123.69, 130.2, 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 63 16.00 O 1652 8.00 N 1542 7.00 C 5805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 39 " - pdb=" SG CYS H 113 " distance=2.03 Simple disulfide: pdb=" SG CYS H 176 " - pdb=" SG CYS H 246 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 180 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 262.1 milliseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 39.5% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 79 through 82 Processing helix chain 'H' and resid 104 through 108 removed outlier: 3.645A pdb=" N THR H 108 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'G' and resid 13 through 25 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.539A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 246 through 262 removed outlier: 3.709A pdb=" N GLN A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 266 removed outlier: 3.707A pdb=" N ARG A 266 " --> pdb=" O ARG A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 266' Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.762A pdb=" N TYR A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 4.350A pdb=" N ARG A 300 " --> pdb=" O PRO A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 335 removed outlier: 4.001A pdb=" N SER A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 374 Processing helix chain 'R' and resid 28 through 60 Processing helix chain 'R' and resid 66 through 84 removed outlier: 4.421A pdb=" N PHE R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 96 removed outlier: 4.272A pdb=" N HIS R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 109 Processing helix chain 'R' and resid 110 through 136 Processing helix chain 'R' and resid 143 through 168 Proline residue: R 164 - end of helix Processing helix chain 'R' and resid 190 through 205 removed outlier: 3.536A pdb=" N HIS R 197 " --> pdb=" O GLU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 225 Processing helix chain 'R' and resid 238 through 274 Proline residue: R 263 - end of helix Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 274 through 279 removed outlier: 4.158A pdb=" N TYR R 278 " --> pdb=" O ASN R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 296 removed outlier: 4.165A pdb=" N GLN R 285 " --> pdb=" O LYS R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 309 removed outlier: 3.611A pdb=" N TYR R 300 " --> pdb=" O SER R 296 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN R 301 " --> pdb=" O SER R 297 " (cutoff:3.500A) Proline residue: R 302 - end of helix Processing helix chain 'R' and resid 309 through 319 removed outlier: 3.859A pdb=" N ARG R 313 " --> pdb=" O ASN R 309 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 20 through 24 Processing sheet with id=AA2, first strand: chain 'H' and resid 27 through 29 removed outlier: 6.765A pdb=" N MET H 51 " --> pdb=" O TYR H 67 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR H 67 " --> pdb=" O MET H 51 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP H 53 " --> pdb=" O VAL H 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 157 through 158 Processing sheet with id=AA4, first strand: chain 'H' and resid 163 through 165 removed outlier: 6.158A pdb=" N LEU H 195 " --> pdb=" O LEU H 204 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU H 204 " --> pdb=" O LEU H 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.452A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.753A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.909A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.548A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.155A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.562A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.248A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 34 through 37 Processing sheet with id=AB4, first strand: chain 'A' and resid 39 through 40 removed outlier: 7.154A pdb=" N LEU A 39 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N ASP A 242 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE A 239 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN A 275 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL A 241 " --> pdb=" O ASN A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'R' and resid 169 through 173 461 hydrogen bonds defined for protein. 1311 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: 1.39 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1689 1.32 - 1.45: 2402 1.45 - 1.57: 5094 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 9279 Sorted by residual: bond pdb=" C VAL B 187 " pdb=" N MET B 188 " ideal model delta sigma weight residual 1.332 1.439 -0.107 1.36e-02 5.41e+03 6.14e+01 bond pdb=" CG ASN R 96 " pdb=" OD1 ASN R 96 " ideal model delta sigma weight residual 1.231 1.323 -0.092 1.90e-02 2.77e+03 2.35e+01 bond pdb=" N PHE R 111 " pdb=" CA PHE R 111 " ideal model delta sigma weight residual 1.463 1.497 -0.033 6.90e-03 2.10e+04 2.34e+01 bond pdb=" CG ASN R 96 " pdb=" ND2 ASN R 96 " ideal model delta sigma weight residual 1.328 1.229 0.099 2.10e-02 2.27e+03 2.24e+01 bond pdb=" C CYS B 103 " pdb=" N ALA B 104 " ideal model delta sigma weight residual 1.330 1.268 0.061 1.41e-02 5.03e+03 1.90e+01 ... (remaining 9274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 10070 2.01 - 4.02: 2426 4.02 - 6.03: 90 6.03 - 8.05: 7 8.05 - 10.06: 3 Bond angle restraints: 12596 Sorted by residual: angle pdb=" CA VAL B 187 " pdb=" C VAL B 187 " pdb=" N MET B 188 " ideal model delta sigma weight residual 116.33 125.15 -8.82 1.03e+00 9.43e-01 7.33e+01 angle pdb=" N ASP B 154 " pdb=" CA ASP B 154 " pdb=" C ASP B 154 " ideal model delta sigma weight residual 113.02 103.88 9.14 1.20e+00 6.94e-01 5.81e+01 angle pdb=" C HIS B 311 " pdb=" N ASP B 312 " pdb=" CA ASP B 312 " ideal model delta sigma weight residual 122.60 112.54 10.06 1.56e+00 4.11e-01 4.16e+01 angle pdb=" O VAL B 187 " pdb=" C VAL B 187 " pdb=" N MET B 188 " ideal model delta sigma weight residual 122.66 116.62 6.04 1.07e+00 8.73e-01 3.19e+01 angle pdb=" N LEU B 152 " pdb=" CA LEU B 152 " pdb=" C LEU B 152 " ideal model delta sigma weight residual 112.68 105.34 7.34 1.33e+00 5.65e-01 3.04e+01 ... (remaining 12591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 5073 16.70 - 33.39: 309 33.39 - 50.09: 64 50.09 - 66.79: 21 66.79 - 83.48: 3 Dihedral angle restraints: 5470 sinusoidal: 2146 harmonic: 3324 Sorted by residual: dihedral pdb=" CB CYS H 39 " pdb=" SG CYS H 39 " pdb=" SG CYS H 113 " pdb=" CB CYS H 113 " ideal model delta sinusoidal sigma weight residual 93.00 60.66 32.34 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" C PHE B 151 " pdb=" N PHE B 151 " pdb=" CA PHE B 151 " pdb=" CB PHE B 151 " ideal model delta harmonic sigma weight residual -122.60 -113.69 -8.91 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" CA TYR H 252 " pdb=" C TYR H 252 " pdb=" N PRO H 253 " pdb=" CA PRO H 253 " ideal model delta harmonic sigma weight residual 0.00 17.10 -17.10 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 459 0.053 - 0.106: 451 0.106 - 0.158: 334 0.158 - 0.211: 136 0.211 - 0.264: 27 Chirality restraints: 1407 Sorted by residual: chirality pdb=" CB VAL R 126 " pdb=" CA VAL R 126 " pdb=" CG1 VAL R 126 " pdb=" CG2 VAL R 126 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1404 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 103 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C CYS B 103 " -0.063 2.00e-02 2.50e+03 pdb=" O CYS B 103 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA B 104 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 245 " -0.011 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C ASP A 245 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP A 245 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR A 246 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 196 " 0.008 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C THR B 196 " -0.030 2.00e-02 2.50e+03 pdb=" O THR B 196 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG B 197 " 0.010 2.00e-02 2.50e+03 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 52 2.65 - 3.21: 8532 3.21 - 3.77: 14544 3.77 - 4.34: 21309 4.34 - 4.90: 33245 Nonbonded interactions: 77682 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.086 3.040 nonbonded pdb=" CD2 PHE R 70 " pdb=" OD2 ASP R 129 " model vdw 2.209 3.340 nonbonded pdb=" N ASP B 154 " pdb=" N ASN B 155 " model vdw 2.506 2.560 nonbonded pdb=" O THR H 161 " pdb=" OG1 THR H 260 " model vdw 2.520 3.040 nonbonded pdb=" N CYS B 166 " pdb=" O CYS B 166 " model vdw 2.561 2.496 ... (remaining 77677 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: 4.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.420 Find NCS groups from input model: 0.060 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:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 : 0.012 0.107 9283 Z= 0.935 Angle : 1.511 10.057 12602 Z= 1.178 Chirality : 0.103 0.264 1407 Planarity : 0.004 0.036 1587 Dihedral : 11.809 83.483 3317 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.12 % Allowed : 7.05 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.72 (0.23), residues: 1120 helix: -0.91 (0.24), residues: 378 sheet: -0.86 (0.31), residues: 236 loop : -1.34 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 177 TYR 0.023 0.002 TYR H 207 PHE 0.021 0.002 PHE B 151 TRP 0.024 0.002 TRP B 82 HIS 0.009 0.002 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.01231 / 0.93 ( 9279) covalent geometry : angle 1.51095 / 1.18 (12596) SS BOND : bond 0.00677 / 0.34 ( 3) SS BOND : angle 1.58961 / 0.71 ( 6) hydrogen bonds : bond 0.16920 / 11.13 ( 461) hydrogen bonds : angle 7.87066 / 5.43 ( 1311) Misc. bond : bond 0.09443 / 4.97 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 256 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 63 GLU cc_start: 0.7576 (tt0) cc_final: 0.7325 (tm-30) REVERT: B 155 ASN cc_start: 0.7592 (t0) cc_final: 0.7196 (t0) REVERT: B 263 THR cc_start: 0.8886 (t) cc_final: 0.8659 (m) REVERT: A 6 SER cc_start: 0.8271 (p) cc_final: 0.7890 (p) REVERT: A 8 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7688 (mm-30) REVERT: A 9 ASP cc_start: 0.7798 (m-30) cc_final: 0.7434 (m-30) REVERT: A 17 LYS cc_start: 0.7843 (mmtp) cc_final: 0.7326 (mtpt) REVERT: A 263 ARG cc_start: 0.7061 (ptm160) cc_final: 0.6829 (ptm160) REVERT: A 368 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6937 (mtt-85) REVERT: A 372 ARG cc_start: 0.7177 (mtt90) cc_final: 0.6755 (tpt-90) REVERT: R 51 VAL cc_start: 0.7563 (t) cc_final: 0.7154 (p) REVERT: R 63 MET cc_start: 0.6860 (mmm) cc_final: 0.6296 (mtt) REVERT: R 109 ASN cc_start: 0.6708 (m-40) cc_final: 0.6060 (m-40) REVERT: R 161 LEU cc_start: 0.7349 (tp) cc_final: 0.7080 (tt) REVERT: R 163 PHE cc_start: 0.6569 (t80) cc_final: 0.6198 (t80) REVERT: R 182 ILE cc_start: 0.7803 (mt) cc_final: 0.7453 (mp) REVERT: P 8 PHE cc_start: 0.8219 (m-80) cc_final: 0.7836 (m-10) outliers start: 11 outliers final: 2 residues processed: 266 average time/residue: 0.4460 time to fit residues: 127.2057 Evaluate side-chains 175 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain A residue 368 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 99 GLN B 17 GLN B 266 HIS A 206 GLN A 211 ASN R 50 ASN R 68 ASN R 274 ASN R 301 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.183543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125722 restraints weight = 10138.153| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.21 r_work: 0.3247 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9283 Z= 0.145 Angle : 0.588 7.027 12602 Z= 0.316 Chirality : 0.043 0.152 1407 Planarity : 0.004 0.047 1587 Dihedral : 4.523 48.484 1261 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.06 % Allowed : 15.42 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.08 (0.24), residues: 1120 helix: 1.50 (0.25), residues: 390 sheet: -0.84 (0.29), residues: 246 loop : -0.57 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 339 TYR 0.020 0.002 TYR R 272 PHE 0.027 0.002 PHE H 85 TRP 0.015 0.001 TRP B 82 HIS 0.010 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 9279) covalent geometry : angle 0.58731 / 0.32 (12596) SS BOND : bond 0.00216 / 0.10 ( 3) SS BOND : angle 1.02640 / 0.54 ( 6) hydrogen bonds : bond 0.05522 / 3.71 ( 461) hydrogen bonds : angle 5.40145 / 3.71 ( 1311) Misc. bond : bond 0.00044 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 106 GLU cc_start: 0.8578 (mp0) cc_final: 0.8366 (mt-10) REVERT: H 180 LYS cc_start: 0.8196 (ttpt) cc_final: 0.7974 (ttpp) REVERT: H 208 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.7019 (mtp180) REVERT: B 155 ASN cc_start: 0.8206 (t0) cc_final: 0.7508 (t0) REVERT: B 195 ASP cc_start: 0.7271 (p0) cc_final: 0.6943 (p0) REVERT: B 197 ARG cc_start: 0.7181 (mmt180) cc_final: 0.6739 (mmp80) REVERT: B 214 ARG cc_start: 0.8151 (ptt180) cc_final: 0.7893 (ptp-170) REVERT: B 219 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.7949 (mmm-85) REVERT: B 226 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8148 (mp0) REVERT: B 247 ASP cc_start: 0.7623 (t0) cc_final: 0.7383 (t0) REVERT: G 18 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6567 (tm-30) REVERT: A 17 LYS cc_start: 0.8247 (mmtp) cc_final: 0.7323 (mtpt) REVERT: A 206 GLN cc_start: 0.7293 (tt0) cc_final: 0.6939 (tm-30) REVERT: A 326 ASP cc_start: 0.7472 (t0) cc_final: 0.7242 (t70) REVERT: A 368 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6823 (mtt180) REVERT: A 369 MET cc_start: 0.7261 (ttm) cc_final: 0.7047 (ttt) REVERT: A 372 ARG cc_start: 0.7245 (mtt90) cc_final: 0.6381 (tpp-160) REVERT: R 63 MET cc_start: 0.6549 (mmm) cc_final: 0.6026 (mtt) REVERT: R 90 PHE cc_start: 0.8668 (t80) cc_final: 0.8444 (t80) REVERT: R 96 ASN cc_start: 0.7584 (t0) cc_final: 0.7377 (t0) REVERT: R 109 ASN cc_start: 0.5811 (m-40) cc_final: 0.5592 (m-40) REVERT: R 121 TYR cc_start: 0.7424 (m-80) cc_final: 0.7215 (m-80) REVERT: R 161 LEU cc_start: 0.7081 (tp) cc_final: 0.6755 (tt) REVERT: R 163 PHE cc_start: 0.6517 (t80) cc_final: 0.6150 (t80) REVERT: R 300 TYR cc_start: 0.6526 (m-80) cc_final: 0.6299 (m-80) REVERT: P 8 PHE cc_start: 0.8174 (m-80) cc_final: 0.7722 (m-10) outliers start: 30 outliers final: 12 residues processed: 227 average time/residue: 0.4671 time to fit residues: 113.5082 Evaluate side-chains 186 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 208 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain R residue 72 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 103 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 74 optimal weight: 0.0670 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 99 GLN B 17 GLN A 22 GLN A 229 GLN A 277 GLN R 50 ASN R 136 HIS R 274 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.186339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130137 restraints weight = 10058.990| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.19 r_work: 0.3201 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9283 Z= 0.129 Angle : 0.546 6.774 12602 Z= 0.293 Chirality : 0.042 0.171 1407 Planarity : 0.004 0.051 1587 Dihedral : 4.465 48.857 1260 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.06 % Allowed : 17.88 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.24), residues: 1120 helix: 1.87 (0.26), residues: 382 sheet: -0.75 (0.28), residues: 257 loop : -0.43 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.016 0.001 TYR B 105 PHE 0.032 0.002 PHE H 85 TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 9279) covalent geometry : angle 0.54550 / 0.29 (12596) SS BOND : bond 0.00283 / 0.14 ( 3) SS BOND : angle 1.18211 / 0.58 ( 6) hydrogen bonds : bond 0.04801 / 3.24 ( 461) hydrogen bonds : angle 5.09084 / 3.48 ( 1311) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 80 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8585 (p) REVERT: H 106 GLU cc_start: 0.8606 (mp0) cc_final: 0.8375 (mt-10) REVERT: B 155 ASN cc_start: 0.8360 (t0) cc_final: 0.8042 (t0) REVERT: B 217 MET cc_start: 0.8262 (pmt) cc_final: 0.7982 (pmm) REVERT: B 219 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7801 (mmm-85) REVERT: B 226 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8217 (mp0) REVERT: B 247 ASP cc_start: 0.7593 (t0) cc_final: 0.7378 (t0) REVERT: G 18 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6862 (tp-100) REVERT: A 17 LYS cc_start: 0.8206 (mmtp) cc_final: 0.7296 (mtpt) REVERT: A 21 LYS cc_start: 0.7890 (mtpt) cc_final: 0.7459 (mtmm) REVERT: A 206 GLN cc_start: 0.7266 (tt0) cc_final: 0.6884 (tm-30) REVERT: A 254 ASN cc_start: 0.8115 (m-40) cc_final: 0.7873 (m110) REVERT: A 290 LYS cc_start: 0.8211 (mppt) cc_final: 0.7945 (mptp) REVERT: A 326 ASP cc_start: 0.7565 (t0) cc_final: 0.7244 (t70) REVERT: R 63 MET cc_start: 0.6498 (mmm) cc_final: 0.6050 (mtt) REVERT: R 81 MET cc_start: 0.7374 (ttm) cc_final: 0.7131 (ptp) REVERT: R 161 LEU cc_start: 0.7066 (tp) cc_final: 0.6743 (tt) REVERT: R 163 PHE cc_start: 0.6471 (t80) cc_final: 0.6125 (t80) REVERT: R 205 TYR cc_start: 0.7802 (t80) cc_final: 0.6843 (t80) REVERT: R 262 LEU cc_start: 0.7735 (tp) cc_final: 0.7320 (tp) REVERT: P 8 PHE cc_start: 0.8223 (m-80) cc_final: 0.7764 (m-10) outliers start: 30 outliers final: 12 residues processed: 192 average time/residue: 0.5413 time to fit residues: 111.0538 Evaluate side-chains 167 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain R residue 72 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN B 259 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.178441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120907 restraints weight = 10137.326| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.11 r_work: 0.3124 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9283 Z= 0.271 Angle : 0.654 9.936 12602 Z= 0.346 Chirality : 0.047 0.146 1407 Planarity : 0.005 0.043 1587 Dihedral : 4.581 28.578 1255 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.80 % Allowed : 17.77 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.24), residues: 1120 helix: 1.64 (0.25), residues: 383 sheet: -0.63 (0.29), residues: 261 loop : -0.43 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 19 TYR 0.021 0.002 TYR B 105 PHE 0.037 0.002 PHE H 85 TRP 0.019 0.002 TRP B 169 HIS 0.006 0.002 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.27 ( 9279) covalent geometry : angle 0.65330 / 0.35 (12596) SS BOND : bond 0.00346 / 0.17 ( 3) SS BOND : angle 1.18352 / 0.64 ( 6) hydrogen bonds : bond 0.05454 / 3.70 ( 461) hydrogen bonds : angle 5.40054 / 3.69 ( 1311) Misc. bond : bond 0.00092 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 106 GLU cc_start: 0.8599 (mp0) cc_final: 0.8369 (mt-10) REVERT: B 52 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8201 (mtt90) REVERT: B 155 ASN cc_start: 0.8522 (t0) cc_final: 0.8163 (t0) REVERT: B 176 GLN cc_start: 0.8676 (mt0) cc_final: 0.8434 (tt0) REVERT: B 217 MET cc_start: 0.8372 (pmt) cc_final: 0.8111 (pmm) REVERT: B 219 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.7890 (mmm-85) REVERT: B 226 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8276 (mp0) REVERT: B 247 ASP cc_start: 0.7871 (t0) cc_final: 0.7634 (t0) REVERT: B 258 ASP cc_start: 0.8231 (t0) cc_final: 0.7828 (t70) REVERT: A 17 LYS cc_start: 0.8353 (mmtp) cc_final: 0.7526 (mtpt) REVERT: A 21 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7600 (mtmm) REVERT: A 26 ASP cc_start: 0.8150 (m-30) cc_final: 0.7647 (m-30) REVERT: A 206 GLN cc_start: 0.7215 (tt0) cc_final: 0.6919 (tm-30) REVERT: A 254 ASN cc_start: 0.8197 (m-40) cc_final: 0.7910 (m110) REVERT: A 290 LYS cc_start: 0.8478 (mppt) cc_final: 0.8211 (mptp) REVERT: A 326 ASP cc_start: 0.7687 (t0) cc_final: 0.7401 (t70) REVERT: R 63 MET cc_start: 0.6620 (mmm) cc_final: 0.6218 (mtt) REVERT: R 81 MET cc_start: 0.7498 (ttm) cc_final: 0.7221 (ptp) REVERT: R 161 LEU cc_start: 0.7073 (tp) cc_final: 0.6676 (tt) REVERT: R 163 PHE cc_start: 0.6601 (t80) cc_final: 0.6257 (t80) REVERT: R 205 TYR cc_start: 0.7853 (t80) cc_final: 0.6856 (t80) REVERT: P 8 PHE cc_start: 0.8302 (m-80) cc_final: 0.8011 (m-80) outliers start: 47 outliers final: 18 residues processed: 191 average time/residue: 0.5457 time to fit residues: 111.2922 Evaluate side-chains 171 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 30 GLN B 17 GLN B 176 GLN B 259 GLN A 229 GLN A 277 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.183352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130357 restraints weight = 10046.365| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.07 r_work: 0.3167 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9283 Z= 0.134 Angle : 0.550 7.940 12602 Z= 0.292 Chirality : 0.042 0.138 1407 Planarity : 0.004 0.039 1587 Dihedral : 4.307 26.058 1255 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.37 % Allowed : 19.31 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.24), residues: 1120 helix: 1.80 (0.25), residues: 387 sheet: -0.75 (0.28), residues: 285 loop : -0.21 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 62 TYR 0.016 0.001 TYR B 59 PHE 0.023 0.001 PHE H 85 TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 9279) covalent geometry : angle 0.55018 / 0.29 (12596) SS BOND : bond 0.00244 / 0.12 ( 3) SS BOND : angle 0.91558 / 0.51 ( 6) hydrogen bonds : bond 0.04599 / 3.13 ( 461) hydrogen bonds : angle 5.07305 / 3.47 ( 1311) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 80 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8710 (p) REVERT: H 106 GLU cc_start: 0.8534 (mp0) cc_final: 0.8313 (mt-10) REVERT: B 52 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7988 (mtt90) REVERT: B 155 ASN cc_start: 0.8489 (t0) cc_final: 0.7958 (t0) REVERT: B 217 MET cc_start: 0.8386 (pmt) cc_final: 0.8142 (pmm) REVERT: B 219 ARG cc_start: 0.8358 (mmm-85) cc_final: 0.7854 (mmm-85) REVERT: B 226 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8180 (mp0) REVERT: B 247 ASP cc_start: 0.7754 (t0) cc_final: 0.7487 (t0) REVERT: B 258 ASP cc_start: 0.8022 (t0) cc_final: 0.7573 (t70) REVERT: A 17 LYS cc_start: 0.8214 (mmtp) cc_final: 0.7396 (mtpt) REVERT: A 21 LYS cc_start: 0.7865 (mtpt) cc_final: 0.7424 (mtmm) REVERT: A 206 GLN cc_start: 0.7256 (tt0) cc_final: 0.6939 (tm-30) REVERT: A 229 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8185 (pp30) REVERT: A 290 LYS cc_start: 0.8472 (mppt) cc_final: 0.8229 (mptp) REVERT: A 326 ASP cc_start: 0.7672 (t0) cc_final: 0.7380 (t70) REVERT: A 368 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6755 (mtt180) REVERT: R 63 MET cc_start: 0.6498 (mmm) cc_final: 0.6195 (mtt) REVERT: R 68 ASN cc_start: 0.7807 (m-40) cc_final: 0.7607 (m110) REVERT: R 89 ASN cc_start: 0.7193 (m-40) cc_final: 0.6741 (m-40) REVERT: R 161 LEU cc_start: 0.7106 (tp) cc_final: 0.6818 (tp) REVERT: R 163 PHE cc_start: 0.6538 (t80) cc_final: 0.6208 (t80) REVERT: R 205 TYR cc_start: 0.7820 (t80) cc_final: 0.6835 (t80) REVERT: R 262 LEU cc_start: 0.7686 (tp) cc_final: 0.7259 (tp) REVERT: R 299 MET cc_start: 0.7410 (ptm) cc_final: 0.6812 (ptt) REVERT: R 300 TYR cc_start: 0.6280 (m-10) cc_final: 0.5943 (m-10) REVERT: R 314 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5866 (mt) REVERT: P 8 PHE cc_start: 0.8291 (m-80) cc_final: 0.8024 (m-80) outliers start: 33 outliers final: 14 residues processed: 194 average time/residue: 0.5385 time to fit residues: 111.7863 Evaluate side-chains 179 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 0.1980 chunk 64 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 62 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN A 229 GLN A 250 GLN A 254 ASN A 277 GLN R 50 ASN R 96 ASN R 274 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.181672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124282 restraints weight = 10057.670| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.10 r_work: 0.3158 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9283 Z= 0.178 Angle : 0.576 8.826 12602 Z= 0.307 Chirality : 0.044 0.209 1407 Planarity : 0.004 0.038 1587 Dihedral : 4.345 26.909 1255 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.98 % Allowed : 19.61 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.25), residues: 1120 helix: 1.76 (0.25), residues: 389 sheet: -0.70 (0.28), residues: 285 loop : -0.21 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.022 0.002 TYR R 104 PHE 0.037 0.002 PHE H 85 TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 9279) covalent geometry : angle 0.57547 / 0.31 (12596) SS BOND : bond 0.00289 / 0.14 ( 3) SS BOND : angle 1.12410 / 0.70 ( 6) hydrogen bonds : bond 0.04828 / 3.27 ( 461) hydrogen bonds : angle 5.15878 / 3.52 ( 1311) Misc. bond : bond 0.00044 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 80 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8707 (p) REVERT: H 106 GLU cc_start: 0.8565 (mp0) cc_final: 0.8349 (mt-10) REVERT: B 52 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8038 (mtt90) REVERT: B 155 ASN cc_start: 0.8528 (t0) cc_final: 0.8287 (t0) REVERT: B 217 MET cc_start: 0.8410 (pmt) cc_final: 0.8204 (pmm) REVERT: B 219 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.7852 (mmm-85) REVERT: B 226 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8252 (mp0) REVERT: B 247 ASP cc_start: 0.7802 (t0) cc_final: 0.7576 (t0) REVERT: B 258 ASP cc_start: 0.8107 (t0) cc_final: 0.7701 (t70) REVERT: A 17 LYS cc_start: 0.8275 (mmtp) cc_final: 0.7461 (mtpt) REVERT: A 21 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7455 (mtmm) REVERT: A 26 ASP cc_start: 0.8130 (m-30) cc_final: 0.7558 (m-30) REVERT: A 206 GLN cc_start: 0.7212 (tt0) cc_final: 0.6906 (tm-30) REVERT: A 229 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8293 (pp30) REVERT: A 290 LYS cc_start: 0.8500 (mppt) cc_final: 0.8260 (mptp) REVERT: A 326 ASP cc_start: 0.7770 (t0) cc_final: 0.7480 (t70) REVERT: A 368 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6774 (mtt180) REVERT: R 63 MET cc_start: 0.6566 (mmm) cc_final: 0.6268 (mtt) REVERT: R 68 ASN cc_start: 0.7863 (m-40) cc_final: 0.7660 (m110) REVERT: R 89 ASN cc_start: 0.7292 (m-40) cc_final: 0.6704 (m-40) REVERT: R 161 LEU cc_start: 0.7123 (tp) cc_final: 0.6830 (tp) REVERT: R 163 PHE cc_start: 0.6529 (t80) cc_final: 0.6202 (t80) REVERT: R 205 TYR cc_start: 0.7846 (t80) cc_final: 0.6828 (t80) REVERT: R 262 LEU cc_start: 0.7735 (tp) cc_final: 0.7302 (tp) REVERT: R 299 MET cc_start: 0.7406 (ptm) cc_final: 0.6732 (ptt) REVERT: R 314 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5864 (mt) REVERT: P 8 PHE cc_start: 0.8297 (m-80) cc_final: 0.8000 (m-80) outliers start: 39 outliers final: 21 residues processed: 187 average time/residue: 0.4705 time to fit residues: 93.9417 Evaluate side-chains 185 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN A 229 GLN A 277 GLN R 50 ASN R 96 ASN R 274 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.182268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125084 restraints weight = 10055.685| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.09 r_work: 0.3147 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9283 Z= 0.158 Angle : 0.563 8.467 12602 Z= 0.300 Chirality : 0.043 0.179 1407 Planarity : 0.004 0.037 1587 Dihedral : 4.313 26.263 1255 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.88 % Allowed : 19.51 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.25), residues: 1120 helix: 1.76 (0.25), residues: 388 sheet: -0.62 (0.28), residues: 282 loop : -0.18 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.024 0.002 TYR R 300 PHE 0.032 0.002 PHE H 85 TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 9279) covalent geometry : angle 0.56271 / 0.30 (12596) SS BOND : bond 0.00288 / 0.14 ( 3) SS BOND : angle 1.15886 / 0.77 ( 6) hydrogen bonds : bond 0.04718 / 3.21 ( 461) hydrogen bonds : angle 5.12063 / 3.50 ( 1311) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 80 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8693 (p) REVERT: H 106 GLU cc_start: 0.8570 (mp0) cc_final: 0.8343 (mt-10) REVERT: B 52 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8002 (mtt90) REVERT: B 155 ASN cc_start: 0.8524 (t0) cc_final: 0.8287 (t0) REVERT: B 217 MET cc_start: 0.8412 (pmt) cc_final: 0.8194 (pmm) REVERT: B 219 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.7876 (mmm-85) REVERT: B 226 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8268 (mp0) REVERT: B 247 ASP cc_start: 0.7773 (t0) cc_final: 0.7531 (t0) REVERT: B 258 ASP cc_start: 0.8092 (t0) cc_final: 0.7653 (t70) REVERT: B 266 HIS cc_start: 0.7526 (t70) cc_final: 0.6637 (OUTLIER) REVERT: A 17 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7442 (mtpt) REVERT: A 21 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7455 (mtmm) REVERT: A 26 ASP cc_start: 0.8093 (m-30) cc_final: 0.7520 (m-30) REVERT: A 206 GLN cc_start: 0.7230 (tt0) cc_final: 0.6910 (tm-30) REVERT: A 229 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8202 (pp30) REVERT: A 290 LYS cc_start: 0.8521 (mppt) cc_final: 0.8263 (mptp) REVERT: A 368 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6743 (mtt180) REVERT: R 63 MET cc_start: 0.6510 (mmm) cc_final: 0.6240 (mtt) REVERT: R 85 ASN cc_start: 0.6402 (t0) cc_final: 0.5838 (t160) REVERT: R 89 ASN cc_start: 0.7307 (m-40) cc_final: 0.6613 (m-40) REVERT: R 161 LEU cc_start: 0.7108 (tp) cc_final: 0.6826 (tp) REVERT: R 163 PHE cc_start: 0.6521 (t80) cc_final: 0.6187 (t80) REVERT: R 205 TYR cc_start: 0.7830 (t80) cc_final: 0.6781 (t80) REVERT: R 262 LEU cc_start: 0.7616 (tp) cc_final: 0.7171 (tp) REVERT: R 314 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5865 (mt) REVERT: P 8 PHE cc_start: 0.8274 (m-80) cc_final: 0.7984 (m-80) outliers start: 38 outliers final: 18 residues processed: 186 average time/residue: 0.4788 time to fit residues: 95.1395 Evaluate side-chains 179 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 97 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 66 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN A 275 ASN A 277 GLN R 68 ASN R 96 ASN R 274 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.184294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126584 restraints weight = 9996.018| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.01 r_work: 0.3182 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9283 Z= 0.126 Angle : 0.550 8.288 12602 Z= 0.291 Chirality : 0.043 0.238 1407 Planarity : 0.004 0.038 1587 Dihedral : 4.217 25.139 1255 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.35 % Allowed : 20.94 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.60 (0.25), residues: 1120 helix: 1.85 (0.25), residues: 382 sheet: -0.57 (0.28), residues: 282 loop : -0.07 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.025 0.001 TYR R 300 PHE 0.028 0.001 PHE H 85 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 9279) covalent geometry : angle 0.54939 / 0.29 (12596) SS BOND : bond 0.00239 / 0.12 ( 3) SS BOND : angle 1.06554 / 0.77 ( 6) hydrogen bonds : bond 0.04442 / 3.02 ( 461) hydrogen bonds : angle 5.00508 / 3.42 ( 1311) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 106 GLU cc_start: 0.8551 (mp0) cc_final: 0.8333 (mt-10) REVERT: B 52 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7980 (mtt90) REVERT: B 155 ASN cc_start: 0.8515 (t0) cc_final: 0.7977 (t0) REVERT: B 217 MET cc_start: 0.8434 (pmt) cc_final: 0.8186 (pmm) REVERT: B 219 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.7881 (mmm-85) REVERT: B 226 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8214 (mp0) REVERT: B 247 ASP cc_start: 0.7743 (t0) cc_final: 0.7460 (t0) REVERT: B 266 HIS cc_start: 0.7433 (t70) cc_final: 0.6811 (OUTLIER) REVERT: G 18 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.7148 (tp-100) REVERT: A 17 LYS cc_start: 0.8264 (mmtp) cc_final: 0.7465 (mtpt) REVERT: A 21 LYS cc_start: 0.7889 (mtpt) cc_final: 0.7448 (mtmm) REVERT: A 26 ASP cc_start: 0.8068 (m-30) cc_final: 0.7841 (m-30) REVERT: A 206 GLN cc_start: 0.7241 (tt0) cc_final: 0.6910 (tm-30) REVERT: A 229 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8229 (pp30) REVERT: A 290 LYS cc_start: 0.8534 (mppt) cc_final: 0.8268 (mptp) REVERT: A 368 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6860 (mtt-85) REVERT: R 63 MET cc_start: 0.6509 (mmm) cc_final: 0.6267 (mtt) REVERT: R 85 ASN cc_start: 0.6391 (t0) cc_final: 0.5848 (t160) REVERT: R 89 ASN cc_start: 0.7293 (m-40) cc_final: 0.6712 (m-40) REVERT: R 161 LEU cc_start: 0.7148 (tp) cc_final: 0.6886 (tp) REVERT: R 163 PHE cc_start: 0.6511 (t80) cc_final: 0.6180 (t80) REVERT: R 174 MET cc_start: 0.6016 (ppp) cc_final: 0.5741 (ppp) REVERT: R 205 TYR cc_start: 0.7855 (t80) cc_final: 0.6831 (t80) REVERT: R 262 LEU cc_start: 0.7597 (tp) cc_final: 0.7144 (tp) REVERT: R 314 LEU cc_start: 0.6244 (tt) cc_final: 0.5881 (mt) REVERT: P 8 PHE cc_start: 0.8311 (m-80) cc_final: 0.8048 (m-80) outliers start: 23 outliers final: 15 residues processed: 187 average time/residue: 0.4438 time to fit residues: 88.3682 Evaluate side-chains 179 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 GLN B 17 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN R 68 ASN R 73 ASN ** R 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 274 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117835 restraints weight = 10010.578| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.18 r_work: 0.3160 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 9283 Z= 0.385 Angle : 0.756 12.499 12602 Z= 0.400 Chirality : 0.051 0.179 1407 Planarity : 0.005 0.049 1587 Dihedral : 4.976 28.552 1255 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.37 % Allowed : 19.20 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.17 (0.24), residues: 1120 helix: 1.23 (0.25), residues: 384 sheet: -0.50 (0.30), residues: 269 loop : -0.32 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 19 TYR 0.028 0.003 TYR R 300 PHE 0.053 0.003 PHE H 85 TRP 0.019 0.002 TRP B 169 HIS 0.009 0.002 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00916 / 0.39 ( 9279) covalent geometry : angle 0.75439 / 0.40 (12596) SS BOND : bond 0.00449 / 0.22 ( 3) SS BOND : angle 2.23358 / 1.38 ( 6) hydrogen bonds : bond 0.05895 / 4.00 ( 461) hydrogen bonds : angle 5.55587 / 3.81 ( 1311) Misc. bond : bond 0.00119 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.212 Fit side-chains REVERT: B 52 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8301 (mtt90) REVERT: B 155 ASN cc_start: 0.8635 (t0) cc_final: 0.8283 (t0) REVERT: B 212 ASP cc_start: 0.8387 (t70) cc_final: 0.7055 (t70) REVERT: B 215 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7516 (mp0) REVERT: B 217 MET cc_start: 0.8453 (pmt) cc_final: 0.8128 (pmm) REVERT: B 219 ARG cc_start: 0.8462 (mmm-85) cc_final: 0.7910 (mmm-85) REVERT: B 258 ASP cc_start: 0.8314 (t0) cc_final: 0.8058 (t0) REVERT: B 266 HIS cc_start: 0.7578 (t70) cc_final: 0.6731 (OUTLIER) REVERT: A 3 CYS cc_start: 0.6219 (m) cc_final: 0.5976 (t) REVERT: A 17 LYS cc_start: 0.8507 (mmtp) cc_final: 0.7764 (mtpt) REVERT: A 26 ASP cc_start: 0.8166 (m-30) cc_final: 0.7640 (m-30) REVERT: A 206 GLN cc_start: 0.7201 (tt0) cc_final: 0.6867 (tm-30) REVERT: A 290 LYS cc_start: 0.8675 (mppt) cc_final: 0.8112 (ttpp) REVERT: A 368 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6954 (mtt180) REVERT: R 63 MET cc_start: 0.6708 (mmm) cc_final: 0.6371 (mtt) REVERT: R 89 ASN cc_start: 0.7326 (m-40) cc_final: 0.6782 (m-40) REVERT: R 161 LEU cc_start: 0.7176 (tp) cc_final: 0.6867 (tp) REVERT: R 163 PHE cc_start: 0.6699 (t80) cc_final: 0.6428 (t80) REVERT: R 205 TYR cc_start: 0.7929 (t80) cc_final: 0.6907 (t80) REVERT: R 262 LEU cc_start: 0.7914 (tp) cc_final: 0.7546 (tp) REVERT: R 314 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5904 (mt) REVERT: P 8 PHE cc_start: 0.8373 (m-80) cc_final: 0.8095 (m-80) outliers start: 33 outliers final: 16 residues processed: 178 average time/residue: 0.4827 time to fit residues: 91.7777 Evaluate side-chains 163 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 266 ILE Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 51 optimal weight: 0.4980 chunk 52 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 GLN B 17 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 266 HIS G 18 GLN A 229 GLN A 275 ASN A 277 GLN R 68 ASN ** R 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.182194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124668 restraints weight = 10018.191| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.15 r_work: 0.3185 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9283 Z= 0.142 Angle : 0.612 10.661 12602 Z= 0.316 Chirality : 0.044 0.220 1407 Planarity : 0.004 0.037 1587 Dihedral : 4.498 24.344 1255 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.15 % Allowed : 21.04 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.25), residues: 1120 helix: 1.56 (0.25), residues: 382 sheet: -0.60 (0.29), residues: 269 loop : -0.15 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 19 TYR 0.026 0.002 TYR R 300 PHE 0.017 0.001 PHE R 264 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 9279) covalent geometry : angle 0.61091 / 0.32 (12596) SS BOND : bond 0.00251 / 0.12 ( 3) SS BOND : angle 1.43900 / 0.98 ( 6) hydrogen bonds : bond 0.04710 / 3.21 ( 461) hydrogen bonds : angle 5.15397 / 3.52 ( 1311) Misc. bond : bond 0.00013 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 60 LYS cc_start: 0.8925 (mmtm) cc_final: 0.8685 (mppt) REVERT: H 63 GLU cc_start: 0.8469 (tt0) cc_final: 0.7855 (pt0) REVERT: B 52 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7990 (mtt90) REVERT: B 155 ASN cc_start: 0.8553 (t0) cc_final: 0.8177 (t0) REVERT: B 217 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8215 (pmm) REVERT: B 219 ARG cc_start: 0.8398 (mmm-85) cc_final: 0.7873 (mmm-85) REVERT: B 266 HIS cc_start: 0.7087 (t-90) cc_final: 0.6841 (OUTLIER) REVERT: A 17 LYS cc_start: 0.8289 (mmtp) cc_final: 0.7497 (mtpt) REVERT: A 26 ASP cc_start: 0.8040 (m-30) cc_final: 0.7464 (m-30) REVERT: A 206 GLN cc_start: 0.7180 (tt0) cc_final: 0.6848 (tm-30) REVERT: A 229 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8343 (pp30) REVERT: A 290 LYS cc_start: 0.8641 (mppt) cc_final: 0.8115 (ttpp) REVERT: A 368 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6783 (mtt180) REVERT: R 63 MET cc_start: 0.6542 (mmm) cc_final: 0.6278 (mtt) REVERT: R 68 ASN cc_start: 0.7917 (m-40) cc_final: 0.7711 (m110) REVERT: R 85 ASN cc_start: 0.6418 (t0) cc_final: 0.5909 (t160) REVERT: R 89 ASN cc_start: 0.7186 (m-40) cc_final: 0.6640 (m-40) REVERT: R 161 LEU cc_start: 0.7179 (tp) cc_final: 0.6950 (tp) REVERT: R 163 PHE cc_start: 0.6560 (t80) cc_final: 0.6310 (t80) REVERT: R 205 TYR cc_start: 0.7831 (t80) cc_final: 0.6823 (t80) REVERT: R 262 LEU cc_start: 0.7624 (tp) cc_final: 0.7182 (tp) REVERT: R 314 LEU cc_start: 0.6207 (tt) cc_final: 0.5852 (mt) REVERT: P 8 PHE cc_start: 0.8314 (m-80) cc_final: 0.8021 (m-80) outliers start: 21 outliers final: 15 residues processed: 180 average time/residue: 0.5124 time to fit residues: 98.7874 Evaluate side-chains 175 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 57 optimal weight: 0.0770 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 GLN B 17 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN A 229 GLN A 275 ASN A 277 GLN R 73 ASN ** R 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.180217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122156 restraints weight = 9934.235| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.15 r_work: 0.3152 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9283 Z= 0.188 Angle : 0.645 13.265 12602 Z= 0.333 Chirality : 0.045 0.252 1407 Planarity : 0.004 0.050 1587 Dihedral : 4.567 26.188 1255 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.66 % Allowed : 21.25 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.43 (0.25), residues: 1120 helix: 1.53 (0.25), residues: 383 sheet: -0.57 (0.29), residues: 269 loop : -0.09 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 19 TYR 0.021 0.002 TYR R 300 PHE 0.018 0.002 PHE H 85 TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 9279) covalent geometry : angle 0.64397 / 0.33 (12596) SS BOND : bond 0.00317 / 0.15 ( 3) SS BOND : angle 1.65609 / 1.09 ( 6) hydrogen bonds : bond 0.04917 / 3.35 ( 461) hydrogen bonds : angle 5.22052 / 3.57 ( 1311) Misc. bond : bond 0.00045 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3807.12 seconds wall clock time: 65 minutes 38.10 seconds (3938.10 seconds total)