Starting phenix.real_space_refine on Thu Sep 18 09:44:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kym_62647/09_2025/9kym_62647.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kym_62647/09_2025/9kym_62647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kym_62647/09_2025/9kym_62647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kym_62647/09_2025/9kym_62647.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kym_62647/09_2025/9kym_62647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kym_62647/09_2025/9kym_62647.map" } resolution = 3.93 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= 0.017 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: 5 Type Number sf(0) Gaussians S 39 5.16 5 C 5066 2.51 5 N 1324 2.21 5 O 1408 1.98 5 H 8012 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15849 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4264 Classifications: {'peptide': 278} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 265} Chain: "B" Number of atoms: 4312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4312 Classifications: {'peptide': 277} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 262} Chain breaks: 1 Chain: "C" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 4364 Classifications: {'peptide': 266} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 255} Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2909 Classifications: {'peptide': 177} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 169} Time building chain proxies: 2.95, per 1000 atoms: 0.19 Number of scatterers: 15849 At special positions: 0 Unit cell: (81.84, 85.36, 136.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 O 1408 8.00 N 1324 7.00 C 5066 6.00 H 8012 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 480.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 64.1% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.745A pdb=" N ASP A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 82 removed outlier: 3.607A pdb=" N GLU A 81 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 4.260A pdb=" N GLY A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 127 removed outlier: 3.796A pdb=" N VAL A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.860A pdb=" N SER A 140 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 141 " --> pdb=" O PRO A 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 141' Processing helix chain 'A' and resid 142 through 158 removed outlier: 3.976A pdb=" N GLN A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 191 Processing helix chain 'A' and resid 200 through 207 removed outlier: 3.918A pdb=" N ALA A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 232 through 238 removed outlier: 3.881A pdb=" N GLU A 236 " --> pdb=" O THR A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.539A pdb=" N ARG A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.577A pdb=" N ILE B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 79 through 85 removed outlier: 4.105A pdb=" N LEU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.615A pdb=" N ASN B 96 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN B 97 " --> pdb=" O PRO B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 93 through 97' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 117 through 132 removed outlier: 3.668A pdb=" N ASP B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 132 " --> pdb=" O MET B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 147 through 161 removed outlier: 3.677A pdb=" N ARG B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 196 removed outlier: 3.507A pdb=" N GLY B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 212 removed outlier: 3.984A pdb=" N VAL B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 236 through 242 removed outlier: 3.533A pdb=" N LEU B 240 " --> pdb=" O ASN B 236 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 260 Processing helix chain 'B' and resid 270 through 286 Processing helix chain 'C' and resid 15 through 19 Processing helix chain 'C' and resid 20 through 38 removed outlier: 3.519A pdb=" N LYS C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 57 Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.831A pdb=" N PHE C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 67 " --> pdb=" O GLY C 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY C 68 " --> pdb=" O PHE C 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 68' Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 72 through 84 Processing helix chain 'C' and resid 103 through 129 removed outlier: 3.650A pdb=" N LEU C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.652A pdb=" N ILE C 136 " --> pdb=" O GLN C 132 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 151 removed outlier: 3.568A pdb=" N TRP C 149 " --> pdb=" O PRO C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 184 Proline residue: C 169 - end of helix Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 201 through 227 Proline residue: C 207 - end of helix Processing helix chain 'C' and resid 243 through 264 removed outlier: 3.877A pdb=" N THR C 247 " --> pdb=" O GLN C 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 31 removed outlier: 4.095A pdb=" N SER D 31 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 45 through 57 removed outlier: 3.838A pdb=" N VAL D 49 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 50 " --> pdb=" O PHE D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 77 Processing helix chain 'D' and resid 81 through 100 removed outlier: 4.057A pdb=" N THR D 85 " --> pdb=" O PHE D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 134 removed outlier: 3.917A pdb=" N THR D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ASN D 125 " --> pdb=" O ASN D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 165 removed outlier: 3.726A pdb=" N LEU D 140 " --> pdb=" O PRO D 136 " (cutoff:3.500A) Proline residue: D 142 - end of helix Proline residue: D 153 - end of helix Processing helix chain 'D' and resid 165 through 177 removed outlier: 3.618A pdb=" N GLN D 169 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG D 174 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 4.016A pdb=" N ASP A 9 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 63 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU A 11 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLN A 61 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.290A pdb=" N GLY A 84 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.637A pdb=" N ALA B 4 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS B 65 " --> pdb=" O ALA B 4 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.497A pdb=" N GLY B 88 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASP B 170 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B 90 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 167 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL B 202 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 169 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TYR B 35 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA B 217 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA B 37 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 35 through 36 402 hydrogen bonds defined for protein. 1152 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: 3.30 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8011 1.02 - 1.22: 1 1.22 - 1.42: 3216 1.42 - 1.62: 4710 1.62 - 1.81: 77 Bond restraints: 16015 Sorted by residual: bond pdb=" NZ LYS D 177 " pdb=" HZ3 LYS D 177 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" NZ LYS D 177 " pdb=" HZ1 LYS D 177 " ideal model delta sigma weight residual 0.890 0.958 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" NZ LYS D 177 " pdb=" HZ2 LYS D 177 " ideal model delta sigma weight residual 0.890 0.957 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" CA ILE B 39 " pdb=" CB ILE B 39 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.05e-02 9.07e+03 1.73e+00 bond pdb=" C ASN A 278 " pdb=" N THR A 279 " ideal model delta sigma weight residual 1.329 1.345 -0.016 1.40e-02 5.10e+03 1.28e+00 ... (remaining 16010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 28191 1.46 - 2.92: 750 2.92 - 4.39: 73 4.39 - 5.85: 10 5.85 - 7.31: 3 Bond angle restraints: 29027 Sorted by residual: angle pdb=" C ALA C 98 " pdb=" CA ALA C 98 " pdb=" CB ALA C 98 " ideal model delta sigma weight residual 116.63 111.28 5.35 1.16e+00 7.43e-01 2.13e+01 angle pdb=" N SER D 139 " pdb=" CA SER D 139 " pdb=" C SER D 139 " ideal model delta sigma weight residual 114.04 108.90 5.14 1.24e+00 6.50e-01 1.72e+01 angle pdb=" N VAL A 95 " pdb=" CA VAL A 95 " pdb=" C VAL A 95 " ideal model delta sigma weight residual 113.71 110.70 3.01 9.50e-01 1.11e+00 1.00e+01 angle pdb=" N LEU C 204 " pdb=" CA LEU C 204 " pdb=" C LEU C 204 " ideal model delta sigma weight residual 114.39 110.52 3.87 1.45e+00 4.76e-01 7.11e+00 angle pdb=" C ASP B 67 " pdb=" CA ASP B 67 " pdb=" CB ASP B 67 " ideal model delta sigma weight residual 110.42 115.66 -5.24 1.99e+00 2.53e-01 6.92e+00 ... (remaining 29022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6469 17.95 - 35.91: 701 35.91 - 53.86: 245 53.86 - 71.81: 53 71.81 - 89.77: 11 Dihedral angle restraints: 7479 sinusoidal: 4092 harmonic: 3387 Sorted by residual: dihedral pdb=" CA THR A 198 " pdb=" C THR A 198 " pdb=" N HIS A 199 " pdb=" CA HIS A 199 " ideal model delta harmonic sigma weight residual 180.00 160.56 19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PRO C 203 " pdb=" C PRO C 203 " pdb=" N LEU C 204 " pdb=" CA LEU C 204 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA PHE B 99 " pdb=" C PHE B 99 " pdb=" N GLU B 100 " pdb=" CA GLU B 100 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 7476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 903 0.033 - 0.067: 270 0.067 - 0.100: 72 0.100 - 0.134: 33 0.134 - 0.167: 3 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CA LYS D 177 " pdb=" N LYS D 177 " pdb=" C LYS D 177 " pdb=" CB LYS D 177 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA THR A 279 " pdb=" N THR A 279 " pdb=" C THR A 279 " pdb=" CB THR A 279 " both_signs ideal model delta sigma weight residual False 2.53 2.68 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE A 197 " pdb=" N ILE A 197 " pdb=" C ILE A 197 " pdb=" CB ILE A 197 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 1278 not shown) Planarity restraints: 2324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 265 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C HIS C 265 " -0.027 2.00e-02 2.50e+03 pdb=" O HIS C 265 " 0.010 2.00e-02 2.50e+03 pdb=" N TRP C 266 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 278 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C ASN A 278 " -0.026 2.00e-02 2.50e+03 pdb=" O ASN A 278 " 0.010 2.00e-02 2.50e+03 pdb=" N THR A 279 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 72 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 73 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " -0.021 5.00e-02 4.00e+02 ... (remaining 2321 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 522 2.13 - 2.75: 28516 2.75 - 3.37: 44225 3.37 - 3.98: 52501 3.98 - 4.60: 82074 Nonbonded interactions: 207838 Sorted by model distance: nonbonded pdb=" H ASN D 37 " pdb=" O ILE D 40 " model vdw 1.516 2.450 nonbonded pdb=" OD1 ASP A 165 " pdb=" H GLU A 166 " model vdw 1.533 2.450 nonbonded pdb=" OE1 GLU B 207 " pdb=" H GLU B 207 " model vdw 1.572 2.450 nonbonded pdb=" OE1 GLU B 238 " pdb=" H GLU B 238 " model vdw 1.602 2.450 nonbonded pdb=" OE1 GLU C 174 " pdb="HH21 ARG C 215 " model vdw 1.633 2.450 ... (remaining 207833 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.920 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 : 0.003 0.038 8003 Z= 0.131 Angle : 0.613 7.309 10883 Z= 0.338 Chirality : 0.038 0.167 1281 Planarity : 0.004 0.036 1374 Dihedral : 18.390 89.768 2898 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.12 % Allowed : 30.97 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.27), residues: 988 helix: 1.11 (0.23), residues: 551 sheet: -1.22 (0.75), residues: 52 loop : -2.38 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 148 TYR 0.009 0.001 TYR D 160 PHE 0.011 0.001 PHE C 29 TRP 0.010 0.001 TRP B 239 HIS 0.014 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8003) covalent geometry : angle 0.61294 (10883) hydrogen bonds : bond 0.16683 ( 402) hydrogen bonds : angle 6.22195 ( 1152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7184 (tp30) cc_final: 0.6788 (tp30) REVERT: D 148 GLU cc_start: 0.8713 (mp0) cc_final: 0.8430 (mp0) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.1537 time to fit residues: 32.4481 Evaluate side-chains 128 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0470 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 189 GLN B 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.091318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.066027 restraints weight = 63125.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.069588 restraints weight = 26713.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.071971 restraints weight = 16083.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.073506 restraints weight = 11772.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.074502 restraints weight = 9697.506| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8003 Z= 0.129 Angle : 0.576 4.693 10883 Z= 0.310 Chirality : 0.038 0.154 1281 Planarity : 0.004 0.041 1374 Dihedral : 4.727 38.299 1066 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.42 % Allowed : 29.79 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.27), residues: 988 helix: 1.24 (0.23), residues: 553 sheet: -1.48 (0.73), residues: 52 loop : -2.40 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 148 TYR 0.008 0.001 TYR A 15 PHE 0.010 0.001 PHE C 213 TRP 0.006 0.001 TRP D 60 HIS 0.009 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8003) covalent geometry : angle 0.57601 (10883) hydrogen bonds : bond 0.05136 ( 402) hydrogen bonds : angle 5.30717 ( 1152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7447 (tp30) cc_final: 0.7166 (tp30) REVERT: C 179 MET cc_start: 0.8995 (tpp) cc_final: 0.8640 (tpp) REVERT: C 205 MET cc_start: 0.8904 (tpt) cc_final: 0.8504 (tpp) REVERT: D 148 GLU cc_start: 0.8644 (mp0) cc_final: 0.8293 (mp0) outliers start: 12 outliers final: 10 residues processed: 144 average time/residue: 0.1425 time to fit residues: 31.5115 Evaluate side-chains 142 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 263 GLN B 41 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.090302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.064672 restraints weight = 65275.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.068245 restraints weight = 28013.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.070654 restraints weight = 16964.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.072034 restraints weight = 12434.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.073123 restraints weight = 10378.105| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8003 Z= 0.159 Angle : 0.556 4.770 10883 Z= 0.301 Chirality : 0.038 0.150 1281 Planarity : 0.004 0.036 1374 Dihedral : 4.638 34.957 1066 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.72 % Allowed : 28.25 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.27), residues: 988 helix: 1.18 (0.23), residues: 553 sheet: -1.55 (0.74), residues: 52 loop : -2.47 (0.27), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 148 TYR 0.009 0.001 TYR D 133 PHE 0.013 0.001 PHE C 213 TRP 0.006 0.001 TRP D 60 HIS 0.004 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8003) covalent geometry : angle 0.55625 (10883) hydrogen bonds : bond 0.04817 ( 402) hydrogen bonds : angle 5.16356 ( 1152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 179 MET cc_start: 0.8976 (tpp) cc_final: 0.8760 (tpp) REVERT: C 205 MET cc_start: 0.8939 (tpt) cc_final: 0.8594 (tpp) REVERT: D 132 MET cc_start: 0.9076 (tmm) cc_final: 0.8572 (tmm) REVERT: D 148 GLU cc_start: 0.8704 (mp0) cc_final: 0.8243 (mp0) outliers start: 23 outliers final: 15 residues processed: 147 average time/residue: 0.1473 time to fit residues: 32.6956 Evaluate side-chains 146 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 130 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 24 optimal weight: 0.0170 chunk 84 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.089591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.064093 restraints weight = 64612.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.067600 restraints weight = 27730.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.069987 restraints weight = 16828.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.071527 restraints weight = 12296.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.072495 restraints weight = 10136.487| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8003 Z= 0.173 Angle : 0.557 5.695 10883 Z= 0.303 Chirality : 0.038 0.153 1281 Planarity : 0.004 0.058 1374 Dihedral : 4.619 33.284 1066 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.60 % Allowed : 28.96 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.27), residues: 988 helix: 1.18 (0.23), residues: 547 sheet: -1.54 (0.73), residues: 53 loop : -2.48 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 101 TYR 0.019 0.001 TYR D 100 PHE 0.016 0.001 PHE C 213 TRP 0.006 0.001 TRP D 60 HIS 0.010 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8003) covalent geometry : angle 0.55653 (10883) hydrogen bonds : bond 0.04591 ( 402) hydrogen bonds : angle 5.09951 ( 1152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8074 (t80) cc_final: 0.7714 (t80) REVERT: B 100 GLU cc_start: 0.7817 (tp30) cc_final: 0.7209 (tp30) REVERT: C 205 MET cc_start: 0.8964 (tpt) cc_final: 0.8606 (tpp) REVERT: D 132 MET cc_start: 0.9130 (tmm) cc_final: 0.8615 (tmm) REVERT: D 148 GLU cc_start: 0.8678 (mp0) cc_final: 0.8241 (mp0) outliers start: 22 outliers final: 19 residues processed: 148 average time/residue: 0.1351 time to fit residues: 30.8179 Evaluate side-chains 151 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 130 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 75 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 54 optimal weight: 0.0670 chunk 73 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.0040 chunk 13 optimal weight: 4.9990 overall best weight: 0.7332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 42 ASN A 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.091233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.065501 restraints weight = 64302.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.069096 restraints weight = 27619.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.071531 restraints weight = 16740.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.073104 restraints weight = 12258.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.074060 restraints weight = 10076.157| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8003 Z= 0.111 Angle : 0.528 5.668 10883 Z= 0.281 Chirality : 0.037 0.150 1281 Planarity : 0.004 0.035 1374 Dihedral : 4.477 29.752 1066 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.84 % Allowed : 28.37 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.27), residues: 988 helix: 1.42 (0.23), residues: 547 sheet: -1.50 (0.73), residues: 53 loop : -2.43 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 101 TYR 0.012 0.001 TYR D 100 PHE 0.011 0.001 PHE C 213 TRP 0.006 0.001 TRP D 60 HIS 0.010 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8003) covalent geometry : angle 0.52759 (10883) hydrogen bonds : bond 0.04285 ( 402) hydrogen bonds : angle 4.81872 ( 1152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8027 (t80) cc_final: 0.7286 (t80) REVERT: A 57 LEU cc_start: 0.8841 (pp) cc_final: 0.8577 (pp) REVERT: B 100 GLU cc_start: 0.7866 (tp30) cc_final: 0.7217 (tp30) REVERT: C 167 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8821 (m-80) REVERT: C 205 MET cc_start: 0.8902 (tpt) cc_final: 0.8514 (tpp) REVERT: D 132 MET cc_start: 0.9126 (tmm) cc_final: 0.8572 (tmm) REVERT: D 148 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8184 (mp0) outliers start: 24 outliers final: 15 residues processed: 154 average time/residue: 0.1419 time to fit residues: 33.4203 Evaluate side-chains 151 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 148 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 84 optimal weight: 0.0020 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 18 optimal weight: 0.0030 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.064923 restraints weight = 64041.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.068481 restraints weight = 27867.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.070879 restraints weight = 17000.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.072427 restraints weight = 12492.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.073422 restraints weight = 10296.776| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8003 Z= 0.127 Angle : 0.528 5.623 10883 Z= 0.282 Chirality : 0.038 0.161 1281 Planarity : 0.004 0.038 1374 Dihedral : 4.397 27.774 1066 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.13 % Allowed : 28.72 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.27), residues: 988 helix: 1.38 (0.23), residues: 550 sheet: -1.35 (0.74), residues: 53 loop : -2.42 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 285 TYR 0.013 0.001 TYR D 100 PHE 0.011 0.001 PHE C 213 TRP 0.006 0.001 TRP D 60 HIS 0.011 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8003) covalent geometry : angle 0.52817 (10883) hydrogen bonds : bond 0.04132 ( 402) hydrogen bonds : angle 4.81814 ( 1152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8024 (t80) cc_final: 0.7678 (t80) REVERT: B 100 GLU cc_start: 0.8025 (tp30) cc_final: 0.7495 (tp30) REVERT: C 167 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8812 (m-80) REVERT: C 205 MET cc_start: 0.8927 (tpt) cc_final: 0.8543 (tpp) REVERT: D 132 MET cc_start: 0.9159 (tmm) cc_final: 0.8580 (tmm) REVERT: D 148 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8199 (mp0) outliers start: 18 outliers final: 15 residues processed: 147 average time/residue: 0.1419 time to fit residues: 31.8559 Evaluate side-chains 153 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 148 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 51 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.090413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.064521 restraints weight = 63907.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.068057 restraints weight = 27564.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.070435 restraints weight = 16755.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.072004 restraints weight = 12320.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.072708 restraints weight = 10125.573| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8003 Z= 0.145 Angle : 0.541 7.369 10883 Z= 0.289 Chirality : 0.038 0.152 1281 Planarity : 0.004 0.033 1374 Dihedral : 4.368 27.126 1066 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.13 % Allowed : 29.43 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.27), residues: 988 helix: 1.32 (0.23), residues: 550 sheet: -1.42 (0.74), residues: 53 loop : -2.41 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 285 TYR 0.013 0.001 TYR D 100 PHE 0.013 0.001 PHE C 213 TRP 0.006 0.001 TRP D 60 HIS 0.012 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8003) covalent geometry : angle 0.54125 (10883) hydrogen bonds : bond 0.04158 ( 402) hydrogen bonds : angle 4.83936 ( 1152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8123 (t80) cc_final: 0.7777 (t80) REVERT: B 100 GLU cc_start: 0.8119 (tp30) cc_final: 0.7575 (tp30) REVERT: C 167 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8864 (m-80) REVERT: C 205 MET cc_start: 0.8923 (tpt) cc_final: 0.8511 (tpp) REVERT: D 132 MET cc_start: 0.9169 (tmm) cc_final: 0.8719 (tmm) REVERT: D 148 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8207 (mp0) outliers start: 18 outliers final: 15 residues processed: 148 average time/residue: 0.1410 time to fit residues: 31.7374 Evaluate side-chains 149 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 148 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.064891 restraints weight = 64308.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.068448 restraints weight = 27548.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.070801 restraints weight = 16623.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.072393 restraints weight = 12188.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.073253 restraints weight = 9988.562| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8003 Z= 0.133 Angle : 0.536 7.429 10883 Z= 0.285 Chirality : 0.038 0.151 1281 Planarity : 0.004 0.034 1374 Dihedral : 4.340 25.642 1066 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.25 % Allowed : 29.20 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.27), residues: 988 helix: 1.32 (0.23), residues: 556 sheet: -1.49 (0.73), residues: 53 loop : -2.38 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 285 TYR 0.012 0.001 TYR D 100 PHE 0.017 0.001 PHE C 117 TRP 0.005 0.001 TRP D 60 HIS 0.013 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8003) covalent geometry : angle 0.53628 (10883) hydrogen bonds : bond 0.04081 ( 402) hydrogen bonds : angle 4.76903 ( 1152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8081 (t80) cc_final: 0.7734 (t80) REVERT: B 100 GLU cc_start: 0.8146 (tp30) cc_final: 0.7602 (tp30) REVERT: C 167 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8809 (m-80) REVERT: C 205 MET cc_start: 0.8905 (tpt) cc_final: 0.8475 (tpp) REVERT: D 132 MET cc_start: 0.9173 (tmm) cc_final: 0.8703 (tmm) REVERT: D 148 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8184 (mp0) outliers start: 19 outliers final: 17 residues processed: 148 average time/residue: 0.1376 time to fit residues: 31.1768 Evaluate side-chains 148 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 148 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 72 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 80 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.064727 restraints weight = 64102.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.068240 restraints weight = 27815.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.070595 restraints weight = 16984.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.072121 restraints weight = 12501.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.073002 restraints weight = 10333.116| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8003 Z= 0.137 Angle : 0.548 7.334 10883 Z= 0.289 Chirality : 0.038 0.152 1281 Planarity : 0.004 0.035 1374 Dihedral : 4.331 24.827 1066 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.48 % Allowed : 29.31 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.27), residues: 988 helix: 1.28 (0.23), residues: 556 sheet: -1.53 (0.72), residues: 53 loop : -2.39 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 152 TYR 0.016 0.001 TYR C 31 PHE 0.013 0.001 PHE C 213 TRP 0.006 0.001 TRP B 239 HIS 0.013 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8003) covalent geometry : angle 0.54771 (10883) hydrogen bonds : bond 0.04071 ( 402) hydrogen bonds : angle 4.76418 ( 1152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8088 (t80) cc_final: 0.7739 (t80) REVERT: B 100 GLU cc_start: 0.8172 (tp30) cc_final: 0.7624 (tp30) REVERT: C 167 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8861 (m-80) REVERT: C 205 MET cc_start: 0.8904 (tpt) cc_final: 0.8468 (tpp) REVERT: D 132 MET cc_start: 0.9188 (tmm) cc_final: 0.8716 (tmm) REVERT: D 148 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8163 (mp0) outliers start: 21 outliers final: 17 residues processed: 145 average time/residue: 0.1504 time to fit residues: 33.0373 Evaluate side-chains 150 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 148 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.091448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.065674 restraints weight = 64132.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.069266 restraints weight = 27849.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.071674 restraints weight = 16962.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.073122 restraints weight = 12437.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.074135 restraints weight = 10358.993| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8003 Z= 0.108 Angle : 0.539 9.966 10883 Z= 0.280 Chirality : 0.038 0.149 1281 Planarity : 0.004 0.037 1374 Dihedral : 4.223 21.898 1066 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.25 % Allowed : 29.43 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.28), residues: 988 helix: 1.44 (0.23), residues: 555 sheet: -1.51 (0.72), residues: 53 loop : -2.32 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 285 TYR 0.018 0.001 TYR C 31 PHE 0.009 0.001 PHE C 213 TRP 0.005 0.001 TRP D 60 HIS 0.013 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8003) covalent geometry : angle 0.53923 (10883) hydrogen bonds : bond 0.03872 ( 402) hydrogen bonds : angle 4.66732 ( 1152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8050 (t80) cc_final: 0.7694 (t80) REVERT: A 268 MET cc_start: 0.9185 (mmt) cc_final: 0.8984 (mmm) REVERT: B 100 GLU cc_start: 0.8194 (tp30) cc_final: 0.7639 (tp30) REVERT: C 167 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8876 (m-80) REVERT: C 205 MET cc_start: 0.8893 (tpt) cc_final: 0.8453 (tpp) REVERT: D 132 MET cc_start: 0.9182 (tmm) cc_final: 0.8714 (tmm) REVERT: D 148 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8158 (mp0) outliers start: 19 outliers final: 15 residues processed: 147 average time/residue: 0.1463 time to fit residues: 32.8514 Evaluate side-chains 149 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 148 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 19 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 90 optimal weight: 0.0370 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.091400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.065573 restraints weight = 63237.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.069129 restraints weight = 27475.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.071529 restraints weight = 16719.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.073070 restraints weight = 12255.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.074031 restraints weight = 10110.828| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8003 Z= 0.116 Angle : 0.543 8.296 10883 Z= 0.284 Chirality : 0.038 0.150 1281 Planarity : 0.004 0.035 1374 Dihedral : 4.181 20.437 1066 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.01 % Allowed : 29.43 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.27), residues: 988 helix: 1.41 (0.23), residues: 555 sheet: -1.50 (0.72), residues: 53 loop : -2.31 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 285 TYR 0.018 0.001 TYR C 31 PHE 0.010 0.001 PHE C 213 TRP 0.006 0.001 TRP D 60 HIS 0.014 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8003) covalent geometry : angle 0.54323 (10883) hydrogen bonds : bond 0.03845 ( 402) hydrogen bonds : angle 4.67378 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2699.89 seconds wall clock time: 46 minutes 42.12 seconds (2802.12 seconds total)