Starting phenix.real_space_refine on Fri Aug 22 17:10:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bmr_16122/08_2025/8bmr_16122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bmr_16122/08_2025/8bmr_16122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bmr_16122/08_2025/8bmr_16122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bmr_16122/08_2025/8bmr_16122.map" model { file = "/net/cci-nas-00/data/ceres_data/8bmr_16122/08_2025/8bmr_16122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bmr_16122/08_2025/8bmr_16122.cif" } resolution = 3.8 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= 0.004 sd= 0.078 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 26 5.16 5 C 4087 2.51 5 N 1050 2.21 5 O 1167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6330 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2129 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2131 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 1 Chain: "C" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2070 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Time building chain proxies: 1.21, per 1000 atoms: 0.19 Number of scatterers: 6330 At special positions: 0 Unit cell: (82.782, 83.804, 116.508, 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 26 16.00 O 1167 8.00 N 1050 7.00 C 4087 6.00 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: 0.38 Conformation dependent library (CDL) restraints added in 312.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1502 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 4 sheets defined 59.4% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 removed outlier: 4.803A pdb=" N SER A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 78 through 85 removed outlier: 3.962A pdb=" N VAL A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 97 removed outlier: 3.619A pdb=" N GLN A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 97 " --> pdb=" O ASP A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 93 through 97' Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 146 through 160 removed outlier: 3.765A pdb=" N GLN A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 194 Processing helix chain 'A' and resid 203 through 208 removed outlier: 4.249A pdb=" N ALA A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 233 through 241 removed outlier: 3.595A pdb=" N LEU A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'B' and resid 45 through 52 removed outlier: 3.757A pdb=" N GLN B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 removed outlier: 4.378A pdb=" N LEU B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.577A pdb=" N ALA B 96 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 110 through 114 Processing helix chain 'B' and resid 117 through 133 Processing helix chain 'B' and resid 135 through 139 removed outlier: 4.028A pdb=" N ILE B 139 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 removed outlier: 5.855A pdb=" N SER B 147 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 161 removed outlier: 3.688A pdb=" N ARG B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 155 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 193 Processing helix chain 'B' and resid 204 through 211 removed outlier: 3.830A pdb=" N VAL B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.686A pdb=" N PHE B 233 " --> pdb=" O PRO B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 242 Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 269 through 282 Processing helix chain 'C' and resid 14 through 19 removed outlier: 3.515A pdb=" N VAL C 19 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 38 Processing helix chain 'C' and resid 40 through 59 Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.847A pdb=" N PHE C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 86 removed outlier: 4.133A pdb=" N ILE C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 108 through 127 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 145 through 149 removed outlier: 3.833A pdb=" N LEU C 148 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 185 removed outlier: 3.732A pdb=" N ARG C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 191 through 197 removed outlier: 3.908A pdb=" N LYS C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 225 removed outlier: 4.177A pdb=" N VAL C 205 " --> pdb=" O VAL C 201 " (cutoff:3.500A) Proline residue: C 206 - end of helix Processing helix chain 'C' and resid 245 through 261 removed outlier: 4.034A pdb=" N VAL C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 11 removed outlier: 3.866A pdb=" N ASN A 4 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A 26 " --> pdb=" O PHE A 8 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS A 10 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER A 24 " --> pdb=" O HIS A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89 removed outlier: 6.198A pdb=" N ILE A 165 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE A 200 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 167 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 213 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN A 224 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 215 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 23 through 30 removed outlier: 6.337A pdb=" N ASP B 24 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER B 9 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU B 26 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.455A pdb=" N SER B 88 " --> pdb=" O CYS B 168 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 36 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU B 219 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.64 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2038 1.35 - 1.46: 1411 1.46 - 1.58: 2958 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 6457 Sorted by residual: bond pdb=" CA ILE C 247 " pdb=" C ILE C 247 " ideal model delta sigma weight residual 1.520 1.529 -0.009 8.80e-03 1.29e+04 1.08e+00 bond pdb=" CB ARG B 85 " pdb=" CG ARG B 85 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.60e-01 bond pdb=" CB GLU A 256 " pdb=" CG GLU A 256 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.45e-01 bond pdb=" CB GLU B 163 " pdb=" CG GLU B 163 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.28e-01 bond pdb=" CA GLU B 163 " pdb=" CB GLU B 163 " ideal model delta sigma weight residual 1.530 1.543 -0.014 1.58e-02 4.01e+03 7.36e-01 ... (remaining 6452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 8468 1.49 - 2.99: 205 2.99 - 4.48: 53 4.48 - 5.98: 13 5.98 - 7.47: 4 Bond angle restraints: 8743 Sorted by residual: angle pdb=" CA ARG B 85 " pdb=" CB ARG B 85 " pdb=" CG ARG B 85 " ideal model delta sigma weight residual 114.10 119.41 -5.31 2.00e+00 2.50e-01 7.06e+00 angle pdb=" N ASP B 170 " pdb=" CA ASP B 170 " pdb=" C ASP B 170 " ideal model delta sigma weight residual 110.53 107.16 3.37 1.29e+00 6.01e-01 6.81e+00 angle pdb=" C GLU A 269 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.70e+00 angle pdb=" CA GLU B 163 " pdb=" CB GLU B 163 " pdb=" CG GLU B 163 " ideal model delta sigma weight residual 114.10 119.16 -5.06 2.00e+00 2.50e-01 6.41e+00 angle pdb=" CB MET C 118 " pdb=" CG MET C 118 " pdb=" SD MET C 118 " ideal model delta sigma weight residual 112.70 120.17 -7.47 3.00e+00 1.11e-01 6.21e+00 ... (remaining 8738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3497 18.00 - 35.99: 334 35.99 - 53.99: 41 53.99 - 71.98: 5 71.98 - 89.98: 3 Dihedral angle restraints: 3880 sinusoidal: 1556 harmonic: 2324 Sorted by residual: dihedral pdb=" CA LEU B 169 " pdb=" C LEU B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA LEU B 98 " pdb=" C LEU B 98 " pdb=" N PHE B 99 " pdb=" CA PHE B 99 " ideal model delta harmonic sigma weight residual 180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA PHE C 188 " pdb=" C PHE C 188 " pdb=" N ASN C 189 " pdb=" CA ASN C 189 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 3877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 599 0.030 - 0.060: 259 0.060 - 0.090: 88 0.090 - 0.120: 55 0.120 - 0.150: 8 Chirality restraints: 1009 Sorted by residual: chirality pdb=" CA ILE B 166 " pdb=" N ILE B 166 " pdb=" C ILE B 166 " pdb=" CB ILE B 166 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA VAL C 201 " pdb=" N VAL C 201 " pdb=" C VAL C 201 " pdb=" CB VAL C 201 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 6 " pdb=" N ILE A 6 " pdb=" C ILE A 6 " pdb=" CB ILE A 6 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1006 not shown) Planarity restraints: 1105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 270 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C LYS A 270 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS A 270 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 271 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 231 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 232 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 20 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 21 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " 0.024 5.00e-02 4.00e+02 ... (remaining 1102 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1023 2.76 - 3.30: 6407 3.30 - 3.83: 10046 3.83 - 4.37: 11065 4.37 - 4.90: 19194 Nonbonded interactions: 47735 Sorted by model distance: nonbonded pdb=" O VAL C 55 " pdb=" OG1 THR C 58 " model vdw 2.228 3.040 nonbonded pdb=" O PHE A 13 " pdb=" OG SER A 18 " model vdw 2.235 3.040 nonbonded pdb=" OG1 THR A 171 " pdb=" OE2 GLU A 206 " model vdw 2.273 3.040 nonbonded pdb=" OE1 GLN A 150 " pdb=" OG SER A 170 " model vdw 2.305 3.040 nonbonded pdb=" OE2 GLU A 111 " pdb=" NH1 ARG C 233 " model vdw 2.314 3.120 ... (remaining 47730 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: 1.110 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 0.034 6457 Z= 0.119 Angle : 0.611 7.473 8743 Z= 0.312 Chirality : 0.042 0.150 1009 Planarity : 0.005 0.052 1105 Dihedral : 13.549 89.979 2378 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -0.04 (0.31), residues: 798 helix: 0.68 (0.26), residues: 414 sheet: 0.19 (0.69), residues: 68 loop : -0.94 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 165 TYR 0.010 0.001 TYR A 248 PHE 0.012 0.001 PHE C 166 TRP 0.012 0.001 TRP B 238 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6457) covalent geometry : angle 0.61106 ( 8743) hydrogen bonds : bond 0.15272 ( 322) hydrogen bonds : angle 6.50125 ( 900) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.190 Fit side-chains REVERT: A 133 MET cc_start: 0.8903 (mmm) cc_final: 0.8617 (mmt) REVERT: B 220 HIS cc_start: 0.7879 (m90) cc_final: 0.7352 (m90) REVERT: B 268 LEU cc_start: 0.9060 (mm) cc_final: 0.8850 (mm) REVERT: C 140 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8417 (tm-30) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.0572 time to fit residues: 10.6938 Evaluate side-chains 113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 196 HIS ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.153377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116666 restraints weight = 10870.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119832 restraints weight = 6938.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.122035 restraints weight = 5118.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123247 restraints weight = 4137.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124379 restraints weight = 3608.248| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 6457 Z= 0.272 Angle : 0.696 11.020 8743 Z= 0.354 Chirality : 0.046 0.148 1009 Planarity : 0.005 0.050 1105 Dihedral : 4.643 20.663 855 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.76 % Allowed : 12.06 % Favored : 85.17 % 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: 0.11 (0.31), residues: 798 helix: 0.99 (0.26), residues: 420 sheet: -0.02 (0.66), residues: 68 loop : -1.15 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 233 TYR 0.012 0.002 TYR C 251 PHE 0.024 0.002 PHE B 99 TRP 0.009 0.001 TRP A 80 HIS 0.014 0.002 HIS A 10 Details of bonding type rmsd covalent geometry : bond 0.00653 ( 6457) covalent geometry : angle 0.69640 ( 8743) hydrogen bonds : bond 0.04176 ( 322) hydrogen bonds : angle 4.92572 ( 900) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.248 Fit side-chains REVERT: B 85 ARG cc_start: 0.8532 (tpt-90) cc_final: 0.8236 (tpt-90) REVERT: B 92 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7973 (tm-30) REVERT: B 220 HIS cc_start: 0.7898 (m90) cc_final: 0.7347 (m90) REVERT: B 268 LEU cc_start: 0.9220 (mm) cc_final: 0.9005 (mm) REVERT: C 116 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7266 (t80) REVERT: C 134 GLU cc_start: 0.8738 (mp0) cc_final: 0.8292 (mp0) REVERT: C 140 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8433 (tm-30) outliers start: 19 outliers final: 13 residues processed: 131 average time/residue: 0.0583 time to fit residues: 10.5758 Evaluate side-chains 124 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 40.0000 chunk 53 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** C 83 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 = 0.3966 r_free = 0.3966 target = 0.157373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121056 restraints weight = 10725.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124402 restraints weight = 6769.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126598 restraints weight = 4949.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.127933 restraints weight = 4003.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.129044 restraints weight = 3475.275| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6457 Z= 0.122 Angle : 0.573 8.926 8743 Z= 0.287 Chirality : 0.042 0.151 1009 Planarity : 0.004 0.050 1105 Dihedral : 4.380 19.352 855 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.33 % Allowed : 16.28 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.31), residues: 798 helix: 1.14 (0.26), residues: 424 sheet: 0.02 (0.66), residues: 68 loop : -1.12 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 239 TYR 0.023 0.001 TYR C 251 PHE 0.028 0.001 PHE B 99 TRP 0.008 0.001 TRP A 80 HIS 0.005 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6457) covalent geometry : angle 0.57316 ( 8743) hydrogen bonds : bond 0.03293 ( 322) hydrogen bonds : angle 4.52392 ( 900) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.160 Fit side-chains REVERT: B 85 ARG cc_start: 0.8486 (tpt-90) cc_final: 0.8126 (tpt-90) REVERT: B 186 GLN cc_start: 0.8790 (tp40) cc_final: 0.8380 (tp40) REVERT: B 220 HIS cc_start: 0.7828 (m90) cc_final: 0.7306 (m90) REVERT: B 268 LEU cc_start: 0.9195 (mm) cc_final: 0.8981 (mm) REVERT: C 34 MET cc_start: 0.7646 (mmp) cc_final: 0.7444 (mmp) REVERT: C 75 MET cc_start: 0.7604 (ppp) cc_final: 0.7242 (ppp) REVERT: C 116 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7089 (t80) REVERT: C 134 GLU cc_start: 0.8751 (mp0) cc_final: 0.8301 (mp0) REVERT: C 140 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8401 (tm-30) REVERT: C 165 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8270 (ttp80) outliers start: 16 outliers final: 11 residues processed: 131 average time/residue: 0.0592 time to fit residues: 10.5747 Evaluate side-chains 126 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** C 83 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 = 0.3985 r_free = 0.3985 target = 0.158859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122692 restraints weight = 10803.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.126114 restraints weight = 6717.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.128400 restraints weight = 4867.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.129917 restraints weight = 3913.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130861 restraints weight = 3369.562| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6457 Z= 0.115 Angle : 0.558 8.435 8743 Z= 0.279 Chirality : 0.042 0.148 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.253 19.303 855 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.05 % Allowed : 18.90 % Favored : 78.05 % 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: 0.44 (0.31), residues: 798 helix: 1.28 (0.26), residues: 424 sheet: 0.15 (0.68), residues: 68 loop : -1.06 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 165 TYR 0.024 0.001 TYR C 251 PHE 0.027 0.001 PHE B 99 TRP 0.009 0.001 TRP B 238 HIS 0.006 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6457) covalent geometry : angle 0.55760 ( 8743) hydrogen bonds : bond 0.02968 ( 322) hydrogen bonds : angle 4.35475 ( 900) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.203 Fit side-chains REVERT: A 195 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8781 (pp) REVERT: B 85 ARG cc_start: 0.8457 (tpt-90) cc_final: 0.8074 (tpt-90) REVERT: B 186 GLN cc_start: 0.8765 (tp40) cc_final: 0.8393 (tp40) REVERT: B 220 HIS cc_start: 0.7830 (m90) cc_final: 0.7332 (m90) REVERT: B 268 LEU cc_start: 0.9208 (mm) cc_final: 0.8991 (mm) REVERT: C 108 ASN cc_start: 0.7725 (p0) cc_final: 0.7518 (p0) REVERT: C 116 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7223 (t80) REVERT: C 134 GLU cc_start: 0.8767 (mp0) cc_final: 0.8367 (mp0) REVERT: C 140 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8414 (tm-30) outliers start: 21 outliers final: 12 residues processed: 136 average time/residue: 0.0629 time to fit residues: 11.8487 Evaluate side-chains 127 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 0.0050 chunk 72 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN ** C 83 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 = 0.3979 r_free = 0.3979 target = 0.158504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122204 restraints weight = 10946.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125550 restraints weight = 6831.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127869 restraints weight = 4978.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.129217 restraints weight = 3992.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130333 restraints weight = 3463.456| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6457 Z= 0.120 Angle : 0.572 9.115 8743 Z= 0.281 Chirality : 0.042 0.164 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.187 19.397 855 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.78 % Allowed : 18.90 % Favored : 77.33 % 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: 0.49 (0.31), residues: 798 helix: 1.25 (0.26), residues: 431 sheet: 0.20 (0.68), residues: 68 loop : -0.98 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 239 TYR 0.023 0.001 TYR C 251 PHE 0.029 0.001 PHE B 99 TRP 0.009 0.001 TRP B 238 HIS 0.006 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6457) covalent geometry : angle 0.57199 ( 8743) hydrogen bonds : bond 0.02893 ( 322) hydrogen bonds : angle 4.28458 ( 900) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.165 Fit side-chains REVERT: A 195 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8788 (pp) REVERT: B 186 GLN cc_start: 0.8770 (tp40) cc_final: 0.8353 (tp40) REVERT: B 205 MET cc_start: 0.8673 (mmm) cc_final: 0.8079 (mmm) REVERT: B 220 HIS cc_start: 0.7865 (m90) cc_final: 0.7321 (m90) REVERT: C 108 ASN cc_start: 0.7806 (p0) cc_final: 0.7574 (p0) REVERT: C 113 PHE cc_start: 0.8215 (t80) cc_final: 0.7726 (t80) REVERT: C 116 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7210 (t80) REVERT: C 134 GLU cc_start: 0.8716 (mp0) cc_final: 0.8319 (mp0) REVERT: C 140 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8475 (tm-30) outliers start: 26 outliers final: 14 residues processed: 140 average time/residue: 0.0574 time to fit residues: 11.2636 Evaluate side-chains 133 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** C 83 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 = 0.3910 r_free = 0.3910 target = 0.152483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117443 restraints weight = 10854.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119916 restraints weight = 7190.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.121139 restraints weight = 5039.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121748 restraints weight = 4406.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.121918 restraints weight = 4182.751| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 6457 Z= 0.273 Angle : 0.719 11.945 8743 Z= 0.357 Chirality : 0.047 0.179 1009 Planarity : 0.005 0.048 1105 Dihedral : 4.675 19.782 855 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.51 % Allowed : 20.06 % Favored : 75.44 % 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: 0.23 (0.31), residues: 798 helix: 1.15 (0.26), residues: 421 sheet: -0.26 (0.65), residues: 68 loop : -1.12 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 165 TYR 0.019 0.002 TYR C 251 PHE 0.029 0.002 PHE B 99 TRP 0.009 0.001 TRP B 128 HIS 0.005 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00657 ( 6457) covalent geometry : angle 0.71875 ( 8743) hydrogen bonds : bond 0.03875 ( 322) hydrogen bonds : angle 4.69294 ( 900) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.245 Fit side-chains REVERT: A 195 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8761 (pp) REVERT: B 85 ARG cc_start: 0.8587 (tpt-90) cc_final: 0.8311 (tpt-90) REVERT: B 186 GLN cc_start: 0.8935 (tp40) cc_final: 0.8564 (tp40) REVERT: B 205 MET cc_start: 0.8647 (mmm) cc_final: 0.8069 (mmm) REVERT: B 220 HIS cc_start: 0.7824 (m90) cc_final: 0.7503 (m90) REVERT: C 108 ASN cc_start: 0.7906 (p0) cc_final: 0.7688 (p0) REVERT: C 113 PHE cc_start: 0.8237 (t80) cc_final: 0.7764 (t80) REVERT: C 140 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8458 (tm-30) outliers start: 31 outliers final: 22 residues processed: 136 average time/residue: 0.0626 time to fit residues: 11.7998 Evaluate side-chains 128 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 63 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** C 83 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 = 0.3967 r_free = 0.3967 target = 0.157349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120916 restraints weight = 10817.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.124320 restraints weight = 6796.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126639 restraints weight = 4928.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128219 restraints weight = 3947.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129107 restraints weight = 3381.801| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6457 Z= 0.119 Angle : 0.603 10.440 8743 Z= 0.293 Chirality : 0.043 0.161 1009 Planarity : 0.004 0.050 1105 Dihedral : 4.339 19.772 855 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.78 % Allowed : 20.93 % Favored : 75.29 % 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: 0.41 (0.31), residues: 798 helix: 1.25 (0.26), residues: 425 sheet: -0.05 (0.66), residues: 68 loop : -1.04 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 165 TYR 0.025 0.001 TYR C 251 PHE 0.028 0.001 PHE B 99 TRP 0.011 0.001 TRP B 238 HIS 0.006 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6457) covalent geometry : angle 0.60343 ( 8743) hydrogen bonds : bond 0.02952 ( 322) hydrogen bonds : angle 4.33770 ( 900) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8680 (pp) REVERT: A 257 ARG cc_start: 0.8467 (tpp-160) cc_final: 0.8240 (tpp80) REVERT: B 85 ARG cc_start: 0.8444 (tpt-90) cc_final: 0.8126 (tpt-90) REVERT: B 177 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7978 (p0) REVERT: B 186 GLN cc_start: 0.8842 (tp40) cc_final: 0.8315 (tp40) REVERT: B 220 HIS cc_start: 0.7909 (m90) cc_final: 0.7382 (m90) REVERT: C 113 PHE cc_start: 0.8231 (t80) cc_final: 0.7801 (t80) REVERT: C 116 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7108 (t80) REVERT: C 134 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8175 (mp0) REVERT: C 140 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8534 (tm-30) outliers start: 26 outliers final: 16 residues processed: 138 average time/residue: 0.0640 time to fit residues: 12.2980 Evaluate side-chains 133 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 30.0000 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** C 83 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 = 0.3930 r_free = 0.3930 target = 0.154199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117369 restraints weight = 10861.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.120561 restraints weight = 6909.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122765 restraints weight = 5104.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124285 restraints weight = 4128.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125059 restraints weight = 3563.709| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6457 Z= 0.202 Angle : 0.659 10.539 8743 Z= 0.323 Chirality : 0.045 0.178 1009 Planarity : 0.004 0.050 1105 Dihedral : 4.448 20.071 855 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.05 % Allowed : 21.80 % Favored : 75.15 % 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: 0.36 (0.31), residues: 798 helix: 1.25 (0.26), residues: 421 sheet: -0.14 (0.66), residues: 68 loop : -1.06 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 165 TYR 0.023 0.001 TYR C 251 PHE 0.029 0.002 PHE B 99 TRP 0.009 0.001 TRP A 80 HIS 0.005 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 6457) covalent geometry : angle 0.65871 ( 8743) hydrogen bonds : bond 0.03377 ( 322) hydrogen bonds : angle 4.47268 ( 900) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 195 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8808 (pp) REVERT: B 85 ARG cc_start: 0.8557 (tpt-90) cc_final: 0.8258 (tpt-90) REVERT: B 186 GLN cc_start: 0.8864 (tp40) cc_final: 0.8464 (tp40) REVERT: B 220 HIS cc_start: 0.7705 (m90) cc_final: 0.7364 (m90) REVERT: B 270 MET cc_start: 0.8691 (mmt) cc_final: 0.8296 (mmt) REVERT: C 113 PHE cc_start: 0.8285 (t80) cc_final: 0.7841 (t80) REVERT: C 116 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7340 (t80) REVERT: C 134 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8244 (mp0) REVERT: C 140 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8482 (tm-30) outliers start: 21 outliers final: 17 residues processed: 128 average time/residue: 0.0633 time to fit residues: 11.1152 Evaluate side-chains 133 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 66 optimal weight: 0.0170 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 0.0020 overall best weight: 0.4226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** C 83 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 = 0.3984 r_free = 0.3984 target = 0.158717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122573 restraints weight = 10883.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125940 restraints weight = 6838.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.128193 restraints weight = 4990.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.129662 restraints weight = 4015.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130733 restraints weight = 3465.627| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6457 Z= 0.111 Angle : 0.605 11.413 8743 Z= 0.292 Chirality : 0.043 0.165 1009 Planarity : 0.004 0.049 1105 Dihedral : 4.217 20.158 855 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.49 % Allowed : 21.66 % Favored : 74.85 % 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: 0.45 (0.31), residues: 798 helix: 1.25 (0.26), residues: 431 sheet: -0.00 (0.66), residues: 68 loop : -1.01 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 165 TYR 0.025 0.001 TYR C 251 PHE 0.025 0.001 PHE B 99 TRP 0.013 0.001 TRP B 238 HIS 0.006 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6457) covalent geometry : angle 0.60510 ( 8743) hydrogen bonds : bond 0.02841 ( 322) hydrogen bonds : angle 4.26792 ( 900) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.208 Fit side-chains REVERT: A 195 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8774 (pp) REVERT: B 85 ARG cc_start: 0.8525 (tpt-90) cc_final: 0.8236 (tpt-90) REVERT: B 186 GLN cc_start: 0.8760 (tp40) cc_final: 0.8348 (tp-100) REVERT: B 220 HIS cc_start: 0.7737 (m90) cc_final: 0.7362 (m90) REVERT: B 270 MET cc_start: 0.8633 (mmt) cc_final: 0.8216 (mmt) REVERT: C 113 PHE cc_start: 0.8247 (t80) cc_final: 0.7652 (t80) REVERT: C 116 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7329 (t80) REVERT: C 134 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8223 (mp0) REVERT: C 140 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8429 (tm-30) outliers start: 24 outliers final: 18 residues processed: 137 average time/residue: 0.0577 time to fit residues: 11.2040 Evaluate side-chains 134 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 38 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** C 83 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 = 0.3984 r_free = 0.3984 target = 0.158839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122746 restraints weight = 10679.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126132 restraints weight = 6640.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128425 restraints weight = 4827.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129954 restraints weight = 3874.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130850 restraints weight = 3323.858| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6457 Z= 0.116 Angle : 0.630 11.597 8743 Z= 0.303 Chirality : 0.042 0.167 1009 Planarity : 0.004 0.049 1105 Dihedral : 4.181 20.275 855 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.05 % Allowed : 21.80 % Favored : 75.15 % 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: 0.59 (0.31), residues: 798 helix: 1.36 (0.26), residues: 431 sheet: 0.05 (0.67), residues: 68 loop : -0.92 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 257 TYR 0.023 0.001 TYR C 251 PHE 0.027 0.001 PHE B 99 TRP 0.012 0.001 TRP B 238 HIS 0.005 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6457) covalent geometry : angle 0.63009 ( 8743) hydrogen bonds : bond 0.02820 ( 322) hydrogen bonds : angle 4.21996 ( 900) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.266 Fit side-chains REVERT: A 195 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8757 (pp) REVERT: B 85 ARG cc_start: 0.8489 (tpt-90) cc_final: 0.8201 (tpt-90) REVERT: B 152 ARG cc_start: 0.8508 (tpp80) cc_final: 0.8198 (ttp80) REVERT: B 186 GLN cc_start: 0.8724 (tp40) cc_final: 0.8325 (tp-100) REVERT: B 220 HIS cc_start: 0.7729 (m90) cc_final: 0.7495 (m90) REVERT: B 270 MET cc_start: 0.8612 (mmt) cc_final: 0.8199 (mmt) REVERT: C 113 PHE cc_start: 0.8245 (t80) cc_final: 0.7650 (t80) REVERT: C 116 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7397 (t80) REVERT: C 134 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8234 (mp0) REVERT: C 140 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8421 (tm-30) outliers start: 21 outliers final: 19 residues processed: 129 average time/residue: 0.0610 time to fit residues: 11.0808 Evaluate side-chains 137 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 259 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** C 83 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 = 0.3957 r_free = 0.3957 target = 0.156325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119778 restraints weight = 10857.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.122993 restraints weight = 6922.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125163 restraints weight = 5103.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126500 restraints weight = 4138.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127556 restraints weight = 3599.578| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6457 Z= 0.168 Angle : 0.664 11.420 8743 Z= 0.322 Chirality : 0.044 0.171 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.265 20.560 855 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.91 % Allowed : 22.53 % Favored : 74.56 % 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: 0.59 (0.31), residues: 798 helix: 1.43 (0.26), residues: 425 sheet: -0.06 (0.66), residues: 68 loop : -0.98 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 165 TYR 0.023 0.001 TYR C 251 PHE 0.025 0.001 PHE B 99 TRP 0.008 0.001 TRP A 80 HIS 0.004 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 6457) covalent geometry : angle 0.66352 ( 8743) hydrogen bonds : bond 0.03144 ( 322) hydrogen bonds : angle 4.34431 ( 900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1024.15 seconds wall clock time: 18 minutes 19.04 seconds (1099.04 seconds total)