Starting phenix.real_space_refine on Tue Feb 11 16:58:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bmr_16122/02_2025/8bmr_16122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bmr_16122/02_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_16122/02_2025/8bmr_16122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bmr_16122/02_2025/8bmr_16122.map" model { file = "/net/cci-nas-00/data/ceres_data/8bmr_16122/02_2025/8bmr_16122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bmr_16122/02_2025/8bmr_16122.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.21, per 1000 atoms: 0.67 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: 1.49 Conformation dependent library (CDL) restraints added in 897.0 milliseconds 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: 0.64 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: 1.65 Time building geometry restraints manager: 1.74 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: 0.720 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.570 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.890 ------------------------------------------------------------------------------- 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= 0.172 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP B 238 HIS 0.003 0.001 HIS A 10 PHE 0.012 0.001 PHE C 166 TYR 0.010 0.001 TYR A 248 ARG 0.005 0.000 ARG C 165 *********************** 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 : 0.569 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: 0.1606 time to fit residues: 29.7135 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 : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.156928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120778 restraints weight = 10745.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124079 restraints weight = 6792.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.126228 restraints weight = 4955.251| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6457 Z= 0.271 Angle : 0.613 8.710 8743 Z= 0.310 Chirality : 0.044 0.152 1009 Planarity : 0.005 0.049 1105 Dihedral : 4.408 18.417 855 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.03 % Allowed : 11.77 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.31), residues: 798 helix: 1.08 (0.26), residues: 424 sheet: 0.16 (0.67), residues: 68 loop : -1.10 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.015 0.002 HIS A 10 PHE 0.022 0.001 PHE B 99 TYR 0.013 0.001 TYR C 251 ARG 0.004 0.000 ARG C 233 *********************** 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 137 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.757 Fit side-chains REVERT: B 85 ARG cc_start: 0.8465 (tpt-90) cc_final: 0.8195 (tpt-90) REVERT: B 184 MET cc_start: 0.8583 (ttm) cc_final: 0.8167 (ttp) REVERT: B 186 GLN cc_start: 0.8771 (tp40) cc_final: 0.8360 (tp40) REVERT: B 220 HIS cc_start: 0.7883 (m90) cc_final: 0.7299 (m90) REVERT: B 268 LEU cc_start: 0.9149 (mm) cc_final: 0.8888 (mm) REVERT: C 134 GLU cc_start: 0.8752 (mp0) cc_final: 0.8357 (mp0) REVERT: C 140 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8442 (tm-30) outliers start: 14 outliers final: 10 residues processed: 131 average time/residue: 0.1646 time to fit residues: 29.3843 Evaluate side-chains 126 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 48 THR 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 61 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 63 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 7 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 1 optimal weight: 0.0970 chunk 4 optimal weight: 0.6980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 97 GLN ** 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 = 0.4016 r_free = 0.4016 target = 0.161667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.125993 restraints weight = 10826.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129416 restraints weight = 6682.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.131660 restraints weight = 4836.851| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6457 Z= 0.142 Angle : 0.549 7.239 8743 Z= 0.274 Chirality : 0.042 0.156 1009 Planarity : 0.004 0.047 1105 Dihedral : 4.179 19.356 855 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.62 % Allowed : 14.83 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.31), residues: 798 helix: 1.17 (0.26), residues: 430 sheet: 0.18 (0.68), residues: 69 loop : -0.98 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 238 HIS 0.012 0.001 HIS A 10 PHE 0.025 0.001 PHE B 99 TYR 0.024 0.001 TYR C 251 ARG 0.004 0.000 ARG A 239 *********************** 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 151 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.858 Fit side-chains REVERT: B 85 ARG cc_start: 0.8442 (tpt-90) cc_final: 0.8129 (tpt-90) REVERT: B 186 GLN cc_start: 0.8692 (tp40) cc_final: 0.8226 (tp40) REVERT: B 220 HIS cc_start: 0.7814 (m90) cc_final: 0.7305 (m90) REVERT: B 268 LEU cc_start: 0.9082 (mm) cc_final: 0.8841 (mm) REVERT: C 116 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7222 (t80) REVERT: C 134 GLU cc_start: 0.8713 (mp0) cc_final: 0.8374 (mp0) REVERT: C 140 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8424 (tm-30) outliers start: 18 outliers final: 12 residues processed: 140 average time/residue: 0.1671 time to fit residues: 31.9189 Evaluate side-chains 134 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain B residue 103 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 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 66 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 0.0570 chunk 51 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 97 GLN ** 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 = 0.3977 r_free = 0.3977 target = 0.158615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122343 restraints weight = 10813.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125665 restraints weight = 6734.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127899 restraints weight = 4928.397| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6457 Z= 0.222 Angle : 0.572 8.249 8743 Z= 0.285 Chirality : 0.043 0.164 1009 Planarity : 0.004 0.047 1105 Dihedral : 4.182 18.529 855 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.05 % Allowed : 17.88 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.31), residues: 798 helix: 1.26 (0.26), residues: 425 sheet: 0.27 (0.68), residues: 68 loop : -0.94 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 238 HIS 0.013 0.001 HIS A 10 PHE 0.028 0.001 PHE B 99 TYR 0.022 0.001 TYR C 251 ARG 0.003 0.000 ARG C 233 *********************** 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 147 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.740 Fit side-chains REVERT: A 195 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8842 (pp) REVERT: A 223 ASP cc_start: 0.6834 (t0) cc_final: 0.6632 (t0) REVERT: B 85 ARG cc_start: 0.8473 (tpt-90) cc_final: 0.8124 (tpt-90) REVERT: B 186 GLN cc_start: 0.8717 (tp40) cc_final: 0.8265 (tp40) REVERT: B 220 HIS cc_start: 0.7795 (m90) cc_final: 0.7290 (m90) REVERT: B 268 LEU cc_start: 0.9163 (mm) cc_final: 0.8908 (mm) REVERT: C 113 PHE cc_start: 0.8187 (t80) cc_final: 0.7663 (t80) REVERT: C 116 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7270 (t80) REVERT: C 140 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8458 (tm-30) outliers start: 21 outliers final: 13 residues processed: 138 average time/residue: 0.1545 time to fit residues: 29.2893 Evaluate side-chains 133 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 195 LEU Chi-restraints excluded: chain A residue 221 LEU 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 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 247 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.154158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.117297 restraints weight = 10813.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120489 restraints weight = 6942.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122632 restraints weight = 5120.323| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6457 Z= 0.358 Angle : 0.656 9.624 8743 Z= 0.328 Chirality : 0.045 0.176 1009 Planarity : 0.005 0.048 1105 Dihedral : 4.508 19.203 855 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.07 % Allowed : 18.17 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.31), residues: 798 helix: 1.22 (0.26), residues: 421 sheet: 0.02 (0.66), residues: 68 loop : -0.96 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.006 0.001 HIS B 141 PHE 0.028 0.002 PHE B 99 TYR 0.022 0.002 TYR C 251 ARG 0.004 0.000 ARG C 233 *********************** 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 145 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.763 Fit side-chains REVERT: A 195 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8858 (pp) REVERT: B 205 MET cc_start: 0.8847 (tpp) cc_final: 0.7875 (mmm) REVERT: B 220 HIS cc_start: 0.7892 (m90) cc_final: 0.7332 (m90) REVERT: C 113 PHE cc_start: 0.8282 (t80) cc_final: 0.7742 (t80) REVERT: C 116 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7244 (t80) REVERT: C 134 GLU cc_start: 0.8936 (mp0) cc_final: 0.8351 (mp0) REVERT: C 140 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8547 (tm-30) outliers start: 28 outliers final: 20 residues processed: 139 average time/residue: 0.1711 time to fit residues: 32.4733 Evaluate side-chains 132 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 195 LEU 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 159 VAL 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 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 174 THR 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 51 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.0670 chunk 40 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.158357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122041 restraints weight = 10743.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125426 restraints weight = 6718.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127636 restraints weight = 4884.777| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1854 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= 0.188 Angle : 0.586 9.965 8743 Z= 0.288 Chirality : 0.043 0.168 1009 Planarity : 0.004 0.049 1105 Dihedral : 4.292 19.397 855 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.49 % Allowed : 20.20 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.31), residues: 798 helix: 1.24 (0.26), residues: 425 sheet: 0.13 (0.66), residues: 68 loop : -1.01 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 238 HIS 0.006 0.001 HIS B 141 PHE 0.027 0.001 PHE B 99 TYR 0.023 0.001 TYR C 251 ARG 0.002 0.000 ARG C 233 *********************** 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 147 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.775 Fit side-chains REVERT: A 195 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8819 (pp) REVERT: B 85 ARG cc_start: 0.8492 (tpt-90) cc_final: 0.8192 (tpt-90) REVERT: B 186 GLN cc_start: 0.8742 (tp40) cc_final: 0.8323 (tp40) REVERT: B 220 HIS cc_start: 0.7880 (m90) cc_final: 0.7305 (m90) REVERT: C 113 PHE cc_start: 0.8280 (t80) cc_final: 0.7815 (t80) REVERT: C 116 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7266 (t80) REVERT: C 134 GLU cc_start: 0.8947 (mp0) cc_final: 0.8324 (mp0) REVERT: C 140 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8475 (tm-30) outliers start: 24 outliers final: 15 residues processed: 137 average time/residue: 0.1625 time to fit residues: 30.5678 Evaluate side-chains 130 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 159 VAL 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 142 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.158097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.121798 restraints weight = 10751.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125161 restraints weight = 6741.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.127434 restraints weight = 4899.325| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6457 Z= 0.203 Angle : 0.597 10.447 8743 Z= 0.293 Chirality : 0.043 0.176 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.279 19.696 855 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.78 % Allowed : 20.64 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.31), residues: 798 helix: 1.29 (0.26), residues: 425 sheet: 0.14 (0.66), residues: 68 loop : -0.99 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 238 HIS 0.006 0.001 HIS B 141 PHE 0.025 0.001 PHE B 99 TYR 0.022 0.001 TYR C 251 ARG 0.008 0.000 ARG C 165 *********************** 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 147 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.750 Fit side-chains REVERT: A 195 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8836 (pp) REVERT: B 85 ARG cc_start: 0.8500 (tpt-90) cc_final: 0.8201 (tpt-90) REVERT: B 186 GLN cc_start: 0.8749 (tp40) cc_final: 0.8336 (tp-100) REVERT: B 220 HIS cc_start: 0.7926 (m90) cc_final: 0.7532 (m90) REVERT: C 76 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6784 (tt) REVERT: C 113 PHE cc_start: 0.8276 (t80) cc_final: 0.7842 (t80) REVERT: C 116 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7194 (t80) REVERT: C 134 GLU cc_start: 0.8935 (mp0) cc_final: 0.8326 (mp0) REVERT: C 140 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8495 (tm-30) outliers start: 26 outliers final: 16 residues processed: 136 average time/residue: 0.1474 time to fit residues: 28.2195 Evaluate side-chains 131 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 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 159 VAL 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 76 ILE 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 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3955 r_free = 0.3955 target = 0.156531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.120236 restraints weight = 10716.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.123512 restraints weight = 6787.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125625 restraints weight = 4968.432| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6457 Z= 0.255 Angle : 0.635 10.778 8743 Z= 0.311 Chirality : 0.044 0.179 1009 Planarity : 0.004 0.047 1105 Dihedral : 4.326 19.905 855 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.34 % Allowed : 22.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.31), residues: 798 helix: 1.29 (0.26), residues: 425 sheet: 0.08 (0.66), residues: 68 loop : -1.00 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.006 0.001 HIS B 141 PHE 0.023 0.001 PHE B 99 TYR 0.022 0.001 TYR C 251 ARG 0.007 0.000 ARG C 165 *********************** 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 142 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.690 Fit side-chains REVERT: A 195 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8831 (pp) REVERT: B 85 ARG cc_start: 0.8544 (tpt-90) cc_final: 0.8247 (tpt-90) REVERT: B 186 GLN cc_start: 0.8764 (tp40) cc_final: 0.8431 (tp40) REVERT: B 220 HIS cc_start: 0.7862 (m90) cc_final: 0.7456 (m90) REVERT: B 270 MET cc_start: 0.8709 (mmt) cc_final: 0.8314 (mmt) REVERT: C 75 MET cc_start: 0.7671 (ppp) cc_final: 0.7218 (ppp) REVERT: C 76 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6646 (tt) REVERT: C 113 PHE cc_start: 0.8273 (t80) cc_final: 0.7851 (t80) REVERT: C 134 GLU cc_start: 0.8947 (mp0) cc_final: 0.8290 (mp0) REVERT: C 140 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8507 (tm-30) outliers start: 23 outliers final: 20 residues processed: 132 average time/residue: 0.1559 time to fit residues: 28.5123 Evaluate side-chains 139 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 159 VAL 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 76 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 76 optimal weight: 0.3980 chunk 78 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.159491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.123338 restraints weight = 10771.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.126776 restraints weight = 6707.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.129058 restraints weight = 4859.392| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6457 Z= 0.184 Angle : 0.610 11.367 8743 Z= 0.298 Chirality : 0.042 0.173 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.228 20.096 855 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.20 % Allowed : 21.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.31), residues: 798 helix: 1.31 (0.26), residues: 431 sheet: 0.16 (0.67), residues: 68 loop : -0.95 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 238 HIS 0.006 0.001 HIS B 141 PHE 0.022 0.001 PHE B 99 TYR 0.024 0.001 TYR C 251 ARG 0.006 0.000 ARG C 165 *********************** 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 142 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.778 Fit side-chains REVERT: B 85 ARG cc_start: 0.8532 (tpt-90) cc_final: 0.8252 (tpt-90) REVERT: B 152 ARG cc_start: 0.8477 (tpp80) cc_final: 0.8204 (ttp80) REVERT: B 186 GLN cc_start: 0.8722 (tp40) cc_final: 0.8328 (tp-100) REVERT: B 220 HIS cc_start: 0.7718 (m90) cc_final: 0.7429 (m90) REVERT: C 113 PHE cc_start: 0.8241 (t80) cc_final: 0.7796 (t80) REVERT: C 134 GLU cc_start: 0.8843 (mp0) cc_final: 0.8168 (mp0) REVERT: C 140 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8418 (tm-30) outliers start: 22 outliers final: 20 residues processed: 131 average time/residue: 0.1647 time to fit residues: 29.3929 Evaluate side-chains 135 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 159 VAL 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 11 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.152466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115427 restraints weight = 10861.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118458 restraints weight = 7083.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.120538 restraints weight = 5317.755| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 6457 Z= 0.457 Angle : 0.762 11.464 8743 Z= 0.378 Chirality : 0.047 0.197 1009 Planarity : 0.005 0.047 1105 Dihedral : 4.689 20.310 855 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.49 % Allowed : 21.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.31), residues: 798 helix: 1.21 (0.26), residues: 420 sheet: -0.25 (0.64), residues: 69 loop : -1.17 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.004 0.001 HIS B 141 PHE 0.021 0.002 PHE B 99 TYR 0.022 0.002 TYR C 251 ARG 0.005 0.001 ARG A 257 ********************** 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 138 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.702 Fit side-chains REVERT: A 195 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8786 (pp) REVERT: B 85 ARG cc_start: 0.8590 (tpt-90) cc_final: 0.8299 (tpt-90) REVERT: B 186 GLN cc_start: 0.8905 (tp40) cc_final: 0.8581 (tp40) REVERT: B 205 MET cc_start: 0.8752 (mmm) cc_final: 0.8426 (mmm) REVERT: B 220 HIS cc_start: 0.7811 (m90) cc_final: 0.7435 (m90) REVERT: B 270 MET cc_start: 0.8733 (mmt) cc_final: 0.8339 (mmt) REVERT: C 113 PHE cc_start: 0.8268 (t80) cc_final: 0.7817 (t80) REVERT: C 134 GLU cc_start: 0.8914 (mp0) cc_final: 0.8157 (mp0) REVERT: C 140 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8518 (tm-30) outliers start: 24 outliers final: 18 residues processed: 132 average time/residue: 0.1585 time to fit residues: 28.8481 Evaluate side-chains 130 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 159 VAL 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 232 VAL 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 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 49 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 11 optimal weight: 0.0980 chunk 12 optimal weight: 0.0470 chunk 39 optimal weight: 3.9990 overall best weight: 0.3078 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.159693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.123369 restraints weight = 10897.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126948 restraints weight = 6807.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.129078 restraints weight = 4916.423| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6457 Z= 0.171 Angle : 0.640 11.813 8743 Z= 0.311 Chirality : 0.043 0.173 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.328 20.993 855 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.18 % Allowed : 22.82 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.31), residues: 798 helix: 1.28 (0.26), residues: 431 sheet: 0.02 (0.66), residues: 68 loop : -1.03 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 238 HIS 0.005 0.001 HIS B 141 PHE 0.020 0.001 PHE B 99 TYR 0.023 0.001 TYR C 251 ARG 0.006 0.000 ARG C 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2038.86 seconds wall clock time: 37 minutes 22.49 seconds (2242.49 seconds total)