Starting phenix.real_space_refine on Fri Dec 27 18:07:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bmr_16122/12_2024/8bmr_16122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bmr_16122/12_2024/8bmr_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_16122/12_2024/8bmr_16122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bmr_16122/12_2024/8bmr_16122.map" model { file = "/net/cci-nas-00/data/ceres_data/8bmr_16122/12_2024/8bmr_16122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bmr_16122/12_2024/8bmr_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-5532/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: 4.35, per 1000 atoms: 0.69 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: 1.69 Conformation dependent library (CDL) restraints added in 961.0 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: 0.67 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: 1.97 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.490 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.920 ------------------------------------------------------------------------------- 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 : 0.776 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: 0.1601 time to fit residues: 29.7358 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 : 0.854 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.788 Fit side-chains REVERT: B 85 ARG cc_start: 0.8460 (tpt-90) cc_final: 0.8192 (tpt-90) REVERT: B 184 MET cc_start: 0.8587 (ttm) cc_final: 0.8163 (ttp) REVERT: B 186 GLN cc_start: 0.8775 (tp40) cc_final: 0.8356 (tp40) REVERT: B 220 HIS cc_start: 0.7884 (m90) cc_final: 0.7300 (m90) REVERT: B 268 LEU cc_start: 0.9147 (mm) cc_final: 0.8887 (mm) REVERT: C 134 GLU cc_start: 0.8749 (mp0) cc_final: 0.8347 (mp0) REVERT: C 140 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8439 (tm-30) outliers start: 14 outliers final: 10 residues processed: 131 average time/residue: 0.1656 time to fit residues: 29.5207 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 : 0.809 ------------------------------------------------------------------------------- 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 39 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 0.0870 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1426 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= 0.182 Angle : 0.562 7.715 8743 Z= 0.280 Chirality : 0.042 0.153 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.256 19.026 855 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.62 % Allowed : 15.26 % Favored : 82.12 % 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: 424 sheet: 0.19 (0.67), residues: 68 loop : -1.04 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 238 HIS 0.013 0.001 HIS A 10 PHE 0.028 0.001 PHE B 99 TYR 0.025 0.001 TYR C 251 ARG 0.003 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 149 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.770 Fit side-chains REVERT: B 85 ARG cc_start: 0.8468 (tpt-90) cc_final: 0.8143 (tpt-90) REVERT: B 186 GLN cc_start: 0.8755 (tp40) cc_final: 0.8241 (tp40) REVERT: B 220 HIS cc_start: 0.7833 (m90) cc_final: 0.7312 (m90) REVERT: B 268 LEU cc_start: 0.9135 (mm) cc_final: 0.8882 (mm) REVERT: C 34 MET cc_start: 0.7760 (mmp) cc_final: 0.7559 (mmp) REVERT: C 116 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7218 (t80) REVERT: C 134 GLU cc_start: 0.8750 (mp0) cc_final: 0.8356 (mp0) REVERT: C 140 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8400 (tm-30) outliers start: 18 outliers final: 13 residues processed: 139 average time/residue: 0.1657 time to fit residues: 31.1805 Evaluate side-chains 133 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 159 VAL 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 37 optimal weight: 3.9990 chunk 7 optimal weight: 0.0370 chunk 34 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 63 optimal weight: 0.0030 chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 0.9270 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1600 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= 0.207 Angle : 0.569 8.472 8743 Z= 0.284 Chirality : 0.042 0.159 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.243 19.031 855 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.20 % Allowed : 17.01 % Favored : 79.80 % 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: 0.48 (0.31), residues: 798 helix: 1.29 (0.26), residues: 424 sheet: 0.23 (0.68), residues: 68 loop : -1.02 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 238 HIS 0.005 0.001 HIS A 10 PHE 0.028 0.001 PHE B 99 TYR 0.020 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 148 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.744 Fit side-chains REVERT: A 195 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8822 (pp) REVERT: B 85 ARG cc_start: 0.8470 (tpt-90) cc_final: 0.8104 (tpt-90) REVERT: B 186 GLN cc_start: 0.8754 (tp40) cc_final: 0.8262 (tp40) REVERT: B 220 HIS cc_start: 0.7860 (m90) cc_final: 0.7288 (m90) REVERT: B 268 LEU cc_start: 0.9168 (mm) cc_final: 0.8905 (mm) REVERT: C 116 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7193 (t80) REVERT: C 134 GLU cc_start: 0.8750 (mp0) cc_final: 0.8317 (mp0) REVERT: C 140 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8439 (tm-30) outliers start: 22 outliers final: 15 residues processed: 138 average time/residue: 0.1637 time to fit residues: 30.5097 Evaluate side-chains 133 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 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 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 56 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 52 optimal weight: 0.0470 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 overall best weight: 1.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6457 Z= 0.287 Angle : 0.609 8.873 8743 Z= 0.305 Chirality : 0.043 0.172 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.369 19.026 855 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.22 % Allowed : 18.31 % Favored : 77.47 % 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: 1.26 (0.26), residues: 425 sheet: 0.13 (0.67), residues: 68 loop : -0.99 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.012 0.002 HIS A 10 PHE 0.030 0.001 PHE B 99 TYR 0.023 0.001 TYR C 251 ARG 0.009 0.000 ARG C 165 *********************** 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 149 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.798 Fit side-chains REVERT: A 195 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8842 (pp) REVERT: B 205 MET cc_start: 0.8826 (tpp) cc_final: 0.7839 (mmm) REVERT: B 220 HIS cc_start: 0.7890 (m90) cc_final: 0.7330 (m90) REVERT: B 268 LEU cc_start: 0.9231 (mm) cc_final: 0.9018 (mm) REVERT: C 113 PHE cc_start: 0.8216 (t80) cc_final: 0.7755 (t80) REVERT: C 116 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7196 (t80) REVERT: C 140 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8509 (tm-30) outliers start: 29 outliers final: 20 residues processed: 140 average time/residue: 0.1603 time to fit residues: 31.0626 Evaluate side-chains 136 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 A residue 268 ASP 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 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 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 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 18 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 73 optimal weight: 0.0060 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1784 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= 0.165 Angle : 0.569 9.835 8743 Z= 0.281 Chirality : 0.042 0.162 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.219 19.653 855 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.34 % Allowed : 19.91 % Favored : 76.74 % 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: 1.33 (0.26), residues: 424 sheet: 0.23 (0.67), residues: 68 loop : -0.95 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 238 HIS 0.006 0.001 HIS B 141 PHE 0.028 0.001 PHE B 99 TYR 0.023 0.001 TYR C 251 ARG 0.005 0.000 ARG C 165 *********************** 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 149 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.710 Fit side-chains REVERT: A 195 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8807 (pp) REVERT: B 85 ARG cc_start: 0.8480 (tpt-90) cc_final: 0.8177 (tpt-90) REVERT: B 186 GLN cc_start: 0.8679 (tp40) cc_final: 0.8284 (tp-100) REVERT: B 220 HIS cc_start: 0.7880 (m90) cc_final: 0.7291 (m90) REVERT: B 268 LEU cc_start: 0.9217 (mm) cc_final: 0.9011 (mm) REVERT: C 113 PHE cc_start: 0.8222 (t80) cc_final: 0.7810 (t80) REVERT: C 116 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7158 (t80) REVERT: C 134 GLU cc_start: 0.8910 (mp0) cc_final: 0.8263 (mp0) REVERT: C 140 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8459 (tm-30) outliers start: 23 outliers final: 12 residues processed: 138 average time/residue: 0.1602 time to fit residues: 30.4843 Evaluate side-chains 128 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 247 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** A 279 ASN B 97 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1871 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= 0.197 Angle : 0.594 10.409 8743 Z= 0.291 Chirality : 0.043 0.182 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.227 19.804 855 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.20 % Allowed : 21.37 % 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 (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: 0.56 (0.31), residues: 798 helix: 1.33 (0.26), residues: 425 sheet: 0.19 (0.68), residues: 68 loop : -0.92 (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 0.026 0.001 PHE B 99 TYR 0.023 0.001 TYR C 251 ARG 0.006 0.000 ARG A 257 *********************** 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 142 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.760 Fit side-chains REVERT: A 195 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8791 (pp) REVERT: B 85 ARG cc_start: 0.8507 (tpt-90) cc_final: 0.8208 (tpt-90) REVERT: B 152 ARG cc_start: 0.8529 (tpp80) cc_final: 0.8197 (ttp80) REVERT: B 186 GLN cc_start: 0.8705 (tp40) cc_final: 0.8288 (tp-100) REVERT: B 220 HIS cc_start: 0.7916 (m90) cc_final: 0.7424 (m90) REVERT: B 268 LEU cc_start: 0.9245 (mm) cc_final: 0.9035 (mm) REVERT: C 113 PHE cc_start: 0.8214 (t80) cc_final: 0.7822 (t80) REVERT: C 134 GLU cc_start: 0.8967 (mp0) cc_final: 0.8328 (mp0) REVERT: C 140 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8471 (tm-30) outliers start: 22 outliers final: 18 residues processed: 131 average time/residue: 0.1510 time to fit residues: 27.3583 Evaluate side-chains 132 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 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 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 207 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 14 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 69 optimal weight: 0.0980 chunk 72 optimal weight: 5.9990 chunk 66 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6457 Z= 0.194 Angle : 0.604 10.759 8743 Z= 0.297 Chirality : 0.043 0.174 1009 Planarity : 0.004 0.047 1105 Dihedral : 4.224 19.918 855 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.05 % Allowed : 22.09 % 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 (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: 0.54 (0.31), residues: 798 helix: 1.27 (0.26), residues: 431 sheet: 0.13 (0.68), residues: 68 loop : -0.90 (0.37), residues: 299 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 0.023 0.001 PHE B 99 TYR 0.022 0.001 TYR C 251 ARG 0.005 0.000 ARG A 257 *********************** 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 141 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.592 Fit side-chains REVERT: A 195 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8790 (pp) REVERT: B 85 ARG cc_start: 0.8518 (tpt-90) cc_final: 0.8222 (tpt-90) REVERT: B 152 ARG cc_start: 0.8487 (tpp80) cc_final: 0.8178 (ttp80) REVERT: B 186 GLN cc_start: 0.8690 (tp40) cc_final: 0.8303 (tp-100) REVERT: B 205 MET cc_start: 0.8745 (mmm) cc_final: 0.8167 (mmm) REVERT: B 220 HIS cc_start: 0.7952 (m90) cc_final: 0.7539 (m90) REVERT: B 268 LEU cc_start: 0.9243 (mm) cc_final: 0.9036 (mm) REVERT: C 113 PHE cc_start: 0.8252 (t80) cc_final: 0.7859 (t80) REVERT: C 134 GLU cc_start: 0.8950 (mp0) cc_final: 0.8322 (mp0) REVERT: C 140 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8472 (tm-30) outliers start: 21 outliers final: 16 residues processed: 132 average time/residue: 0.1530 time to fit residues: 27.6593 Evaluate side-chains 133 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 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 247 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6457 Z= 0.294 Angle : 0.652 11.234 8743 Z= 0.322 Chirality : 0.044 0.179 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.365 20.034 855 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.63 % Allowed : 20.93 % 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 (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: 0.50 (0.31), residues: 798 helix: 1.33 (0.26), residues: 425 sheet: 0.04 (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 B 128 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 0.009 0.001 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 138 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.735 Fit side-chains REVERT: A 195 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8826 (pp) REVERT: B 85 ARG cc_start: 0.8547 (tpt-90) cc_final: 0.8250 (tpt-90) REVERT: B 186 GLN cc_start: 0.8800 (tp40) cc_final: 0.8438 (tp40) REVERT: B 205 MET cc_start: 0.8725 (mmm) cc_final: 0.8196 (mmm) REVERT: B 220 HIS cc_start: 0.7848 (m90) cc_final: 0.7445 (m90) REVERT: B 270 MET cc_start: 0.8704 (mmt) cc_final: 0.8319 (mmt) REVERT: C 113 PHE cc_start: 0.8262 (t80) cc_final: 0.7870 (t80) REVERT: C 116 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7297 (t80) REVERT: C 134 GLU cc_start: 0.8978 (mp0) cc_final: 0.8314 (mp0) REVERT: C 140 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8508 (tm-30) outliers start: 25 outliers final: 16 residues processed: 128 average time/residue: 0.1583 time to fit residues: 27.9793 Evaluate side-chains 132 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 232 VAL 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 247 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 62 optimal weight: 30.0000 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 9 optimal weight: 0.0060 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2042 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= 0.195 Angle : 0.625 11.749 8743 Z= 0.305 Chirality : 0.043 0.176 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.281 20.153 855 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.47 % Allowed : 22.53 % 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: 0.57 (0.31), residues: 798 helix: 1.37 (0.26), residues: 425 sheet: 0.06 (0.66), residues: 68 loop : -0.93 (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 0.023 0.001 PHE B 99 TYR 0.023 0.001 TYR C 251 ARG 0.009 0.000 ARG C 165 ********************** 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 137 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.681 Fit side-chains REVERT: A 195 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8787 (pp) REVERT: B 85 ARG cc_start: 0.8528 (tpt-90) cc_final: 0.8239 (tpt-90) REVERT: B 186 GLN cc_start: 0.8742 (tp40) cc_final: 0.8398 (tp40) REVERT: B 205 MET cc_start: 0.8696 (mmm) cc_final: 0.8131 (mmm) REVERT: B 220 HIS cc_start: 0.7811 (m90) cc_final: 0.7416 (m90) REVERT: B 270 MET cc_start: 0.8672 (mmt) cc_final: 0.8286 (mmt) REVERT: C 113 PHE cc_start: 0.8253 (t80) cc_final: 0.7873 (t80) REVERT: C 116 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7290 (t80) REVERT: C 134 GLU cc_start: 0.8914 (mp0) cc_final: 0.8290 (mp0) REVERT: C 140 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8487 (tm-30) outliers start: 17 outliers final: 14 residues processed: 130 average time/residue: 0.1644 time to fit residues: 29.2223 Evaluate side-chains 135 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 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 247 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 30.0000 chunk 26 optimal weight: 0.0980 chunk 64 optimal weight: 9.9990 chunk 7 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 0.0170 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.159399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.123453 restraints weight = 10561.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.126810 restraints weight = 6595.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129061 restraints weight = 4806.660| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2082 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= 0.182 Angle : 0.625 11.936 8743 Z= 0.303 Chirality : 0.043 0.182 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.204 20.244 855 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.47 % Allowed : 22.38 % 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: 0.65 (0.31), residues: 798 helix: 1.43 (0.26), residues: 425 sheet: 0.07 (0.66), residues: 68 loop : -0.89 (0.37), residues: 305 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 0.024 0.001 PHE B 93 TYR 0.023 0.001 TYR C 251 ARG 0.009 0.000 ARG C 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1491.58 seconds wall clock time: 28 minutes 33.53 seconds (1713.53 seconds total)