Starting phenix.real_space_refine on Thu Jun 5 13:56:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bmr_16122/06_2025/8bmr_16122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bmr_16122/06_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_16122/06_2025/8bmr_16122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bmr_16122/06_2025/8bmr_16122.map" model { file = "/net/cci-nas-00/data/ceres_data/8bmr_16122/06_2025/8bmr_16122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bmr_16122/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 4.45, per 1000 atoms: 0.70 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: 1.47 Conformation dependent library (CDL) restraints added in 954.7 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: 0.68 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: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2038 1.35 - 1.46: 1411 1.46 - 1.58: 2958 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 6457 Sorted by residual: bond pdb=" CA ILE C 247 " pdb=" C ILE C 247 " ideal model delta sigma weight residual 1.520 1.529 -0.009 8.80e-03 1.29e+04 1.08e+00 bond pdb=" CB ARG B 85 " pdb=" CG ARG B 85 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.60e-01 bond pdb=" CB GLU A 256 " pdb=" CG GLU A 256 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.45e-01 bond pdb=" CB GLU B 163 " pdb=" CG GLU B 163 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.28e-01 bond pdb=" CA GLU B 163 " pdb=" CB GLU B 163 " ideal model delta sigma weight residual 1.530 1.543 -0.014 1.58e-02 4.01e+03 7.36e-01 ... (remaining 6452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 8468 1.49 - 2.99: 205 2.99 - 4.48: 53 4.48 - 5.98: 13 5.98 - 7.47: 4 Bond angle restraints: 8743 Sorted by residual: angle pdb=" CA ARG B 85 " pdb=" CB ARG B 85 " pdb=" CG ARG B 85 " ideal model delta sigma weight residual 114.10 119.41 -5.31 2.00e+00 2.50e-01 7.06e+00 angle pdb=" N ASP B 170 " pdb=" CA ASP B 170 " pdb=" C ASP B 170 " ideal model delta sigma weight residual 110.53 107.16 3.37 1.29e+00 6.01e-01 6.81e+00 angle pdb=" C GLU A 269 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.70e+00 angle pdb=" CA GLU B 163 " pdb=" CB GLU B 163 " pdb=" CG GLU B 163 " ideal model delta sigma weight residual 114.10 119.16 -5.06 2.00e+00 2.50e-01 6.41e+00 angle pdb=" CB MET C 118 " pdb=" CG MET C 118 " pdb=" SD MET C 118 " ideal model delta sigma weight residual 112.70 120.17 -7.47 3.00e+00 1.11e-01 6.21e+00 ... (remaining 8738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3497 18.00 - 35.99: 334 35.99 - 53.99: 41 53.99 - 71.98: 5 71.98 - 89.98: 3 Dihedral angle restraints: 3880 sinusoidal: 1556 harmonic: 2324 Sorted by residual: dihedral pdb=" CA LEU B 169 " pdb=" C LEU B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA LEU B 98 " pdb=" C LEU B 98 " pdb=" N PHE B 99 " pdb=" CA PHE B 99 " ideal model delta harmonic sigma weight residual 180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA PHE C 188 " pdb=" C PHE C 188 " pdb=" N ASN C 189 " pdb=" CA ASN C 189 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 3877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 599 0.030 - 0.060: 259 0.060 - 0.090: 88 0.090 - 0.120: 55 0.120 - 0.150: 8 Chirality restraints: 1009 Sorted by residual: chirality pdb=" CA ILE B 166 " pdb=" N ILE B 166 " pdb=" C ILE B 166 " pdb=" CB ILE B 166 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA VAL C 201 " pdb=" N VAL C 201 " pdb=" C VAL C 201 " pdb=" CB VAL C 201 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 6 " pdb=" N ILE A 6 " pdb=" C ILE A 6 " pdb=" CB ILE A 6 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1006 not shown) Planarity restraints: 1105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 270 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C LYS A 270 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS A 270 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 271 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 231 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 232 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 20 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 21 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " 0.024 5.00e-02 4.00e+02 ... (remaining 1102 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1023 2.76 - 3.30: 6407 3.30 - 3.83: 10046 3.83 - 4.37: 11065 4.37 - 4.90: 19194 Nonbonded interactions: 47735 Sorted by model distance: nonbonded pdb=" O VAL C 55 " pdb=" OG1 THR C 58 " model vdw 2.228 3.040 nonbonded pdb=" O PHE A 13 " pdb=" OG SER A 18 " model vdw 2.235 3.040 nonbonded pdb=" OG1 THR A 171 " pdb=" OE2 GLU A 206 " model vdw 2.273 3.040 nonbonded pdb=" OE1 GLN A 150 " pdb=" OG SER A 170 " model vdw 2.305 3.040 nonbonded pdb=" OE2 GLU A 111 " pdb=" NH1 ARG C 233 " model vdw 2.314 3.120 ... (remaining 47730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.610 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6457 Z= 0.119 Angle : 0.611 7.473 8743 Z= 0.312 Chirality : 0.042 0.150 1009 Planarity : 0.005 0.052 1105 Dihedral : 13.549 89.979 2378 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.15272 ( 322) hydrogen bonds : angle 6.50125 ( 900) covalent geometry : bond 0.00262 ( 6457) covalent geometry : angle 0.61106 ( 8743) *********************** 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 : 0.913 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: 0.2211 time to fit residues: 40.8581 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 : 0.685 ------------------------------------------------------------------------------- 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 = 66)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120773 restraints weight = 10745.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.124039 restraints weight = 6768.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126246 restraints weight = 4949.581| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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= 0.173 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 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 322) hydrogen bonds : angle 4.70393 ( 900) covalent geometry : bond 0.00414 ( 6457) covalent geometry : angle 0.61349 ( 8743) *********************** 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 : 0.617 Fit side-chains REVERT: B 85 ARG cc_start: 0.8465 (tpt-90) cc_final: 0.8199 (tpt-90) REVERT: B 184 MET cc_start: 0.8568 (ttm) cc_final: 0.8163 (ttp) REVERT: B 186 GLN cc_start: 0.8763 (tp40) cc_final: 0.8359 (tp40) REVERT: B 220 HIS cc_start: 0.7866 (m90) cc_final: 0.7304 (m90) REVERT: B 268 LEU cc_start: 0.9152 (mm) cc_final: 0.8892 (mm) REVERT: C 134 GLU cc_start: 0.8748 (mp0) cc_final: 0.8363 (mp0) REVERT: C 140 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8436 (tm-30) outliers start: 14 outliers final: 10 residues processed: 131 average time/residue: 0.2449 time to fit residues: 43.5208 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 : 0.836 ------------------------------------------------------------------------------- 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: 0.6980 chunk 63 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.157374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120889 restraints weight = 10810.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.124263 restraints weight = 6798.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126497 restraints weight = 4935.803| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1446 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= 0.143 Angle : 0.577 7.977 8743 Z= 0.290 Chirality : 0.043 0.152 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.322 18.625 855 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.05 % Allowed : 14.83 % 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: 0.35 (0.31), residues: 798 helix: 1.19 (0.26), residues: 424 sheet: 0.14 (0.67), residues: 68 loop : -1.08 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.012 0.001 HIS A 10 PHE 0.028 0.001 PHE B 99 TYR 0.024 0.001 TYR C 251 ARG 0.003 0.000 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.03267 ( 322) hydrogen bonds : angle 4.48984 ( 900) covalent geometry : bond 0.00344 ( 6457) covalent geometry : angle 0.57731 ( 8743) *********************** 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 146 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.931 Fit side-chains REVERT: B 85 ARG cc_start: 0.8489 (tpt-90) cc_final: 0.8159 (tpt-90) REVERT: B 186 GLN cc_start: 0.8810 (tp40) cc_final: 0.8393 (tp40) REVERT: B 220 HIS cc_start: 0.7843 (m90) cc_final: 0.7330 (m90) REVERT: B 268 LEU cc_start: 0.9163 (mm) cc_final: 0.8893 (mm) REVERT: C 116 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7256 (t80) REVERT: C 134 GLU cc_start: 0.8744 (mp0) cc_final: 0.8341 (mp0) REVERT: C 140 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8418 (tm-30) outliers start: 21 outliers final: 15 residues processed: 136 average time/residue: 0.2297 time to fit residues: 43.0219 Evaluate side-chains 136 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 A residue 268 ASP 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 78 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: 5.9990 chunk 20 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3937 r_free = 0.3937 target = 0.154924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117818 restraints weight = 10850.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.121255 restraints weight = 6964.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123486 restraints weight = 5094.128| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6457 Z= 0.205 Angle : 0.622 9.203 8743 Z= 0.314 Chirality : 0.044 0.152 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.442 18.580 855 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.49 % Allowed : 17.44 % 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: 0.29 (0.31), residues: 798 helix: 1.16 (0.26), residues: 425 sheet: -0.03 (0.66), residues: 68 loop : -1.12 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 80 HIS 0.010 0.001 HIS A 10 PHE 0.030 0.002 PHE B 99 TYR 0.023 0.001 TYR C 251 ARG 0.004 0.000 ARG C 233 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 322) hydrogen bonds : angle 4.56406 ( 900) covalent geometry : bond 0.00498 ( 6457) covalent geometry : angle 0.62247 ( 8743) *********************** 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: 24 poor density : 123 time to evaluate : 0.686 Fit side-chains REVERT: A 195 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8682 (pp) REVERT: B 92 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7573 (tm-30) REVERT: B 93 PHE cc_start: 0.7133 (m-10) cc_final: 0.6799 (m-10) REVERT: B 186 GLN cc_start: 0.8849 (tp40) cc_final: 0.8326 (tp40) REVERT: B 220 HIS cc_start: 0.7976 (m90) cc_final: 0.7225 (m90) REVERT: B 268 LEU cc_start: 0.9130 (mm) cc_final: 0.8903 (mm) REVERT: C 116 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7101 (t80) REVERT: C 134 GLU cc_start: 0.8786 (mp0) cc_final: 0.8266 (mp0) REVERT: C 140 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8510 (tm-30) outliers start: 24 outliers final: 15 residues processed: 139 average time/residue: 0.1786 time to fit residues: 34.4394 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 : 0.995 ------------------------------------------------------------------------------- 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 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 78 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 14 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 2 optimal weight: 0.0970 chunk 61 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.156519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119981 restraints weight = 10746.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123337 restraints weight = 6777.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125574 restraints weight = 4942.243| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6457 Z= 0.149 Angle : 0.588 9.135 8743 Z= 0.294 Chirality : 0.043 0.162 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.362 18.861 855 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.07 % Allowed : 18.46 % 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: 0.38 (0.31), residues: 798 helix: 1.25 (0.26), residues: 424 sheet: 0.01 (0.66), residues: 68 loop : -1.10 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.012 0.001 HIS A 10 PHE 0.030 0.001 PHE B 99 TYR 0.023 0.001 TYR C 251 ARG 0.003 0.000 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 322) hydrogen bonds : angle 4.42342 ( 900) covalent geometry : bond 0.00360 ( 6457) covalent geometry : angle 0.58801 ( 8743) *********************** 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 151 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.729 Fit side-chains REVERT: A 195 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8793 (pp) REVERT: B 85 ARG cc_start: 0.8507 (tpt-90) cc_final: 0.8200 (tpt-90) REVERT: B 186 GLN cc_start: 0.8839 (tp40) cc_final: 0.8351 (tp40) REVERT: B 205 MET cc_start: 0.8694 (mmm) cc_final: 0.8056 (mmm) REVERT: B 220 HIS cc_start: 0.7944 (m90) cc_final: 0.7327 (m90) REVERT: C 113 PHE cc_start: 0.8225 (t80) cc_final: 0.7728 (t80) REVERT: C 116 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7190 (t80) REVERT: C 134 GLU cc_start: 0.8769 (mp0) cc_final: 0.8297 (mp0) REVERT: C 140 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8519 (tm-30) outliers start: 28 outliers final: 17 residues processed: 138 average time/residue: 0.1582 time to fit residues: 29.9392 Evaluate side-chains 133 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 40 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.158944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122707 restraints weight = 10717.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.126108 restraints weight = 6661.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.128440 restraints weight = 4836.522| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6457 Z= 0.113 Angle : 0.571 9.708 8743 Z= 0.282 Chirality : 0.042 0.165 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.239 19.686 855 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.20 % Allowed : 19.91 % Favored : 76.89 % 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: 0.53 (0.31), residues: 798 helix: 1.35 (0.26), residues: 424 sheet: 0.18 (0.67), residues: 68 loop : -1.00 (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 0.027 0.001 PHE B 99 TYR 0.023 0.001 TYR C 251 ARG 0.010 0.000 ARG C 165 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 322) hydrogen bonds : angle 4.28857 ( 900) covalent geometry : bond 0.00265 ( 6457) covalent geometry : angle 0.57053 ( 8743) *********************** 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 145 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.033 Fit side-chains REVERT: A 195 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8708 (pp) REVERT: A 223 ASP cc_start: 0.7165 (t0) cc_final: 0.6908 (t0) REVERT: A 257 ARG cc_start: 0.8463 (tpp-160) cc_final: 0.8217 (tpp80) REVERT: B 85 ARG cc_start: 0.8497 (tpt-90) cc_final: 0.8176 (tpt-90) REVERT: B 205 MET cc_start: 0.8566 (mmm) cc_final: 0.7725 (mmm) REVERT: B 220 HIS cc_start: 0.8044 (m90) cc_final: 0.7526 (m90) REVERT: C 113 PHE cc_start: 0.8188 (t80) cc_final: 0.7764 (t80) REVERT: C 116 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7178 (t80) REVERT: C 134 GLU cc_start: 0.8781 (mp0) cc_final: 0.8553 (mp0) REVERT: C 140 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8494 (tm-30) outliers start: 22 outliers final: 14 residues processed: 136 average time/residue: 0.1670 time to fit residues: 32.0254 Evaluate side-chains 129 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 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 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.0370 chunk 68 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- 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 ** 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 = 0.3972 r_free = 0.3972 target = 0.157813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.121442 restraints weight = 10761.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.124787 restraints weight = 6767.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127065 restraints weight = 4932.192| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1911 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= 0.139 Angle : 0.601 10.460 8743 Z= 0.294 Chirality : 0.043 0.172 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.278 19.965 855 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.07 % Allowed : 20.49 % 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: 0.51 (0.31), residues: 798 helix: 1.31 (0.26), residues: 425 sheet: 0.12 (0.66), residues: 68 loop : -0.98 (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 0.022 0.001 TYR C 251 ARG 0.006 0.000 ARG C 165 Details of bonding type rmsd hydrogen bonds : bond 0.02951 ( 322) hydrogen bonds : angle 4.31059 ( 900) covalent geometry : bond 0.00337 ( 6457) covalent geometry : angle 0.60102 ( 8743) *********************** 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 146 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.587 Fit side-chains REVERT: A 195 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8808 (pp) REVERT: A 223 ASP cc_start: 0.6933 (t0) cc_final: 0.6701 (t0) REVERT: B 85 ARG cc_start: 0.8543 (tpt-90) cc_final: 0.8233 (tpt-90) REVERT: B 186 GLN cc_start: 0.8732 (tp40) cc_final: 0.8402 (tp-100) REVERT: B 205 MET cc_start: 0.8560 (mmm) cc_final: 0.7880 (mmm) REVERT: B 220 HIS cc_start: 0.7798 (m90) cc_final: 0.7433 (m90) REVERT: C 75 MET cc_start: 0.7618 (ppp) cc_final: 0.7197 (ppp) REVERT: C 76 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6762 (tt) REVERT: C 113 PHE cc_start: 0.8242 (t80) cc_final: 0.7832 (t80) REVERT: C 140 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8460 (tm-30) REVERT: C 181 GLN cc_start: 0.8586 (tp40) cc_final: 0.8095 (tp40) outliers start: 28 outliers final: 16 residues processed: 133 average time/residue: 0.1731 time to fit residues: 32.9205 Evaluate side-chains 130 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.157612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.121374 restraints weight = 10696.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.124696 restraints weight = 6751.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.126988 restraints weight = 4934.654| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2001 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= 0.137 Angle : 0.613 10.828 8743 Z= 0.301 Chirality : 0.043 0.170 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.274 20.409 855 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.49 % Allowed : 21.95 % 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: 0.51 (0.31), residues: 798 helix: 1.30 (0.26), residues: 425 sheet: 0.10 (0.66), residues: 68 loop : -0.95 (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 0.030 0.001 PHE B 99 TYR 0.023 0.001 TYR C 251 ARG 0.006 0.000 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 322) hydrogen bonds : angle 4.30170 ( 900) covalent geometry : bond 0.00332 ( 6457) covalent geometry : angle 0.61307 ( 8743) *********************** 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: 24 poor density : 118 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 195 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8801 (pp) REVERT: A 223 ASP cc_start: 0.6920 (t0) cc_final: 0.6688 (t0) REVERT: B 85 ARG cc_start: 0.8545 (tpt-90) cc_final: 0.8229 (tpt-90) REVERT: B 186 GLN cc_start: 0.8713 (tp40) cc_final: 0.8316 (tp-100) REVERT: B 220 HIS cc_start: 0.7799 (m90) cc_final: 0.7453 (m90) REVERT: C 75 MET cc_start: 0.7625 (ppp) cc_final: 0.7200 (ppp) REVERT: C 76 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6655 (tt) REVERT: C 113 PHE cc_start: 0.8227 (t80) cc_final: 0.7829 (t80) REVERT: C 134 GLU cc_start: 0.8897 (mp0) cc_final: 0.8196 (mp0) REVERT: C 140 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8459 (tm-30) REVERT: C 181 GLN cc_start: 0.8515 (tp40) cc_final: 0.8308 (tp40) outliers start: 24 outliers final: 17 residues processed: 131 average time/residue: 0.1483 time to fit residues: 27.8859 Evaluate side-chains 133 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 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 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 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: 0.8980 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.157383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.120864 restraints weight = 10815.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124184 restraints weight = 6795.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126475 restraints weight = 4971.250| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6457 Z= 0.147 Angle : 0.623 11.571 8743 Z= 0.306 Chirality : 0.043 0.170 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.294 20.569 855 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.78 % Allowed : 21.80 % Favored : 74.42 % 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: 0.45 (0.31), residues: 798 helix: 1.23 (0.26), residues: 431 sheet: 0.07 (0.66), residues: 68 loop : -0.99 (0.37), residues: 299 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 0.029 0.001 PHE B 99 TYR 0.023 0.001 TYR C 251 ARG 0.006 0.000 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 322) hydrogen bonds : angle 4.31406 ( 900) covalent geometry : bond 0.00357 ( 6457) covalent geometry : angle 0.62332 ( 8743) *********************** 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 144 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 195 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8817 (pp) REVERT: A 223 ASP cc_start: 0.6976 (t0) cc_final: 0.6738 (t0) REVERT: B 85 ARG cc_start: 0.8554 (tpt-90) cc_final: 0.8249 (tpt-90) REVERT: B 152 ARG cc_start: 0.8532 (tpp80) cc_final: 0.8224 (ttp80) REVERT: B 186 GLN cc_start: 0.8717 (tp40) cc_final: 0.8387 (tp40) REVERT: B 220 HIS cc_start: 0.7730 (m90) cc_final: 0.7418 (m90) REVERT: B 270 MET cc_start: 0.8660 (mmt) cc_final: 0.8303 (mmt) REVERT: C 75 MET cc_start: 0.7641 (ppp) cc_final: 0.7219 (ppp) REVERT: C 76 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6735 (tt) REVERT: C 113 PHE cc_start: 0.8239 (t80) cc_final: 0.7847 (t80) REVERT: C 134 GLU cc_start: 0.8896 (mp0) cc_final: 0.8247 (mp0) REVERT: C 140 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8409 (tm-30) outliers start: 26 outliers final: 21 residues processed: 133 average time/residue: 0.1528 time to fit residues: 27.9833 Evaluate side-chains 139 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 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 76 ILE Chi-restraints excluded: chain C residue 116 PHE 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 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: 0.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN B 113 ASN ** 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 = 0.3930 r_free = 0.3930 target = 0.154212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117212 restraints weight = 10811.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120494 restraints weight = 6948.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.122609 restraints weight = 5088.103| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6457 Z= 0.210 Angle : 0.687 11.500 8743 Z= 0.338 Chirality : 0.045 0.179 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.540 20.225 855 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.34 % Allowed : 22.24 % Favored : 74.42 % 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: 0.42 (0.31), residues: 798 helix: 1.30 (0.26), residues: 421 sheet: -0.14 (0.65), residues: 68 loop : -1.04 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 80 HIS 0.005 0.001 HIS B 141 PHE 0.026 0.002 PHE B 99 TYR 0.022 0.001 TYR C 251 ARG 0.005 0.001 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 322) hydrogen bonds : angle 4.50741 ( 900) covalent geometry : bond 0.00510 ( 6457) covalent geometry : angle 0.68740 ( 8743) ********************** 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 134 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.669 Fit side-chains REVERT: A 195 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8680 (pp) REVERT: A 223 ASP cc_start: 0.7533 (t0) cc_final: 0.7233 (t0) REVERT: A 256 GLU cc_start: 0.8645 (tp30) cc_final: 0.8366 (tm-30) REVERT: B 220 HIS cc_start: 0.7826 (m90) cc_final: 0.7272 (m90) REVERT: B 270 MET cc_start: 0.8820 (mmt) cc_final: 0.8406 (mmt) REVERT: C 75 MET cc_start: 0.7625 (ppp) cc_final: 0.7237 (ppp) REVERT: C 76 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6879 (tt) REVERT: C 113 PHE cc_start: 0.8213 (t80) cc_final: 0.7800 (t80) REVERT: C 134 GLU cc_start: 0.8836 (mp0) cc_final: 0.8113 (mp0) REVERT: C 140 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8501 (tm-30) outliers start: 23 outliers final: 18 residues processed: 127 average time/residue: 0.1468 time to fit residues: 26.2420 Evaluate side-chains 129 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 170 ASP 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 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 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: 0.5980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 chunk 39 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN B 113 ASN ** 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 = 0.3976 r_free = 0.3976 target = 0.158244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.121678 restraints weight = 10917.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125036 restraints weight = 6833.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.127370 restraints weight = 4967.502| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2175 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= 0.120 Angle : 0.641 11.770 8743 Z= 0.307 Chirality : 0.043 0.173 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.321 21.395 855 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.62 % Allowed : 22.97 % Favored : 74.42 % 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: 1.35 (0.26), residues: 425 sheet: -0.08 (0.65), residues: 68 loop : -1.00 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 238 HIS 0.005 0.001 HIS B 141 PHE 0.024 0.001 PHE B 99 TYR 0.025 0.001 TYR C 251 ARG 0.006 0.000 ARG C 165 Details of bonding type rmsd hydrogen bonds : bond 0.02927 ( 322) hydrogen bonds : angle 4.30641 ( 900) covalent geometry : bond 0.00284 ( 6457) covalent geometry : angle 0.64074 ( 8743) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2613.50 seconds wall clock time: 47 minutes 51.52 seconds (2871.52 seconds total)