Starting phenix.real_space_refine on Fri Aug 22 16:22:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p0a_17331/08_2025/8p0a_17331.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p0a_17331/08_2025/8p0a_17331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p0a_17331/08_2025/8p0a_17331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p0a_17331/08_2025/8p0a_17331.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p0a_17331/08_2025/8p0a_17331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p0a_17331/08_2025/8p0a_17331.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 21 5.16 5 C 3656 2.51 5 N 989 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5764 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2805 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 355, 2796 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 14, 'TRANS': 340} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 355, 2796 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 14, 'TRANS': 340} Chain breaks: 1 bond proxies already assigned to first conformer: 2836 Chain: "B" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2507 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain breaks: 2 Chain: "C" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 388 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN A 137 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 137 " occ=0.50 Time building chain proxies: 2.07, per 1000 atoms: 0.36 Number of scatterers: 5764 At special positions: 0 Unit cell: (75.684, 93.704, 99.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 6 15.00 Mg 2 11.99 O 1090 8.00 N 989 7.00 C 3656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 424.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1354 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 38.4% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 37 through 48 removed outlier: 3.874A pdb=" N LEU A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.813A pdb=" N VAL A 70 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 71 " --> pdb=" O ALA A 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 67 through 71' Processing helix chain 'A' and resid 113 through 123 Processing helix chain 'A' and resid 138 through 144 removed outlier: 3.717A pdb=" N ALA A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 4.122A pdb=" N ALA A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 167 removed outlier: 5.059A pdb=" N GLN A 166 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.795A pdb=" N LYS A 172 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1057 Processing helix chain 'A' and resid 1059 through 1090 removed outlier: 3.774A pdb=" N LYS A1063 " --> pdb=" O PHE A1059 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1128 removed outlier: 3.600A pdb=" N ASN A1127 " --> pdb=" O PRO A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1142 removed outlier: 3.750A pdb=" N THR A1134 " --> pdb=" O GLY A1130 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A1135 " --> pdb=" O GLY A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1178 removed outlier: 4.043A pdb=" N GLY A1168 " --> pdb=" O ASN A1164 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LYS A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1196 removed outlier: 3.661A pdb=" N TYR A1194 " --> pdb=" O LYS A1190 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A1196 " --> pdb=" O GLU A1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 117 through 120 Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 151 through 162 removed outlier: 3.544A pdb=" N ARG B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1048 Processing helix chain 'B' and resid 1111 through 1115 Processing helix chain 'B' and resid 1118 through 1135 Processing helix chain 'B' and resid 1150 through 1163 removed outlier: 4.090A pdb=" N MET B1160 " --> pdb=" O ALA B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1183 removed outlier: 3.873A pdb=" N GLU B1181 " --> pdb=" O GLU B1178 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B1182 " --> pdb=" O LEU B1179 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B1183 " --> pdb=" O LEU B1180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1178 through 1183' Processing helix chain 'B' and resid 1202 through 1212 removed outlier: 4.107A pdb=" N ASP B1212 " --> pdb=" O ASP B1208 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 589 through 603 Processing helix chain 'C' and resid 604 through 607 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 5.705A pdb=" N LEU A 4 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER A 85 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU A 6 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 78 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR A 105 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 6.235A pdb=" N PHE A1153 " --> pdb=" O ILE A1185 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE A1187 " --> pdb=" O PHE A1153 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU A1155 " --> pdb=" O ILE A1187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1095 through 1100 Processing sheet with id=AA4, first strand: chain 'A' and resid 1202 through 1206 Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.698A pdb=" N GLN B 5 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 78 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1139 through 1143 removed outlier: 5.999A pdb=" N ASN B 28 " --> pdb=" O THR B1172 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N TYR B1187 " --> pdb=" O HIS B 27 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 29 " --> pdb=" O TYR B1187 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL B1189 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL B 31 " --> pdb=" O VAL B1189 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N PHE B1191 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG B1192 " --> pdb=" O VAL B1195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1054 through 1057 Processing sheet with id=AA8, first strand: chain 'C' and resid 609 through 610 removed outlier: 3.635A pdb=" N THR C 623 " --> pdb=" O GLU C 610 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1881 1.34 - 1.46: 996 1.46 - 1.58: 2944 1.58 - 1.69: 9 1.69 - 1.81: 36 Bond restraints: 5866 Sorted by residual: bond pdb=" CB LYS B 105 " pdb=" CG LYS B 105 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" O3B ATP B2000 " pdb=" PB ATP B2000 " ideal model delta sigma weight residual 1.592 1.564 0.028 3.00e-02 1.11e+03 8.60e-01 bond pdb=" C ALA A 68 " pdb=" N PRO A 69 " ideal model delta sigma weight residual 1.339 1.370 -0.031 3.40e-02 8.65e+02 8.42e-01 bond pdb=" CG LYS B 105 " pdb=" CD LYS B 105 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.88e-01 bond pdb=" CB ASN A1071 " pdb=" CG ASN A1071 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.16e-01 ... (remaining 5861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 7701 1.80 - 3.61: 176 3.61 - 5.41: 18 5.41 - 7.21: 4 7.21 - 9.02: 5 Bond angle restraints: 7904 Sorted by residual: angle pdb=" C LYS A1056 " pdb=" N GLN A1057 " pdb=" CA GLN A1057 " ideal model delta sigma weight residual 121.94 115.15 6.79 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CB LYS B 105 " pdb=" CG LYS B 105 " pdb=" CD LYS B 105 " ideal model delta sigma weight residual 111.30 118.57 -7.27 2.30e+00 1.89e-01 9.98e+00 angle pdb=" CB MET A 145 " pdb=" CG MET A 145 " pdb=" SD MET A 145 " ideal model delta sigma weight residual 112.70 121.72 -9.02 3.00e+00 1.11e-01 9.04e+00 angle pdb=" N PHE B 53 " pdb=" CA PHE B 53 " pdb=" C PHE B 53 " ideal model delta sigma weight residual 114.04 110.40 3.64 1.24e+00 6.50e-01 8.60e+00 angle pdb=" C LYS A 59 " pdb=" N THR A 60 " pdb=" CA THR A 60 " ideal model delta sigma weight residual 121.54 126.73 -5.19 1.91e+00 2.74e-01 7.37e+00 ... (remaining 7899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 3179 17.72 - 35.44: 346 35.44 - 53.16: 66 53.16 - 70.88: 27 70.88 - 88.60: 8 Dihedral angle restraints: 3626 sinusoidal: 1535 harmonic: 2091 Sorted by residual: dihedral pdb=" CA GLU A 174 " pdb=" C GLU A 174 " pdb=" N MET A 175 " pdb=" CA MET A 175 " ideal model delta harmonic sigma weight residual 180.00 161.63 18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA GLN A1157 " pdb=" C GLN A1157 " pdb=" N ILE A1158 " pdb=" CA ILE A1158 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA VAL A1186 " pdb=" C VAL A1186 " pdb=" N ILE A1187 " pdb=" CA ILE A1187 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 3623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 578 0.041 - 0.083: 199 0.083 - 0.124: 84 0.124 - 0.165: 9 0.165 - 0.206: 2 Chirality restraints: 872 Sorted by residual: chirality pdb=" CB ILE B 138 " pdb=" CA ILE B 138 " pdb=" CG1 ILE B 138 " pdb=" CG2 ILE B 138 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE A 126 " pdb=" CA ILE A 126 " pdb=" CG1 ILE A 126 " pdb=" CG2 ILE A 126 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" CA ILE B 138 " pdb=" N ILE B 138 " pdb=" C ILE B 138 " pdb=" CB ILE B 138 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 869 not shown) Planarity restraints: 1015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 21 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO B 22 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 22 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 22 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 57 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 58 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 58 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 58 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 145 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.00e+00 pdb=" C MET A 145 " 0.024 2.00e-02 2.50e+03 pdb=" O MET A 145 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS A 146 " -0.008 2.00e-02 2.50e+03 ... (remaining 1012 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 103 2.61 - 3.18: 5329 3.18 - 3.75: 9352 3.75 - 4.33: 12558 4.33 - 4.90: 20141 Nonbonded interactions: 47483 Sorted by model distance: nonbonded pdb=" O1G ATP B2000 " pdb="MG MG B2001 " model vdw 2.036 2.170 nonbonded pdb=" O1B ATP A2000 " pdb="MG MG A2001 " model vdw 2.036 2.170 nonbonded pdb=" O3B ATP B2000 " pdb="MG MG B2001 " model vdw 2.078 2.170 nonbonded pdb=" O2B ATP B2000 " pdb="MG MG B2001 " model vdw 2.126 2.170 nonbonded pdb=" OG1 THR A1217 " pdb=" O PRO C 616 " model vdw 2.134 3.040 ... (remaining 47478 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=0.50 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.920 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 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 0.032 5866 Z= 0.142 Angle : 0.655 9.018 7904 Z= 0.343 Chirality : 0.048 0.206 872 Planarity : 0.004 0.043 1015 Dihedral : 16.306 88.597 2272 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.31), residues: 709 helix: -1.39 (0.31), residues: 244 sheet: -0.82 (0.46), residues: 144 loop : -1.32 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 160 TYR 0.016 0.002 TYR A1194 PHE 0.012 0.002 PHE A1067 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 5866) covalent geometry : angle 0.65468 ( 7904) hydrogen bonds : bond 0.17653 ( 215) hydrogen bonds : angle 7.44300 ( 591) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7279 (ptm) cc_final: 0.6985 (ptm) REVERT: A 1217 THR cc_start: 0.8498 (p) cc_final: 0.8261 (p) REVERT: B 1202 THR cc_start: 0.7696 (m) cc_final: 0.7446 (m) REVERT: C 607 GLN cc_start: 0.7137 (pp30) cc_final: 0.6702 (pp30) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0851 time to fit residues: 13.6901 Evaluate side-chains 100 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.201984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.167171 restraints weight = 22292.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.175368 restraints weight = 10373.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.179848 restraints weight = 5317.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.180911 restraints weight = 3869.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.182599 restraints weight = 3748.861| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4242 r_free = 0.4242 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4243 r_free = 0.4243 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5866 Z= 0.148 Angle : 0.662 10.524 7904 Z= 0.342 Chirality : 0.049 0.183 872 Planarity : 0.004 0.043 1015 Dihedral : 11.937 89.377 841 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.97 % Allowed : 11.81 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.31), residues: 709 helix: -0.88 (0.32), residues: 236 sheet: -0.69 (0.46), residues: 143 loop : -1.17 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 160 TYR 0.016 0.002 TYR A1194 PHE 0.022 0.002 PHE C 600 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5866) covalent geometry : angle 0.66186 ( 7904) hydrogen bonds : bond 0.04522 ( 215) hydrogen bonds : angle 5.87801 ( 591) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 160 ARG cc_start: 0.8263 (mmm160) cc_final: 0.7923 (mmm-85) REVERT: B 1115 LEU cc_start: 0.8056 (mm) cc_final: 0.7853 (mm) REVERT: C 596 LYS cc_start: 0.8330 (ptpp) cc_final: 0.7952 (ptpp) REVERT: C 607 GLN cc_start: 0.7185 (pp30) cc_final: 0.6787 (pp30) outliers start: 6 outliers final: 4 residues processed: 113 average time/residue: 0.0778 time to fit residues: 11.8474 Evaluate side-chains 107 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 1055 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1080 ASN A1112 ASN B1119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.202223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.165865 restraints weight = 26170.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.175000 restraints weight = 11489.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.181723 restraints weight = 5600.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.181722 restraints weight = 3847.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.183219 restraints weight = 3580.103| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4241 r_free = 0.4241 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4241 r_free = 0.4241 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5866 Z= 0.134 Angle : 0.635 10.474 7904 Z= 0.324 Chirality : 0.048 0.182 872 Planarity : 0.004 0.049 1015 Dihedral : 11.138 87.942 841 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.78 % Allowed : 15.86 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.32), residues: 709 helix: -0.91 (0.32), residues: 243 sheet: -0.68 (0.46), residues: 142 loop : -1.07 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1066 TYR 0.017 0.002 TYR A1194 PHE 0.024 0.001 PHE B 47 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5866) covalent geometry : angle 0.63541 ( 7904) hydrogen bonds : bond 0.04069 ( 215) hydrogen bonds : angle 5.62914 ( 591) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1115 LEU cc_start: 0.8062 (mm) cc_final: 0.7855 (mm) REVERT: B 1211 GLU cc_start: 0.7881 (tt0) cc_final: 0.7582 (tp30) REVERT: C 607 GLN cc_start: 0.7238 (pp30) cc_final: 0.6794 (pp30) outliers start: 11 outliers final: 9 residues processed: 117 average time/residue: 0.0803 time to fit residues: 12.4285 Evaluate side-chains 108 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 1055 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN B1193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.197271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.161834 restraints weight = 22108.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.169361 restraints weight = 10810.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.174009 restraints weight = 5720.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.175858 restraints weight = 4271.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.176897 restraints weight = 3996.044| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4181 r_free = 0.4181 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4181 r_free = 0.4181 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5866 Z= 0.189 Angle : 0.678 11.997 7904 Z= 0.345 Chirality : 0.049 0.197 872 Planarity : 0.004 0.046 1015 Dihedral : 11.047 89.033 841 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.91 % Allowed : 17.64 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.31), residues: 709 helix: -0.95 (0.32), residues: 239 sheet: -0.98 (0.46), residues: 138 loop : -1.21 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1066 TYR 0.014 0.002 TYR B 137 PHE 0.022 0.002 PHE B 47 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 5866) covalent geometry : angle 0.67753 ( 7904) hydrogen bonds : bond 0.04328 ( 215) hydrogen bonds : angle 5.60916 ( 591) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLN cc_start: 0.6671 (mp10) cc_final: 0.6378 (mp10) REVERT: A 82 MET cc_start: 0.7413 (ptm) cc_final: 0.7140 (ptm) REVERT: B 1 MET cc_start: 0.5848 (ptp) cc_final: 0.5644 (ptp) REVERT: B 105 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7987 (mmmt) REVERT: B 1211 GLU cc_start: 0.7958 (tt0) cc_final: 0.7565 (tp30) REVERT: C 607 GLN cc_start: 0.7310 (pp30) cc_final: 0.6757 (pp30) outliers start: 18 outliers final: 12 residues processed: 119 average time/residue: 0.0797 time to fit residues: 12.7050 Evaluate side-chains 115 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1149 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.200287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.165047 restraints weight = 18756.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.170578 restraints weight = 10188.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.175746 restraints weight = 5788.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.176315 restraints weight = 3983.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.178399 restraints weight = 3942.896| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4206 r_free = 0.4206 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4206 r_free = 0.4206 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5866 Z= 0.139 Angle : 0.646 12.222 7904 Z= 0.329 Chirality : 0.048 0.197 872 Planarity : 0.004 0.048 1015 Dihedral : 10.806 89.274 841 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.91 % Allowed : 18.28 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.32), residues: 709 helix: -0.85 (0.32), residues: 240 sheet: -0.71 (0.46), residues: 145 loop : -1.14 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 160 TYR 0.017 0.002 TYR A1194 PHE 0.024 0.002 PHE B 47 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 5866) covalent geometry : angle 0.64641 ( 7904) hydrogen bonds : bond 0.04033 ( 215) hydrogen bonds : angle 5.51395 ( 591) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7448 (ptm) cc_final: 0.7138 (ptm) REVERT: A 160 ARG cc_start: 0.8338 (mmm160) cc_final: 0.8017 (mmm-85) REVERT: B 1211 GLU cc_start: 0.7891 (tt0) cc_final: 0.7544 (tp30) REVERT: C 607 GLN cc_start: 0.7277 (pp30) cc_final: 0.6758 (pp30) outliers start: 18 outliers final: 15 residues processed: 116 average time/residue: 0.0847 time to fit residues: 13.0779 Evaluate side-chains 107 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1149 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 59 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.197959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.157391 restraints weight = 21382.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.165079 restraints weight = 9715.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.170209 restraints weight = 5843.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.173899 restraints weight = 4132.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.176503 restraints weight = 3220.824| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4194 r_free = 0.4194 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4194 r_free = 0.4194 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5866 Z= 0.172 Angle : 0.676 10.999 7904 Z= 0.347 Chirality : 0.049 0.210 872 Planarity : 0.004 0.041 1015 Dihedral : 10.850 89.160 841 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.56 % Allowed : 19.58 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.31), residues: 709 helix: -0.81 (0.32), residues: 239 sheet: -1.08 (0.45), residues: 141 loop : -1.21 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 160 TYR 0.017 0.002 TYR A1173 PHE 0.023 0.002 PHE A1067 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 5866) covalent geometry : angle 0.67621 ( 7904) hydrogen bonds : bond 0.04194 ( 215) hydrogen bonds : angle 5.47302 ( 591) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7460 (ptm) cc_final: 0.7116 (ptm) REVERT: A 160 ARG cc_start: 0.8303 (mmm160) cc_final: 0.8031 (mmm-85) REVERT: B 125 LEU cc_start: 0.8890 (pp) cc_final: 0.8685 (pp) REVERT: B 1033 PHE cc_start: 0.7613 (t80) cc_final: 0.7373 (t80) REVERT: B 1178 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7288 (mm-30) REVERT: B 1211 GLU cc_start: 0.7817 (tt0) cc_final: 0.7564 (tp30) REVERT: C 607 GLN cc_start: 0.7306 (pp30) cc_final: 0.6788 (pp30) outliers start: 22 outliers final: 18 residues processed: 116 average time/residue: 0.0893 time to fit residues: 13.7067 Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1198 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 6 optimal weight: 0.0270 chunk 57 optimal weight: 2.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.198778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.163191 restraints weight = 20278.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.170541 restraints weight = 10010.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.175638 restraints weight = 5348.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.176112 restraints weight = 4018.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.177345 restraints weight = 3572.931| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4191 r_free = 0.4191 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4191 r_free = 0.4191 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5866 Z= 0.147 Angle : 0.671 11.258 7904 Z= 0.343 Chirality : 0.049 0.208 872 Planarity : 0.004 0.042 1015 Dihedral : 10.695 87.959 841 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.07 % Allowed : 20.87 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.31), residues: 709 helix: -0.84 (0.32), residues: 239 sheet: -0.98 (0.46), residues: 139 loop : -1.19 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 160 TYR 0.019 0.002 TYR A1194 PHE 0.026 0.001 PHE B 47 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5866) covalent geometry : angle 0.67120 ( 7904) hydrogen bonds : bond 0.04056 ( 215) hydrogen bonds : angle 5.48001 ( 591) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7447 (ptm) cc_final: 0.7096 (ptm) REVERT: A 160 ARG cc_start: 0.8237 (mmm160) cc_final: 0.8033 (mmm-85) REVERT: B 125 LEU cc_start: 0.8884 (pp) cc_final: 0.8679 (pp) REVERT: B 1211 GLU cc_start: 0.7971 (tt0) cc_final: 0.7542 (tp30) REVERT: C 607 GLN cc_start: 0.7318 (pp30) cc_final: 0.6826 (pp30) outliers start: 19 outliers final: 16 residues processed: 112 average time/residue: 0.0848 time to fit residues: 12.5321 Evaluate side-chains 108 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1149 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 51 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.0370 chunk 56 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 GLN B1144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.202142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.159827 restraints weight = 23044.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.168629 restraints weight = 9820.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.174555 restraints weight = 5703.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.178589 restraints weight = 3913.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.181446 restraints weight = 2990.197| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4240 r_free = 0.4240 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4240 r_free = 0.4240 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5866 Z= 0.126 Angle : 0.679 12.095 7904 Z= 0.344 Chirality : 0.049 0.224 872 Planarity : 0.004 0.041 1015 Dihedral : 10.357 84.944 841 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.75 % Allowed : 22.17 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.32), residues: 709 helix: -0.73 (0.33), residues: 239 sheet: -0.85 (0.46), residues: 139 loop : -1.12 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 171 TYR 0.021 0.002 TYR A1194 PHE 0.028 0.002 PHE A1067 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5866) covalent geometry : angle 0.67948 ( 7904) hydrogen bonds : bond 0.03849 ( 215) hydrogen bonds : angle 5.33646 ( 591) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7412 (ptm) cc_final: 0.7007 (ptm) REVERT: B 141 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7201 (tp-100) REVERT: B 1033 PHE cc_start: 0.7571 (t80) cc_final: 0.7370 (t80) REVERT: B 1115 LEU cc_start: 0.8247 (mt) cc_final: 0.7812 (mm) REVERT: B 1178 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7213 (mm-30) REVERT: B 1211 GLU cc_start: 0.7882 (tt0) cc_final: 0.7523 (tp30) REVERT: C 607 GLN cc_start: 0.7327 (pp30) cc_final: 0.6879 (pp30) outliers start: 17 outliers final: 12 residues processed: 114 average time/residue: 0.0790 time to fit residues: 11.9484 Evaluate side-chains 107 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1149 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.198856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.162163 restraints weight = 29252.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.171160 restraints weight = 13602.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.177112 restraints weight = 6244.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.178144 restraints weight = 4277.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.179517 restraints weight = 3806.168| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4190 r_free = 0.4190 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4190 r_free = 0.4190 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5866 Z= 0.158 Angle : 0.718 14.033 7904 Z= 0.361 Chirality : 0.049 0.210 872 Planarity : 0.004 0.041 1015 Dihedral : 10.545 85.916 841 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.59 % Allowed : 22.17 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.32), residues: 709 helix: -0.71 (0.33), residues: 239 sheet: -0.91 (0.46), residues: 139 loop : -1.15 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 171 TYR 0.016 0.002 TYR A1194 PHE 0.021 0.002 PHE B 47 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5866) covalent geometry : angle 0.71839 ( 7904) hydrogen bonds : bond 0.04013 ( 215) hydrogen bonds : angle 5.32006 ( 591) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7310 (ptm) cc_final: 0.6967 (ptm) REVERT: B 1178 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7236 (mm-30) REVERT: B 1211 GLU cc_start: 0.8032 (tt0) cc_final: 0.7551 (tp30) REVERT: C 607 GLN cc_start: 0.7290 (pp30) cc_final: 0.6824 (pp30) outliers start: 16 outliers final: 15 residues processed: 107 average time/residue: 0.0732 time to fit residues: 10.6342 Evaluate side-chains 105 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1218 PHE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1149 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 7 optimal weight: 0.0060 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.201813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.166377 restraints weight = 20697.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.173768 restraints weight = 9793.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.178835 restraints weight = 5305.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.179350 restraints weight = 3938.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.180653 restraints weight = 3529.493| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4217 r_free = 0.4217 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4217 r_free = 0.4217 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5866 Z= 0.133 Angle : 0.725 13.708 7904 Z= 0.360 Chirality : 0.049 0.234 872 Planarity : 0.004 0.042 1015 Dihedral : 10.404 84.868 841 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.27 % Allowed : 22.98 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.32), residues: 709 helix: -0.71 (0.33), residues: 238 sheet: -0.81 (0.46), residues: 139 loop : -1.11 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 171 TYR 0.019 0.002 TYR A1194 PHE 0.044 0.002 PHE C 600 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 5866) covalent geometry : angle 0.72526 ( 7904) hydrogen bonds : bond 0.03834 ( 215) hydrogen bonds : angle 5.38950 ( 591) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7387 (ptm) cc_final: 0.7018 (ptm) REVERT: B 1115 LEU cc_start: 0.8293 (mt) cc_final: 0.7881 (mm) REVERT: B 1176 ARG cc_start: 0.8081 (mmp80) cc_final: 0.7807 (mmm160) REVERT: B 1178 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7091 (mm-30) REVERT: B 1211 GLU cc_start: 0.8043 (tt0) cc_final: 0.7530 (tp30) REVERT: C 596 LYS cc_start: 0.8269 (ptpp) cc_final: 0.7977 (ptpp) REVERT: C 607 GLN cc_start: 0.7266 (pp30) cc_final: 0.6843 (pp30) outliers start: 14 outliers final: 14 residues processed: 106 average time/residue: 0.0806 time to fit residues: 11.3368 Evaluate side-chains 106 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1218 PHE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1149 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 0.0060 chunk 56 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.201996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.167501 restraints weight = 15918.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.173654 restraints weight = 8293.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.180918 restraints weight = 4719.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.181388 restraints weight = 2931.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.182036 restraints weight = 2855.802| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4236 r_free = 0.4236 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4237 r_free = 0.4237 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5866 Z= 0.138 Angle : 0.722 13.810 7904 Z= 0.361 Chirality : 0.049 0.235 872 Planarity : 0.004 0.042 1015 Dihedral : 10.397 84.205 841 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.43 % Allowed : 22.49 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.32), residues: 709 helix: -0.60 (0.33), residues: 237 sheet: -0.81 (0.46), residues: 139 loop : -1.14 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 171 TYR 0.018 0.002 TYR A1194 PHE 0.023 0.001 PHE B 47 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5866) covalent geometry : angle 0.72194 ( 7904) hydrogen bonds : bond 0.03888 ( 215) hydrogen bonds : angle 5.31992 ( 591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1273.53 seconds wall clock time: 22 minutes 46.55 seconds (1366.55 seconds total)