Starting phenix.real_space_refine on Tue Mar 3 18:39:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ahc_11782/03_2026/7ahc_11782.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ahc_11782/03_2026/7ahc_11782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ahc_11782/03_2026/7ahc_11782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ahc_11782/03_2026/7ahc_11782.map" model { file = "/net/cci-nas-00/data/ceres_data/7ahc_11782/03_2026/7ahc_11782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ahc_11782/03_2026/7ahc_11782.cif" } resolution = 3.3 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= 0.007 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 40 5.16 5 C 5288 2.51 5 N 1358 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8170 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2016 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain: "B" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2016 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain: "D" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2069 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain: "C" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2069 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Time building chain proxies: 1.79, per 1000 atoms: 0.22 Number of scatterers: 8170 At special positions: 0 Unit cell: (94.116, 106.26, 104.236, 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 40 16.00 O 1484 8.00 N 1358 7.00 C 5288 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: 0.75 Conformation dependent library (CDL) restraints added in 275.4 milliseconds 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 68.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 10 through 26 removed outlier: 3.584A pdb=" N TRP A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 45 removed outlier: 3.860A pdb=" N VAL A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 72 through 89 removed outlier: 4.120A pdb=" N LEU A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 removed outlier: 3.800A pdb=" N SER A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 122 Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 122 through 139 removed outlier: 3.812A pdb=" N ALA A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Proline residue: A 131 - end of helix removed outlier: 3.539A pdb=" N MET A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.597A pdb=" N VAL A 143 " --> pdb=" O PRO A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 193 removed outlier: 3.765A pdb=" N VAL A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 removed outlier: 3.576A pdb=" N PHE A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 212 through 232 removed outlier: 3.948A pdb=" N MET A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 removed outlier: 4.177A pdb=" N GLY A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 276 Processing helix chain 'B' and resid 10 through 26 removed outlier: 3.584A pdb=" N TRP B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 45 removed outlier: 3.861A pdb=" N VAL B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 69 Processing helix chain 'B' and resid 72 through 89 removed outlier: 4.120A pdb=" N LEU B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.800A pdb=" N SER B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 122 Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 122 through 139 removed outlier: 3.812A pdb=" N ALA B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.538A pdb=" N MET B 139 " --> pdb=" O PHE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.597A pdb=" N VAL B 143 " --> pdb=" O PRO B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 Processing helix chain 'B' and resid 156 through 180 Proline residue: B 169 - end of helix Processing helix chain 'B' and resid 183 through 193 removed outlier: 3.765A pdb=" N VAL B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 3.576A pdb=" N PHE B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A) Proline residue: B 207 - end of helix Processing helix chain 'B' and resid 212 through 232 removed outlier: 3.949A pdb=" N MET B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.177A pdb=" N GLY B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 276 Processing helix chain 'D' and resid 17 through 27 removed outlier: 3.571A pdb=" N LYS D 27 " --> pdb=" O THR D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 38 removed outlier: 4.094A pdb=" N ILE D 34 " --> pdb=" O PRO D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 75 removed outlier: 3.849A pdb=" N LEU D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 removed outlier: 3.557A pdb=" N THR D 94 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 137 through 153 Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'D' and resid 166 through 181 removed outlier: 4.270A pdb=" N ASN D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 214 Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.595A pdb=" N ALA D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 27 removed outlier: 3.566A pdb=" N LYS C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 37 removed outlier: 4.088A pdb=" N ILE C 34 " --> pdb=" O PRO C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 75 removed outlier: 4.305A pdb=" N LEU C 71 " --> pdb=" O LYS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 137 through 151 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 166 through 181 removed outlier: 4.210A pdb=" N ASN C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 214 Processing helix chain 'C' and resid 224 through 232 Processing sheet with id=AA1, first strand: chain 'D' and resid 50 through 51 removed outlier: 3.544A pdb=" N ILE D 51 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU D 10 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N SER D 82 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 110 through 111 removed outlier: 6.232A pdb=" N LEU D 186 " --> pdb=" O ILE D 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AA4, first strand: chain 'C' and resid 50 through 51 removed outlier: 4.364A pdb=" N LEU C 10 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER C 82 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 59 removed outlier: 3.892A pdb=" N PHE C 220 " --> pdb=" O PHE C 57 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU C 186 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL C 221 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N MET C 188 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 239 475 hydrogen bonds defined for protein. 1377 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: 1.07 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2624 1.34 - 1.46: 1618 1.46 - 1.58: 3976 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 8298 Sorted by residual: bond pdb=" CB VAL A 228 " pdb=" CG2 VAL A 228 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.16e+00 bond pdb=" CB VAL B 228 " pdb=" CG2 VAL B 228 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.07e+00 bond pdb=" CB THR A 175 " pdb=" CG2 THR A 175 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.78e+00 bond pdb=" CG LEU A 186 " pdb=" CD1 LEU A 186 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.75e+00 bond pdb=" CB THR B 175 " pdb=" CG2 THR B 175 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.74e+00 ... (remaining 8293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 10840 1.43 - 2.85: 329 2.85 - 4.28: 45 4.28 - 5.70: 6 5.70 - 7.13: 2 Bond angle restraints: 11222 Sorted by residual: angle pdb=" N VAL B 113 " pdb=" CA VAL B 113 " pdb=" C VAL B 113 " ideal model delta sigma weight residual 112.67 108.99 3.68 1.25e+00 6.40e-01 8.69e+00 angle pdb=" N VAL A 113 " pdb=" CA VAL A 113 " pdb=" C VAL A 113 " ideal model delta sigma weight residual 112.67 109.04 3.63 1.25e+00 6.40e-01 8.45e+00 angle pdb=" N LYS A 70 " pdb=" CA LYS A 70 " pdb=" C LYS A 70 " ideal model delta sigma weight residual 114.04 110.61 3.43 1.24e+00 6.50e-01 7.66e+00 angle pdb=" N LYS B 70 " pdb=" CA LYS B 70 " pdb=" C LYS B 70 " ideal model delta sigma weight residual 114.04 110.63 3.41 1.24e+00 6.50e-01 7.57e+00 angle pdb=" CA GLY D 61 " pdb=" C GLY D 61 " pdb=" N LEU D 62 " ideal model delta sigma weight residual 114.66 117.19 -2.53 1.10e+00 8.26e-01 5.28e+00 ... (remaining 11217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4414 17.65 - 35.30: 466 35.30 - 52.96: 124 52.96 - 70.61: 22 70.61 - 88.26: 8 Dihedral angle restraints: 5034 sinusoidal: 2008 harmonic: 3026 Sorted by residual: dihedral pdb=" CA MET B 95 " pdb=" C MET B 95 " pdb=" N SER B 96 " pdb=" CA SER B 96 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA MET A 95 " pdb=" C MET A 95 " pdb=" N SER A 96 " pdb=" CA SER A 96 " ideal model delta harmonic sigma weight residual 180.00 155.19 24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ILE B 128 " pdb=" C ILE B 128 " pdb=" N VAL B 129 " pdb=" CA VAL B 129 " ideal model delta harmonic sigma weight residual -180.00 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 700 0.027 - 0.054: 370 0.054 - 0.081: 159 0.081 - 0.107: 92 0.107 - 0.134: 39 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CB VAL B 164 " pdb=" CA VAL B 164 " pdb=" CG1 VAL B 164 " pdb=" CG2 VAL B 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CB VAL A 164 " pdb=" CA VAL A 164 " pdb=" CG1 VAL A 164 " pdb=" CG2 VAL A 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE C 87 " pdb=" N ILE C 87 " pdb=" C ILE C 87 " pdb=" CB ILE C 87 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1357 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 74 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO B 75 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 74 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 136 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO C 137 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 137 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 137 " 0.019 5.00e-02 4.00e+02 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 280 2.69 - 3.24: 9129 3.24 - 3.80: 12638 3.80 - 4.35: 16891 4.35 - 4.90: 28538 Nonbonded interactions: 67476 Sorted by model distance: nonbonded pdb=" NZ LYS C 242 " pdb=" O ILE C 243 " model vdw 2.141 3.120 nonbonded pdb=" NH2 ARG D 76 " pdb=" OE1 GLU D 79 " model vdw 2.195 3.120 nonbonded pdb=" NZ LYS C 6 " pdb=" O ILE C 7 " model vdw 2.225 3.120 nonbonded pdb=" OG SER B 195 " pdb=" OH TYR C 129 " model vdw 2.233 3.040 nonbonded pdb=" NZ LYS D 6 " pdb=" O ILE D 7 " model vdw 2.244 3.120 ... (remaining 67471 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 1.260 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: 0.070 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.230 Find NCS groups from input model: 0.130 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.008 0.053 8298 Z= 0.297 Angle : 0.609 7.129 11222 Z= 0.346 Chirality : 0.045 0.134 1360 Planarity : 0.004 0.041 1406 Dihedral : 15.793 88.260 3078 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.11 % Allowed : 19.98 % Favored : 79.91 % 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 are not related in a simple way. whole: -4.17 (0.21), residues: 1056 helix: -2.12 (0.17), residues: 654 sheet: -4.79 (0.34), residues: 74 loop : -3.24 (0.27), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 17 TYR 0.009 0.001 TYR D 45 PHE 0.019 0.001 PHE B 135 TRP 0.003 0.000 TRP A 91 HIS 0.003 0.001 HIS D 223 Details of bonding type rmsd covalent geometry : bond 0.00765 ( 8298) covalent geometry : angle 0.60930 (11222) hydrogen bonds : bond 0.14251 ( 475) hydrogen bonds : angle 6.59656 ( 1377) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 44 ILE cc_start: 0.8378 (pt) cc_final: 0.7798 (pt) REVERT: B 44 ILE cc_start: 0.8327 (pt) cc_final: 0.7794 (pt) REVERT: C 62 LEU cc_start: 0.8267 (mp) cc_final: 0.7969 (mp) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.0874 time to fit residues: 19.6668 Evaluate side-chains 104 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN D 135 ASN D 181 ASN D 215 GLN C 52 ASN C 164 GLN C 170 GLN C 181 ASN C 211 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.183187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 132)---------------| | r_work = 0.3653 r_free = 0.3653 target = 0.145634 restraints weight = 10030.065| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.16 r_work: 0.3440 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8298 Z= 0.151 Angle : 0.646 7.813 11222 Z= 0.335 Chirality : 0.045 0.203 1360 Planarity : 0.005 0.044 1406 Dihedral : 5.071 48.120 1114 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.90 % Allowed : 17.52 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.26), residues: 1056 helix: -0.30 (0.20), residues: 650 sheet: -3.83 (0.45), residues: 80 loop : -2.09 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 201 TYR 0.007 0.001 TYR D 45 PHE 0.011 0.001 PHE B 77 TRP 0.011 0.001 TRP B 54 HIS 0.001 0.000 HIS D 9 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8298) covalent geometry : angle 0.64559 (11222) hydrogen bonds : bond 0.04032 ( 475) hydrogen bonds : angle 4.90978 ( 1377) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7977 (mp) REVERT: A 199 GLN cc_start: 0.8190 (mt0) cc_final: 0.7926 (mp10) REVERT: B 48 LEU cc_start: 0.3540 (OUTLIER) cc_final: 0.3162 (tt) REVERT: B 127 LYS cc_start: 0.7860 (ttpp) cc_final: 0.7628 (ttpp) REVERT: B 177 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8067 (mp) REVERT: D 71 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8065 (mp) REVERT: C 62 LEU cc_start: 0.8412 (mp) cc_final: 0.8192 (mt) outliers start: 26 outliers final: 8 residues processed: 165 average time/residue: 0.0682 time to fit residues: 16.0548 Evaluate side-chains 117 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 67 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 103 optimal weight: 0.0770 chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 86 optimal weight: 0.0570 chunk 48 optimal weight: 0.6980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN C 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.183511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 128)---------------| | r_work = 0.3674 r_free = 0.3674 target = 0.147230 restraints weight = 10045.122| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.14 r_work: 0.3515 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8298 Z= 0.125 Angle : 0.595 7.559 11222 Z= 0.310 Chirality : 0.044 0.147 1360 Planarity : 0.004 0.046 1406 Dihedral : 4.956 48.502 1114 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.24 % Allowed : 17.08 % Favored : 79.69 % 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 are not related in a simple way. whole: -0.91 (0.27), residues: 1056 helix: 0.41 (0.21), residues: 650 sheet: -3.08 (0.52), residues: 82 loop : -1.86 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 201 TYR 0.003 0.001 TYR C 260 PHE 0.015 0.001 PHE B 77 TRP 0.006 0.001 TRP B 54 HIS 0.002 0.000 HIS D 223 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8298) covalent geometry : angle 0.59474 (11222) hydrogen bonds : bond 0.03593 ( 475) hydrogen bonds : angle 4.55164 ( 1377) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8363 (mp) REVERT: B 48 LEU cc_start: 0.3546 (OUTLIER) cc_final: 0.3264 (tt) REVERT: B 177 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8107 (mp) REVERT: D 60 MET cc_start: 0.7432 (mtp) cc_final: 0.7073 (mmm) REVERT: D 226 ASN cc_start: 0.7434 (p0) cc_final: 0.6920 (t0) REVERT: D 231 ILE cc_start: 0.5705 (OUTLIER) cc_final: 0.5237 (tp) REVERT: C 38 THR cc_start: -0.1275 (OUTLIER) cc_final: -0.1850 (m) REVERT: C 229 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8236 (mm) REVERT: C 259 ASP cc_start: 0.6599 (m-30) cc_final: 0.5957 (p0) outliers start: 29 outliers final: 11 residues processed: 157 average time/residue: 0.0756 time to fit residues: 16.6489 Evaluate side-chains 122 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 229 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 chunk 41 optimal weight: 0.0070 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN D 211 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.182319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149257 restraints weight = 10266.834| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.33 r_work: 0.3454 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8298 Z= 0.120 Angle : 0.580 7.720 11222 Z= 0.299 Chirality : 0.043 0.148 1360 Planarity : 0.004 0.046 1406 Dihedral : 4.875 44.894 1114 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.12 % Allowed : 18.97 % Favored : 77.90 % 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 are not related in a simple way. whole: -0.51 (0.27), residues: 1056 helix: 0.64 (0.21), residues: 656 sheet: -2.67 (0.55), residues: 82 loop : -1.62 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 144 TYR 0.006 0.001 TYR C 260 PHE 0.013 0.001 PHE B 77 TRP 0.005 0.001 TRP A 54 HIS 0.001 0.000 HIS C 9 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8298) covalent geometry : angle 0.58015 (11222) hydrogen bonds : bond 0.03320 ( 475) hydrogen bonds : angle 4.41897 ( 1377) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.255 Fit side-chains REVERT: A 107 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8418 (mp) REVERT: A 177 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8211 (mp) REVERT: B 107 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8429 (mp) REVERT: B 239 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8117 (mt) REVERT: D 60 MET cc_start: 0.7474 (mtp) cc_final: 0.7067 (mmm) REVERT: D 71 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7877 (mt) REVERT: D 226 ASN cc_start: 0.7384 (p0) cc_final: 0.6888 (t0) REVERT: D 231 ILE cc_start: 0.5887 (OUTLIER) cc_final: 0.5484 (tp) outliers start: 28 outliers final: 11 residues processed: 166 average time/residue: 0.0753 time to fit residues: 17.3852 Evaluate side-chains 135 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 149 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 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 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.177779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.142323 restraints weight = 10240.542| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.44 r_work: 0.3264 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8298 Z= 0.154 Angle : 0.601 7.671 11222 Z= 0.313 Chirality : 0.045 0.173 1360 Planarity : 0.004 0.047 1406 Dihedral : 4.923 41.404 1114 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.35 % Allowed : 19.64 % Favored : 77.01 % 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 are not related in a simple way. whole: -0.41 (0.26), residues: 1056 helix: 0.66 (0.21), residues: 654 sheet: -2.45 (0.56), residues: 82 loop : -1.48 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 172 TYR 0.006 0.001 TYR D 45 PHE 0.014 0.001 PHE B 135 TRP 0.007 0.001 TRP B 54 HIS 0.001 0.000 HIS C 9 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8298) covalent geometry : angle 0.60122 (11222) hydrogen bonds : bond 0.03595 ( 475) hydrogen bonds : angle 4.50239 ( 1377) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.194 Fit side-chains REVERT: A 70 LYS cc_start: 0.8078 (mmtm) cc_final: 0.7749 (tppt) REVERT: A 107 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8542 (mp) REVERT: A 177 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8214 (mp) REVERT: B 107 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8535 (mp) REVERT: B 177 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8197 (mp) REVERT: D 31 LYS cc_start: 0.6257 (pttt) cc_final: 0.5851 (pttt) REVERT: D 71 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7929 (mt) REVERT: D 226 ASN cc_start: 0.7567 (p0) cc_final: 0.6858 (t0) REVERT: D 231 ILE cc_start: 0.5820 (OUTLIER) cc_final: 0.5391 (tp) REVERT: C 38 THR cc_start: -0.1284 (OUTLIER) cc_final: -0.1951 (m) outliers start: 30 outliers final: 15 residues processed: 157 average time/residue: 0.0867 time to fit residues: 18.4873 Evaluate side-chains 140 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 67 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 57 optimal weight: 0.0770 chunk 44 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN B 130 GLN D 134 GLN D 160 GLN C 245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.179642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146183 restraints weight = 10157.287| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.56 r_work: 0.3374 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8298 Z= 0.124 Angle : 0.583 7.498 11222 Z= 0.299 Chirality : 0.043 0.176 1360 Planarity : 0.004 0.047 1406 Dihedral : 4.808 36.270 1114 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.46 % Allowed : 20.20 % Favored : 76.34 % 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 are not related in a simple way. whole: -0.24 (0.26), residues: 1056 helix: 0.78 (0.21), residues: 654 sheet: -2.23 (0.57), residues: 82 loop : -1.43 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 230 TYR 0.004 0.001 TYR D 45 PHE 0.024 0.001 PHE A 53 TRP 0.003 0.001 TRP B 54 HIS 0.001 0.000 HIS D 120 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8298) covalent geometry : angle 0.58265 (11222) hydrogen bonds : bond 0.03321 ( 475) hydrogen bonds : angle 4.37312 ( 1377) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.241 Fit side-chains REVERT: A 70 LYS cc_start: 0.8012 (mmtm) cc_final: 0.7741 (tppt) REVERT: A 107 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8476 (mp) REVERT: A 177 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8262 (mp) REVERT: B 107 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8506 (mp) REVERT: B 139 MET cc_start: 0.8349 (ptp) cc_final: 0.8039 (ptp) REVERT: B 177 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8197 (mp) REVERT: D 31 LYS cc_start: 0.6250 (pttt) cc_final: 0.5903 (pttt) REVERT: D 60 MET cc_start: 0.7268 (tpp) cc_final: 0.6744 (mmm) REVERT: D 71 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7889 (mt) REVERT: D 169 MET cc_start: 0.7106 (tpp) cc_final: 0.5990 (tpp) REVERT: D 226 ASN cc_start: 0.7541 (p0) cc_final: 0.6801 (t0) REVERT: C 38 THR cc_start: -0.1452 (OUTLIER) cc_final: -0.2177 (m) REVERT: C 244 MET cc_start: 0.6934 (mtt) cc_final: 0.6594 (mtt) outliers start: 31 outliers final: 19 residues processed: 160 average time/residue: 0.0814 time to fit residues: 17.7462 Evaluate side-chains 146 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 245 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN D 120 HIS C 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.176190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.143118 restraints weight = 10297.666| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.82 r_work: 0.3252 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8298 Z= 0.172 Angle : 0.611 7.700 11222 Z= 0.316 Chirality : 0.045 0.209 1360 Planarity : 0.004 0.049 1406 Dihedral : 4.765 20.840 1110 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.46 % Allowed : 20.87 % Favored : 75.67 % 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 are not related in a simple way. whole: -0.35 (0.26), residues: 1056 helix: 0.69 (0.20), residues: 662 sheet: -2.21 (0.56), residues: 82 loop : -1.53 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 172 TYR 0.007 0.001 TYR D 45 PHE 0.024 0.002 PHE B 53 TRP 0.004 0.001 TRP B 14 HIS 0.002 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8298) covalent geometry : angle 0.61104 (11222) hydrogen bonds : bond 0.03628 ( 475) hydrogen bonds : angle 4.49595 ( 1377) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.227 Fit side-chains REVERT: A 45 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8856 (t) REVERT: A 70 LYS cc_start: 0.8085 (mmtm) cc_final: 0.7849 (tppt) REVERT: A 107 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8492 (mp) REVERT: A 177 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8253 (mp) REVERT: B 107 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8508 (mp) REVERT: B 139 MET cc_start: 0.8328 (ptp) cc_final: 0.8015 (ptp) REVERT: B 177 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8209 (mp) REVERT: D 31 LYS cc_start: 0.6463 (pttt) cc_final: 0.6217 (pttt) REVERT: D 71 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7793 (mp) REVERT: D 226 ASN cc_start: 0.7713 (p0) cc_final: 0.6909 (t0) REVERT: D 231 ILE cc_start: 0.5903 (OUTLIER) cc_final: 0.5474 (tp) REVERT: C 244 MET cc_start: 0.6896 (mtt) cc_final: 0.6674 (mtt) outliers start: 31 outliers final: 16 residues processed: 144 average time/residue: 0.0755 time to fit residues: 15.1049 Evaluate side-chains 139 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 131 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 67 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 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 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.178611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145777 restraints weight = 10247.531| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.53 r_work: 0.3379 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8298 Z= 0.124 Angle : 0.591 9.899 11222 Z= 0.303 Chirality : 0.043 0.150 1360 Planarity : 0.004 0.048 1406 Dihedral : 4.687 20.380 1110 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.35 % Allowed : 21.65 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.27), residues: 1056 helix: 0.83 (0.20), residues: 666 sheet: -2.02 (0.58), residues: 82 loop : -1.52 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 172 TYR 0.004 0.001 TYR D 45 PHE 0.023 0.001 PHE A 53 TRP 0.004 0.001 TRP B 54 HIS 0.001 0.000 HIS C 9 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8298) covalent geometry : angle 0.59061 (11222) hydrogen bonds : bond 0.03353 ( 475) hydrogen bonds : angle 4.37888 ( 1377) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.247 Fit side-chains REVERT: A 45 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8871 (t) REVERT: A 70 LYS cc_start: 0.8149 (mmtm) cc_final: 0.7875 (tppt) REVERT: A 107 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8560 (mp) REVERT: A 177 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8210 (mp) REVERT: B 107 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8539 (mp) REVERT: B 139 MET cc_start: 0.8370 (ptp) cc_final: 0.8042 (ptp) REVERT: B 177 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8164 (mp) REVERT: D 31 LYS cc_start: 0.6660 (pttt) cc_final: 0.6361 (pttt) REVERT: D 60 MET cc_start: 0.7480 (tpp) cc_final: 0.6800 (mmm) REVERT: D 71 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7877 (mt) REVERT: D 208 LEU cc_start: 0.8407 (tp) cc_final: 0.8034 (mt) REVERT: D 226 ASN cc_start: 0.7713 (p0) cc_final: 0.6887 (t0) REVERT: C 238 MET cc_start: 0.6665 (mtp) cc_final: 0.6441 (mtm) REVERT: C 244 MET cc_start: 0.6693 (mtt) cc_final: 0.6446 (mtt) REVERT: C 259 ASP cc_start: 0.6473 (m-30) cc_final: 0.6235 (p0) outliers start: 30 outliers final: 18 residues processed: 150 average time/residue: 0.0716 time to fit residues: 15.0547 Evaluate side-chains 142 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain C residue 60 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 102 optimal weight: 9.9990 chunk 91 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.178438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.147399 restraints weight = 10262.066| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.69 r_work: 0.3292 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8298 Z= 0.127 Angle : 0.602 9.396 11222 Z= 0.306 Chirality : 0.044 0.159 1360 Planarity : 0.004 0.050 1406 Dihedral : 4.701 20.914 1110 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.68 % Allowed : 21.99 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.27), residues: 1056 helix: 0.90 (0.20), residues: 666 sheet: -1.87 (0.59), residues: 82 loop : -1.51 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 172 TYR 0.005 0.001 TYR A 144 PHE 0.024 0.001 PHE B 53 TRP 0.005 0.001 TRP A 54 HIS 0.000 0.000 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8298) covalent geometry : angle 0.60175 (11222) hydrogen bonds : bond 0.03333 ( 475) hydrogen bonds : angle 4.36405 ( 1377) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.241 Fit side-chains REVERT: A 45 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8810 (t) REVERT: A 107 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8499 (mp) REVERT: A 177 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8168 (mp) REVERT: A 199 GLN cc_start: 0.8034 (pm20) cc_final: 0.7783 (pm20) REVERT: B 107 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8504 (mp) REVERT: B 139 MET cc_start: 0.8279 (ptp) cc_final: 0.7955 (ptp) REVERT: B 177 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8140 (mp) REVERT: D 31 LYS cc_start: 0.6487 (pttt) cc_final: 0.6218 (pttt) REVERT: D 60 MET cc_start: 0.7408 (tpp) cc_final: 0.6823 (mmm) REVERT: D 208 LEU cc_start: 0.8234 (tp) cc_final: 0.7981 (mt) REVERT: D 226 ASN cc_start: 0.7594 (p0) cc_final: 0.6823 (t0) REVERT: C 244 MET cc_start: 0.6605 (mtt) cc_final: 0.6368 (mtt) outliers start: 24 outliers final: 17 residues processed: 145 average time/residue: 0.0758 time to fit residues: 15.5157 Evaluate side-chains 140 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain C residue 60 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 0.0670 chunk 14 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.0050 chunk 85 optimal weight: 0.7980 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.180044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.148319 restraints weight = 10248.046| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.73 r_work: 0.3371 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8298 Z= 0.117 Angle : 0.597 8.943 11222 Z= 0.302 Chirality : 0.043 0.156 1360 Planarity : 0.004 0.051 1406 Dihedral : 4.623 20.548 1110 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.46 % Allowed : 21.99 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.27), residues: 1056 helix: 1.04 (0.21), residues: 666 sheet: -1.74 (0.59), residues: 84 loop : -1.46 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 172 TYR 0.005 0.001 TYR C 45 PHE 0.023 0.001 PHE B 53 TRP 0.003 0.000 TRP B 54 HIS 0.001 0.000 HIS C 9 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8298) covalent geometry : angle 0.59707 (11222) hydrogen bonds : bond 0.03140 ( 475) hydrogen bonds : angle 4.25683 ( 1377) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.313 Fit side-chains REVERT: A 41 MET cc_start: 0.7955 (tpp) cc_final: 0.7559 (tpt) REVERT: A 45 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8701 (t) REVERT: A 107 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8523 (mp) REVERT: B 107 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8507 (mp) REVERT: B 139 MET cc_start: 0.8260 (ptp) cc_final: 0.7950 (ptp) REVERT: D 31 LYS cc_start: 0.6442 (pttt) cc_final: 0.6076 (pttt) REVERT: D 60 MET cc_start: 0.7320 (tpp) cc_final: 0.6701 (mmm) REVERT: D 205 ASP cc_start: 0.6789 (t0) cc_final: 0.6524 (m-30) REVERT: D 208 LEU cc_start: 0.8299 (tp) cc_final: 0.7980 (mt) REVERT: D 226 ASN cc_start: 0.7615 (p0) cc_final: 0.6849 (t0) REVERT: C 244 MET cc_start: 0.6535 (mtt) cc_final: 0.6302 (mtt) outliers start: 22 outliers final: 16 residues processed: 146 average time/residue: 0.0728 time to fit residues: 15.1833 Evaluate side-chains 140 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 0.3980 chunk 60 optimal weight: 0.0570 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** 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 = 0.4011 r_free = 0.4011 target = 0.178592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144052 restraints weight = 10386.493| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.85 r_work: 0.3297 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 8298 Z= 0.156 Angle : 0.923 59.198 11222 Z= 0.544 Chirality : 0.043 0.250 1360 Planarity : 0.004 0.051 1406 Dihedral : 4.674 26.631 1110 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.34 % Allowed : 22.32 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.27), residues: 1056 helix: 1.04 (0.21), residues: 666 sheet: -1.71 (0.59), residues: 84 loop : -1.46 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 172 TYR 0.004 0.001 TYR D 45 PHE 0.023 0.001 PHE B 53 TRP 0.003 0.000 TRP B 54 HIS 0.002 0.000 HIS C 9 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8298) covalent geometry : angle 0.92304 (11222) hydrogen bonds : bond 0.03160 ( 475) hydrogen bonds : angle 4.25411 ( 1377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2044.37 seconds wall clock time: 35 minutes 38.10 seconds (2138.10 seconds total)