Starting phenix.real_space_refine on Wed Mar 12 16:00:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ahc_11782/03_2025/7ahc_11782.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ahc_11782/03_2025/7ahc_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_2025/7ahc_11782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ahc_11782/03_2025/7ahc_11782.map" model { file = "/net/cci-nas-00/data/ceres_data/7ahc_11782/03_2025/7ahc_11782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ahc_11782/03_2025/7ahc_11782.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.43, per 1000 atoms: 0.66 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: 2.17 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.83 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: 2.18 Time building geometry restraints manager: 2.53 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: 0.04 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: 1.210 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.230 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.250 ------------------------------------------------------------------------------- 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= 0.493 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.003 0.000 TRP A 91 HIS 0.003 0.001 HIS D 223 PHE 0.019 0.001 PHE B 135 TYR 0.009 0.001 TYR D 45 ARG 0.002 0.000 ARG C 17 *********************** 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 : 0.839 Fit side-chains revert: symmetry clash REVERT: A 44 ILE cc_start: 0.8378 (pt) cc_final: 0.7796 (pt) REVERT: B 44 ILE cc_start: 0.8327 (pt) cc_final: 0.7793 (pt) REVERT: C 62 LEU cc_start: 0.8267 (mp) cc_final: 0.7968 (mp) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.2139 time to fit residues: 48.0017 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 : 0.937 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4044 r_free = 0.4044 target = 0.183829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153980 restraints weight = 9978.254| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.15 r_work: 0.3547 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8298 Z= 0.215 Angle : 0.648 7.670 11222 Z= 0.336 Chirality : 0.045 0.169 1360 Planarity : 0.005 0.043 1406 Dihedral : 5.086 48.514 1114 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.26), residues: 1056 helix: -0.28 (0.20), residues: 650 sheet: -3.78 (0.46), residues: 80 loop : -2.08 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 54 HIS 0.001 0.000 HIS D 9 PHE 0.010 0.001 PHE B 77 TYR 0.008 0.001 TYR D 45 ARG 0.003 0.000 ARG C 76 *********************** 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 166 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8016 (mp) REVERT: B 48 LEU cc_start: 0.3653 (OUTLIER) cc_final: 0.3281 (tt) REVERT: B 127 LYS cc_start: 0.7915 (ttpp) cc_final: 0.7695 (ttpp) REVERT: B 177 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8115 (mp) REVERT: D 71 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8147 (mp) REVERT: C 62 LEU cc_start: 0.8397 (mp) cc_final: 0.8190 (mt) outliers start: 26 outliers final: 7 residues processed: 162 average time/residue: 0.1823 time to fit residues: 41.1007 Evaluate side-chains 113 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 C 171 GLN ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.180709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.148539 restraints weight = 10205.928| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.49 r_work: 0.3397 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8298 Z= 0.218 Angle : 0.605 7.637 11222 Z= 0.316 Chirality : 0.045 0.150 1360 Planarity : 0.004 0.047 1406 Dihedral : 5.001 47.182 1114 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.46 % Allowed : 16.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.26), residues: 1056 helix: 0.30 (0.21), residues: 650 sheet: -3.08 (0.52), residues: 82 loop : -1.87 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 54 HIS 0.001 0.000 HIS D 223 PHE 0.013 0.001 PHE A 77 TYR 0.004 0.001 TYR C 260 ARG 0.003 0.000 ARG C 144 *********************** 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 174 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 177 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8185 (mp) REVERT: B 48 LEU cc_start: 0.3935 (OUTLIER) cc_final: 0.3726 (tt) REVERT: B 107 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8485 (mp) REVERT: B 177 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8154 (mp) REVERT: D 71 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8046 (mp) REVERT: D 226 ASN cc_start: 0.7561 (p0) cc_final: 0.6906 (t0) REVERT: D 231 ILE cc_start: 0.5823 (OUTLIER) cc_final: 0.5356 (tp) REVERT: C 38 THR cc_start: -0.1036 (OUTLIER) cc_final: -0.1680 (m) REVERT: C 165 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7740 (mp) REVERT: C 229 LEU cc_start: 0.8453 (mm) cc_final: 0.8216 (mm) outliers start: 31 outliers final: 11 residues processed: 165 average time/residue: 0.1842 time to fit residues: 42.3829 Evaluate side-chains 132 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 177 LEU 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 107 LEU Chi-restraints excluded: chain B residue 124 LEU 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 71 LEU 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 165 LEU Chi-restraints excluded: chain C residue 188 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 48 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 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 211 GLN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.180645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.145565 restraints weight = 10028.862| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.21 r_work: 0.3369 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3024 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= 0.192 Angle : 0.589 8.282 11222 Z= 0.304 Chirality : 0.044 0.159 1360 Planarity : 0.004 0.047 1406 Dihedral : 4.911 43.889 1114 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.01 % Allowed : 19.53 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.26), residues: 1056 helix: 0.54 (0.21), residues: 654 sheet: -2.73 (0.55), residues: 82 loop : -1.70 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 118 HIS 0.001 0.000 HIS D 223 PHE 0.015 0.001 PHE B 77 TYR 0.006 0.001 TYR C 260 ARG 0.002 0.000 ARG D 144 *********************** 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 168 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.227 Fit side-chains REVERT: A 107 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 177 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8214 (mp) REVERT: B 107 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8493 (mp) REVERT: D 60 MET cc_start: 0.7081 (tpp) cc_final: 0.6445 (mmm) REVERT: D 71 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7847 (mt) REVERT: D 226 ASN cc_start: 0.7482 (p0) cc_final: 0.6823 (t0) REVERT: D 231 ILE cc_start: 0.5563 (OUTLIER) cc_final: 0.5077 (tp) REVERT: C 165 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7586 (mp) outliers start: 27 outliers final: 13 residues processed: 164 average time/residue: 0.2128 time to fit residues: 48.5473 Evaluate side-chains 132 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 177 LEU 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 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 8 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 0.0980 chunk 84 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 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 = 0.4017 r_free = 0.4017 target = 0.180664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.145089 restraints weight = 10040.169| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.21 r_work: 0.3409 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8298 Z= 0.171 Angle : 0.575 7.527 11222 Z= 0.298 Chirality : 0.043 0.184 1360 Planarity : 0.004 0.047 1406 Dihedral : 4.850 40.911 1114 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.57 % Allowed : 19.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.27), residues: 1056 helix: 0.75 (0.21), residues: 654 sheet: -2.52 (0.55), residues: 82 loop : -1.51 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 118 HIS 0.002 0.000 HIS C 223 PHE 0.012 0.001 PHE B 77 TYR 0.004 0.001 TYR D 45 ARG 0.001 0.000 ARG C 172 *********************** 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 164 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 8 GLN cc_start: 0.6366 (mp10) cc_final: 0.5744 (mp10) REVERT: A 107 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8453 (mp) REVERT: B 107 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8475 (mp) REVERT: B 139 MET cc_start: 0.8220 (ptp) cc_final: 0.7917 (ptp) REVERT: B 177 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8178 (mp) REVERT: B 239 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8155 (mt) REVERT: D 60 MET cc_start: 0.7219 (tpp) cc_final: 0.6658 (mmm) REVERT: D 208 LEU cc_start: 0.8415 (tp) cc_final: 0.8190 (mp) REVERT: D 226 ASN cc_start: 0.7429 (p0) cc_final: 0.6739 (t0) REVERT: C 38 THR cc_start: -0.1464 (OUTLIER) cc_final: -0.2099 (m) REVERT: C 165 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7642 (mp) outliers start: 32 outliers final: 18 residues processed: 157 average time/residue: 0.2055 time to fit residues: 43.7991 Evaluate side-chains 141 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 212 THR 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 239 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 3 VAL 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 Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 48 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN A 218 ASN B 130 GLN B 218 ASN D 120 HIS D 134 GLN D 160 GLN C 245 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.172636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141206 restraints weight = 10226.234| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.76 r_work: 0.3265 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8298 Z= 0.385 Angle : 0.677 7.945 11222 Z= 0.352 Chirality : 0.048 0.171 1360 Planarity : 0.005 0.047 1406 Dihedral : 5.205 41.059 1114 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.57 % Allowed : 19.75 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.26), residues: 1056 helix: 0.21 (0.20), residues: 676 sheet: -2.47 (0.56), residues: 82 loop : -1.42 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 14 HIS 0.002 0.001 HIS D 223 PHE 0.017 0.002 PHE B 135 TYR 0.012 0.001 TYR D 45 ARG 0.005 0.001 ARG C 230 *********************** 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 159 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.919 Fit side-chains REVERT: A 70 LYS cc_start: 0.8175 (mmtm) cc_final: 0.7907 (tppt) REVERT: A 107 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8614 (mp) REVERT: A 177 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8255 (mp) REVERT: B 107 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8571 (mp) REVERT: B 139 MET cc_start: 0.8413 (ptp) cc_final: 0.8089 (ptp) REVERT: B 177 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8228 (mp) REVERT: D 71 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7891 (mp) REVERT: D 226 ASN cc_start: 0.7603 (p0) cc_final: 0.6727 (t0) REVERT: D 231 ILE cc_start: 0.5975 (OUTLIER) cc_final: 0.5527 (tp) REVERT: C 165 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7386 (mp) outliers start: 32 outliers final: 15 residues processed: 147 average time/residue: 0.1980 time to fit residues: 39.6761 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 : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU 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 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 154 ILE Chi-restraints excluded: chain B residue 177 LEU 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 60 MET Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 165 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 71 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 56 optimal weight: 0.0870 chunk 89 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.177009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145562 restraints weight = 10263.570| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.63 r_work: 0.3281 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8298 Z= 0.183 Angle : 0.591 7.411 11222 Z= 0.306 Chirality : 0.043 0.185 1360 Planarity : 0.004 0.047 1406 Dihedral : 4.964 37.908 1114 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.35 % Allowed : 20.42 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1056 helix: 0.70 (0.20), residues: 660 sheet: -2.33 (0.57), residues: 82 loop : -1.52 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 21 HIS 0.001 0.000 HIS C 9 PHE 0.013 0.001 PHE B 77 TYR 0.006 0.001 TYR D 45 ARG 0.006 0.000 ARG C 172 *********************** 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 160 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.857 Fit side-chains REVERT: A 45 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8904 (t) REVERT: A 70 LYS cc_start: 0.8190 (mmtm) cc_final: 0.7872 (tppt) REVERT: A 107 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8552 (mp) REVERT: A 177 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8239 (mp) REVERT: B 107 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8549 (mp) REVERT: B 177 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8205 (mp) REVERT: D 31 LYS cc_start: 0.6351 (pttt) cc_final: 0.6054 (pttt) REVERT: D 60 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6724 (mmm) REVERT: D 71 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7864 (mt) REVERT: D 205 ASP cc_start: 0.6958 (t0) cc_final: 0.6642 (m-30) REVERT: D 226 ASN cc_start: 0.7663 (p0) cc_final: 0.6856 (t0) REVERT: D 231 ILE cc_start: 0.5996 (OUTLIER) cc_final: 0.5502 (tp) REVERT: C 165 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7216 (mp) REVERT: C 244 MET cc_start: 0.7017 (mtt) cc_final: 0.6704 (mtt) outliers start: 30 outliers final: 17 residues processed: 154 average time/residue: 0.1908 time to fit residues: 40.8966 Evaluate side-chains 141 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 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 A residue 206 PHE Chi-restraints excluded: chain A residue 212 THR 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 177 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 60 MET 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 67 LYS Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 84 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.174319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140138 restraints weight = 10256.436| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.74 r_work: 0.3163 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3884 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= 0.274 Angle : 0.623 7.647 11222 Z= 0.321 Chirality : 0.045 0.152 1360 Planarity : 0.004 0.049 1406 Dihedral : 5.040 36.746 1114 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.57 % Allowed : 20.42 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 1056 helix: 0.55 (0.20), residues: 676 sheet: -2.30 (0.58), residues: 82 loop : -1.40 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 14 HIS 0.001 0.000 HIS C 223 PHE 0.016 0.001 PHE B 135 TYR 0.008 0.001 TYR D 45 ARG 0.005 0.000 ARG C 230 *********************** 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 150 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.867 Fit side-chains REVERT: A 45 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8997 (t) REVERT: A 70 LYS cc_start: 0.8238 (mmtm) cc_final: 0.7929 (tppt) REVERT: A 107 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8610 (mp) REVERT: A 177 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8310 (mp) REVERT: B 107 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8602 (mp) REVERT: B 139 MET cc_start: 0.8463 (ptp) cc_final: 0.8124 (ptp) REVERT: B 174 MET cc_start: 0.8938 (mmm) cc_final: 0.8539 (mmm) REVERT: B 177 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8232 (mp) REVERT: D 31 LYS cc_start: 0.6547 (pttt) cc_final: 0.6171 (pttt) REVERT: D 60 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6807 (mmm) REVERT: D 71 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7909 (mt) REVERT: D 205 ASP cc_start: 0.7071 (t0) cc_final: 0.6709 (m-30) REVERT: D 226 ASN cc_start: 0.7705 (p0) cc_final: 0.6873 (t0) REVERT: D 231 ILE cc_start: 0.5873 (OUTLIER) cc_final: 0.5386 (tp) REVERT: C 165 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7251 (mp) outliers start: 32 outliers final: 17 residues processed: 143 average time/residue: 0.1936 time to fit residues: 38.1606 Evaluate side-chains 138 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 154 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 212 THR 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 177 LEU Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 60 MET 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 5 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 94 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.177158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144447 restraints weight = 10403.038| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.64 r_work: 0.3351 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8298 Z= 0.201 Angle : 0.611 10.145 11222 Z= 0.311 Chirality : 0.043 0.153 1360 Planarity : 0.004 0.050 1406 Dihedral : 4.754 21.049 1110 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.79 % Allowed : 20.76 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.27), residues: 1056 helix: 0.83 (0.20), residues: 662 sheet: -2.21 (0.59), residues: 82 loop : -1.50 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 54 HIS 0.001 0.000 HIS C 9 PHE 0.013 0.001 PHE B 135 TYR 0.005 0.001 TYR D 45 ARG 0.003 0.000 ARG C 172 *********************** 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 146 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.932 Fit side-chains REVERT: A 45 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8915 (t) REVERT: A 70 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7949 (tppt) REVERT: A 107 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8564 (mp) REVERT: A 177 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8198 (mp) REVERT: B 107 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8566 (mp) REVERT: B 139 MET cc_start: 0.8410 (ptp) cc_final: 0.8100 (ptp) REVERT: D 31 LYS cc_start: 0.6443 (pttt) cc_final: 0.6085 (pttt) REVERT: D 60 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.6976 (mmm) REVERT: D 71 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7820 (mt) REVERT: D 205 ASP cc_start: 0.6949 (t0) cc_final: 0.6616 (m-30) REVERT: D 226 ASN cc_start: 0.7692 (p0) cc_final: 0.6831 (t0) REVERT: D 231 ILE cc_start: 0.5974 (OUTLIER) cc_final: 0.5467 (tp) REVERT: C 165 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7252 (mp) REVERT: C 238 MET cc_start: 0.6747 (mtp) cc_final: 0.6528 (mtm) REVERT: C 244 MET cc_start: 0.6950 (mtt) cc_final: 0.6670 (mtt) outliers start: 25 outliers final: 16 residues processed: 141 average time/residue: 0.1880 time to fit residues: 37.0096 Evaluate side-chains 139 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 177 LEU Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 212 THR 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 D residue 3 VAL Chi-restraints excluded: chain D residue 60 MET 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 123 ILE Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 63 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 70 optimal weight: 0.0870 chunk 87 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.177997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144411 restraints weight = 10178.300| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.69 r_work: 0.3304 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8298 Z= 0.191 Angle : 0.616 10.300 11222 Z= 0.313 Chirality : 0.044 0.155 1360 Planarity : 0.004 0.052 1406 Dihedral : 4.740 20.927 1110 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.79 % Allowed : 20.76 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.27), residues: 1056 helix: 0.88 (0.20), residues: 668 sheet: -2.10 (0.60), residues: 82 loop : -1.47 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 54 HIS 0.001 0.000 HIS C 223 PHE 0.014 0.001 PHE B 135 TYR 0.004 0.001 TYR C 45 ARG 0.007 0.000 ARG A 198 ********************** 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 143 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.935 Fit side-chains REVERT: A 45 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8857 (t) REVERT: A 107 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8552 (mp) REVERT: B 107 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8549 (mp) REVERT: B 139 MET cc_start: 0.8327 (ptp) cc_final: 0.7996 (ptp) REVERT: D 31 LYS cc_start: 0.6394 (pttt) cc_final: 0.6075 (pttt) REVERT: D 60 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6749 (mmm) REVERT: D 71 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7720 (mt) REVERT: D 205 ASP cc_start: 0.6866 (t0) cc_final: 0.6577 (m-30) REVERT: D 208 LEU cc_start: 0.8452 (tp) cc_final: 0.8119 (mt) REVERT: D 226 ASN cc_start: 0.7641 (p0) cc_final: 0.6823 (t0) REVERT: D 231 ILE cc_start: 0.6026 (OUTLIER) cc_final: 0.5799 (tp) REVERT: C 165 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7184 (mp) REVERT: C 238 MET cc_start: 0.6688 (mtp) cc_final: 0.6472 (mtm) REVERT: C 244 MET cc_start: 0.6572 (mtt) cc_final: 0.6304 (mtt) outliers start: 25 outliers final: 15 residues processed: 137 average time/residue: 0.1862 time to fit residues: 35.8067 Evaluate side-chains 138 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 206 PHE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 60 MET 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 123 ILE Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 96 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 69 optimal weight: 6.9990 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 = 0.4005 r_free = 0.4005 target = 0.178005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.145577 restraints weight = 10475.473| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.59 r_work: 0.3344 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8298 Z= 0.195 Angle : 0.613 9.363 11222 Z= 0.312 Chirality : 0.044 0.157 1360 Planarity : 0.004 0.051 1406 Dihedral : 4.733 20.778 1110 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.90 % Allowed : 21.21 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.27), residues: 1056 helix: 0.90 (0.20), residues: 676 sheet: -1.97 (0.60), residues: 82 loop : -1.40 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 54 HIS 0.001 0.000 HIS C 9 PHE 0.013 0.001 PHE B 135 TYR 0.004 0.001 TYR C 45 ARG 0.003 0.000 ARG C 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4419.07 seconds wall clock time: 77 minutes 23.76 seconds (4643.76 seconds total)