Starting phenix.real_space_refine on Tue Jan 14 04:15:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yi7_39311/01_2025/8yi7_39311_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yi7_39311/01_2025/8yi7_39311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yi7_39311/01_2025/8yi7_39311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yi7_39311/01_2025/8yi7_39311.map" model { file = "/net/cci-nas-00/data/ceres_data/8yi7_39311/01_2025/8yi7_39311_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yi7_39311/01_2025/8yi7_39311_neut.cif" } resolution = 3.57 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= 0.003 sd= 0.049 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 43 5.16 5 C 3514 2.51 5 N 943 2.21 5 O 1086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 5586 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1485 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "B" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2413 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 288} Chain breaks: 1 Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 764 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 94} Chain: "D" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.13, per 1000 atoms: 0.74 Number of scatterers: 5586 At special positions: 0 Unit cell: (117.41, 97.4064, 101.755, 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 43 16.00 O 1086 8.00 N 943 7.00 C 3514 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 110 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS B 199 " distance=2.25 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 327 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 114 " distance=2.02 Simple disulfide: pdb=" SG CYS C 51 " - pdb=" SG CYS C 101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 105 " distance=2.04 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 86 " distance=2.05 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG C 401 " - " ASN C 48 " " NAG E 1 " - " ASN B 222 " Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 683.6 milliseconds 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 13 sheets defined 17.4% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 35 through 59 Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 117 through 147 removed outlier: 4.010A pdb=" N MET A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.937A pdb=" N THR A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 228 through 233 Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE B 23 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLU B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU B 25 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 32 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 27 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B 31 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS B 105 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 33 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS B 107 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 35 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS B 92 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS B 91 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 70 " --> pdb=" O TRP B 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE B 23 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLU B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU B 25 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 32 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 27 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B 31 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS B 105 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 33 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS B 107 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 35 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AA4, first strand: chain 'B' and resid 130 through 133 removed outlier: 6.526A pdb=" N GLU B 188 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 160 Processing sheet with id=AA7, first strand: chain 'B' and resid 239 through 245 removed outlier: 5.333A pdb=" N ASN B 240 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU B 257 " --> pdb=" O ASN B 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 289 through 291 removed outlier: 4.262A pdb=" N ALA B 304 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS B 327 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 306 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 31 through 34 Processing sheet with id=AB1, first strand: chain 'C' and resid 40 through 42 removed outlier: 5.755A pdb=" N ILE C 41 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN C 112 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU C 103 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS C 114 " --> pdb=" O CYS C 101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 95 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU C 68 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE C 79 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU C 70 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 56 removed outlier: 4.035A pdb=" N LEU D 50 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER D 63 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS D 52 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU D 61 " --> pdb=" O CYS D 52 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ARG D 54 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG D 59 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AB4, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.765A pdb=" N VAL D 111 " --> pdb=" O LEU D 131 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 543 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: 1.44 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1072 1.32 - 1.45: 1396 1.45 - 1.57: 3181 1.57 - 1.69: 0 1.69 - 1.82: 55 Bond restraints: 5704 Sorted by residual: bond pdb=" CA VAL D 107 " pdb=" CB VAL D 107 " ideal model delta sigma weight residual 1.537 1.479 0.058 1.24e-02 6.50e+03 2.20e+01 bond pdb=" CA VAL D 105 " pdb=" CB VAL D 105 " ideal model delta sigma weight residual 1.541 1.488 0.053 1.30e-02 5.92e+03 1.65e+01 bond pdb=" CA PRO B 237 " pdb=" C PRO B 237 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.60e+01 bond pdb=" N VAL B 325 " pdb=" CA VAL B 325 " ideal model delta sigma weight residual 1.457 1.493 -0.035 9.00e-03 1.23e+04 1.54e+01 bond pdb=" N THR B 52 " pdb=" CA THR B 52 " ideal model delta sigma weight residual 1.453 1.489 -0.035 9.20e-03 1.18e+04 1.49e+01 ... (remaining 5699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 6213 2.13 - 4.26: 1422 4.26 - 6.38: 77 6.38 - 8.51: 7 8.51 - 10.64: 2 Bond angle restraints: 7721 Sorted by residual: angle pdb=" N ARG C 65 " pdb=" CA ARG C 65 " pdb=" C ARG C 65 " ideal model delta sigma weight residual 114.62 106.84 7.78 1.14e+00 7.69e-01 4.65e+01 angle pdb=" C THR D 123 " pdb=" CA THR D 123 " pdb=" CB THR D 123 " ideal model delta sigma weight residual 110.78 100.14 10.64 1.60e+00 3.91e-01 4.42e+01 angle pdb=" CA GLY B 72 " pdb=" C GLY B 72 " pdb=" O GLY B 72 " ideal model delta sigma weight residual 122.23 117.93 4.30 6.90e-01 2.10e+00 3.89e+01 angle pdb=" CA THR D 112 " pdb=" C THR D 112 " pdb=" O THR D 112 " ideal model delta sigma weight residual 121.81 115.62 6.19 1.18e+00 7.18e-01 2.75e+01 angle pdb=" N SER D 106 " pdb=" CA SER D 106 " pdb=" C SER D 106 " ideal model delta sigma weight residual 109.59 117.10 -7.51 1.47e+00 4.63e-01 2.61e+01 ... (remaining 7716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.20: 3301 20.20 - 40.40: 196 40.40 - 60.60: 37 60.60 - 80.80: 8 80.80 - 101.00: 6 Dihedral angle restraints: 3548 sinusoidal: 1498 harmonic: 2050 Sorted by residual: dihedral pdb=" CB CYS C 59 " pdb=" SG CYS C 59 " pdb=" SG CYS C 105 " pdb=" CB CYS C 105 " ideal model delta sinusoidal sigma weight residual 93.00 166.24 -73.24 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS B 300 " pdb=" SG CYS B 300 " pdb=" SG CYS B 327 " pdb=" CB CYS B 327 " ideal model delta sinusoidal sigma weight residual -86.00 -147.42 61.42 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CB CYS B 50 " pdb=" SG CYS B 50 " pdb=" SG CYS B 90 " pdb=" CB CYS B 90 " ideal model delta sinusoidal sigma weight residual 93.00 153.54 -60.54 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 3545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 396 0.076 - 0.151: 318 0.151 - 0.227: 119 0.227 - 0.302: 38 0.302 - 0.378: 3 Chirality restraints: 874 Sorted by residual: chirality pdb=" CA THR D 123 " pdb=" N THR D 123 " pdb=" C THR D 123 " pdb=" CB THR D 123 " both_signs ideal model delta sigma weight residual False 2.53 2.90 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA ASN B 184 " pdb=" N ASN B 184 " pdb=" C ASN B 184 " pdb=" CB ASN B 184 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB VAL B 180 " pdb=" CA VAL B 180 " pdb=" CG1 VAL B 180 " pdb=" CG2 VAL B 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 871 not shown) Planarity restraints: 979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 100 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.22e+00 pdb=" C SER D 100 " 0.053 2.00e-02 2.50e+03 pdb=" O SER D 100 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP D 101 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 196 " -0.014 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C ASP B 196 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP B 196 " -0.019 2.00e-02 2.50e+03 pdb=" N SER B 197 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 265 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C PRO B 265 " -0.048 2.00e-02 2.50e+03 pdb=" O PRO B 265 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS B 266 " 0.016 2.00e-02 2.50e+03 ... (remaining 976 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 138 2.68 - 3.23: 4878 3.23 - 3.79: 8010 3.79 - 4.34: 11305 4.34 - 4.90: 17923 Nonbonded interactions: 42254 Sorted by model distance: nonbonded pdb=" CD2 LEU B 117 " pdb=" CG2 THR B 146 " model vdw 2.122 3.880 nonbonded pdb=" CG2 THR B 141 " pdb=" OE1 GLU B 192 " model vdw 2.338 3.460 nonbonded pdb=" O ASP A 187 " pdb=" OD1 ASP A 187 " model vdw 2.339 3.040 nonbonded pdb=" NZ LYS B 157 " pdb=" OD2 ASP B 213 " model vdw 2.340 3.120 nonbonded pdb=" O5 NAG C 401 " pdb=" O6 NAG C 401 " model vdw 2.447 2.432 ... (remaining 42249 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.010 Find NCS groups from input model: 0.050 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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 : 0.013 0.058 5704 Z= 0.861 Angle : 1.602 10.638 7721 Z= 1.206 Chirality : 0.114 0.378 874 Planarity : 0.005 0.030 977 Dihedral : 13.654 100.996 2174 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.75 % Allowed : 10.81 % Favored : 87.44 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.32), residues: 687 helix: 3.02 (0.48), residues: 119 sheet: 0.51 (0.35), residues: 230 loop : -0.76 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 60 HIS 0.004 0.001 HIS A 71 PHE 0.026 0.002 PHE D 99 TYR 0.025 0.002 TYR B 268 ARG 0.004 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 THR cc_start: 0.8516 (p) cc_final: 0.8123 (p) REVERT: B 114 THR cc_start: 0.8475 (m) cc_final: 0.8270 (p) REVERT: B 271 LEU cc_start: 0.8973 (mt) cc_final: 0.8768 (mt) REVERT: B 275 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8017 (m) REVERT: B 276 GLN cc_start: 0.7301 (tt0) cc_final: 0.7020 (pp30) REVERT: D 51 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7787 (ptp-110) REVERT: D 63 SER cc_start: 0.8564 (t) cc_final: 0.8130 (m) REVERT: D 65 GLN cc_start: 0.7776 (tt0) cc_final: 0.7498 (mt0) REVERT: D 96 ARG cc_start: 0.7965 (ptp-170) cc_final: 0.7495 (ptp90) REVERT: D 98 GLN cc_start: 0.8315 (mt0) cc_final: 0.7879 (mt0) outliers start: 11 outliers final: 1 residues processed: 183 average time/residue: 0.1978 time to fit residues: 45.3780 Evaluate side-chains 113 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain D residue 107 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.0470 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.0670 chunk 61 optimal weight: 4.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN B 87 GLN B 99 HIS D 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.171401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141536 restraints weight = 6761.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.140768 restraints weight = 6315.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141493 restraints weight = 5860.542| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5704 Z= 0.205 Angle : 0.590 7.245 7721 Z= 0.319 Chirality : 0.042 0.157 874 Planarity : 0.004 0.040 977 Dihedral : 7.781 64.229 836 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.38 % Allowed : 16.53 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.67 (0.32), residues: 687 helix: 3.55 (0.43), residues: 109 sheet: 0.59 (0.35), residues: 226 loop : -0.67 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 118 HIS 0.008 0.001 HIS B 91 PHE 0.012 0.001 PHE A 118 TYR 0.024 0.002 TYR B 314 ARG 0.005 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6775 (OUTLIER) cc_final: 0.6441 (mp10) REVERT: B 114 THR cc_start: 0.8430 (m) cc_final: 0.8072 (p) REVERT: B 271 LEU cc_start: 0.8870 (mt) cc_final: 0.8651 (mt) REVERT: B 288 ARG cc_start: 0.7347 (ptp-170) cc_final: 0.6691 (mtt180) REVERT: D 98 GLN cc_start: 0.8429 (mt0) cc_final: 0.8205 (mt0) REVERT: D 123 THR cc_start: 0.7222 (OUTLIER) cc_final: 0.7020 (m) outliers start: 15 outliers final: 7 residues processed: 114 average time/residue: 0.1860 time to fit residues: 27.4143 Evaluate side-chains 102 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 0.9990 chunk 21 optimal weight: 0.0670 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.164880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.133081 restraints weight = 6922.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132653 restraints weight = 7288.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.133737 restraints weight = 6633.099| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5704 Z= 0.193 Angle : 0.529 6.991 7721 Z= 0.286 Chirality : 0.041 0.185 874 Planarity : 0.004 0.040 977 Dihedral : 5.514 37.877 834 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.34 % Allowed : 19.08 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.67 (0.32), residues: 687 helix: 3.44 (0.45), residues: 112 sheet: 0.56 (0.34), residues: 232 loop : -0.67 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 60 HIS 0.010 0.001 HIS B 91 PHE 0.011 0.001 PHE B 228 TYR 0.016 0.002 TYR C 71 ARG 0.004 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.650 Fit side-chains REVERT: A 157 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.6391 (mp10) REVERT: B 114 THR cc_start: 0.8527 (m) cc_final: 0.8024 (p) REVERT: B 288 ARG cc_start: 0.7511 (ptp-170) cc_final: 0.7115 (mtt180) REVERT: D 122 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7348 (mp10) outliers start: 21 outliers final: 9 residues processed: 117 average time/residue: 0.1732 time to fit residues: 26.4461 Evaluate side-chains 103 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 135 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 0.0040 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 22 optimal weight: 0.0870 chunk 66 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 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 = 0.3793 r_free = 0.3793 target = 0.162713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.129015 restraints weight = 7042.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130517 restraints weight = 5853.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.131714 restraints weight = 5224.474| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5704 Z= 0.173 Angle : 0.519 8.815 7721 Z= 0.276 Chirality : 0.039 0.169 874 Planarity : 0.004 0.039 977 Dihedral : 4.358 25.592 834 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.70 % Allowed : 19.87 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.59 (0.32), residues: 687 helix: 3.13 (0.46), residues: 109 sheet: 0.70 (0.34), residues: 226 loop : -0.72 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 60 HIS 0.012 0.001 HIS B 91 PHE 0.015 0.001 PHE A 35 TYR 0.013 0.001 TYR C 71 ARG 0.003 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.6570 (mp10) REVERT: B 114 THR cc_start: 0.8324 (m) cc_final: 0.7945 (p) REVERT: B 118 LYS cc_start: 0.8198 (ptmt) cc_final: 0.7889 (ptmt) REVERT: B 288 ARG cc_start: 0.7529 (ptp-170) cc_final: 0.7179 (mtt180) outliers start: 17 outliers final: 10 residues processed: 103 average time/residue: 0.1846 time to fit residues: 24.8850 Evaluate side-chains 102 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 135 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN B 91 HIS B 99 HIS B 166 GLN B 276 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.154754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.121002 restraints weight = 6910.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.120790 restraints weight = 7261.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.122295 restraints weight = 6734.915| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 5704 Z= 0.321 Angle : 0.588 6.019 7721 Z= 0.313 Chirality : 0.043 0.244 874 Planarity : 0.004 0.041 977 Dihedral : 4.444 18.004 834 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.86 % Allowed : 20.51 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.32), residues: 687 helix: 3.15 (0.47), residues: 112 sheet: 0.65 (0.35), residues: 214 loop : -0.84 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 256 HIS 0.011 0.002 HIS B 91 PHE 0.023 0.002 PHE B 228 TYR 0.015 0.002 TYR B 189 ARG 0.005 0.001 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.8988 (t80) cc_final: 0.8699 (t80) REVERT: B 114 THR cc_start: 0.8423 (m) cc_final: 0.8056 (p) REVERT: B 288 ARG cc_start: 0.7808 (ptp-170) cc_final: 0.7529 (mtt180) REVERT: D 85 ARG cc_start: 0.7860 (mtp-110) cc_final: 0.7553 (mtp-110) outliers start: 18 outliers final: 10 residues processed: 107 average time/residue: 0.1700 time to fit residues: 24.0092 Evaluate side-chains 100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 19 optimal weight: 0.0270 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 0.0570 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN B 91 HIS B 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.158330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132770 restraints weight = 6854.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130801 restraints weight = 10619.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.131184 restraints weight = 9851.910| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 5704 Z= 0.161 Angle : 0.511 6.174 7721 Z= 0.270 Chirality : 0.039 0.189 874 Planarity : 0.004 0.041 977 Dihedral : 4.165 17.735 834 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.91 % Allowed : 21.78 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.32), residues: 687 helix: 2.81 (0.47), residues: 118 sheet: 0.78 (0.36), residues: 211 loop : -0.82 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.013 0.001 HIS B 91 PHE 0.010 0.001 PHE B 140 TYR 0.012 0.001 TYR C 71 ARG 0.003 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6469 (OUTLIER) cc_final: 0.6267 (mp10) REVERT: B 114 THR cc_start: 0.8163 (m) cc_final: 0.7787 (p) REVERT: D 128 GLU cc_start: 0.7461 (pp20) cc_final: 0.6697 (pp20) outliers start: 12 outliers final: 5 residues processed: 99 average time/residue: 0.1974 time to fit residues: 24.9896 Evaluate side-chains 94 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 101 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 0.0870 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN B 91 HIS ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN D 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.153084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117299 restraints weight = 6912.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.118907 restraints weight = 5742.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119346 restraints weight = 4922.264| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5704 Z= 0.264 Angle : 0.546 6.321 7721 Z= 0.287 Chirality : 0.040 0.222 874 Planarity : 0.004 0.044 977 Dihedral : 4.221 18.502 834 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.23 % Allowed : 21.78 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.40 (0.32), residues: 687 helix: 2.81 (0.48), residues: 118 sheet: 0.66 (0.36), residues: 217 loop : -0.92 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 256 HIS 0.012 0.002 HIS B 91 PHE 0.019 0.002 PHE B 228 TYR 0.012 0.001 TYR C 71 ARG 0.008 0.001 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.570 Fit side-chains REVERT: B 258 TYR cc_start: 0.8720 (m-80) cc_final: 0.8401 (m-80) REVERT: D 128 GLU cc_start: 0.7543 (pp20) cc_final: 0.6739 (pp20) outliers start: 14 outliers final: 10 residues processed: 93 average time/residue: 0.2001 time to fit residues: 23.8809 Evaluate side-chains 94 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 52 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** B 99 HIS ** 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 = 0.3690 r_free = 0.3690 target = 0.154308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.118282 restraints weight = 6911.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.119702 restraints weight = 5688.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.121154 restraints weight = 5066.575| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 5704 Z= 0.194 Angle : 0.510 7.468 7721 Z= 0.270 Chirality : 0.039 0.242 874 Planarity : 0.004 0.046 977 Dihedral : 4.101 17.755 834 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.23 % Allowed : 22.26 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 (0.32), residues: 687 helix: 2.79 (0.48), residues: 118 sheet: 0.68 (0.36), residues: 215 loop : -0.91 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.012 0.001 HIS B 91 PHE 0.011 0.001 PHE B 228 TYR 0.012 0.001 TYR D 53 ARG 0.008 0.001 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6721 (mp10) REVERT: B 114 THR cc_start: 0.8255 (m) cc_final: 0.7850 (p) REVERT: B 258 TYR cc_start: 0.8715 (m-80) cc_final: 0.8419 (m-80) REVERT: D 128 GLU cc_start: 0.7492 (pp20) cc_final: 0.6844 (pp20) outliers start: 14 outliers final: 11 residues processed: 94 average time/residue: 0.1827 time to fit residues: 22.3643 Evaluate side-chains 99 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.152291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115227 restraints weight = 6965.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117209 restraints weight = 5549.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118493 restraints weight = 4830.173| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 5704 Z= 0.237 Angle : 0.542 9.676 7721 Z= 0.282 Chirality : 0.040 0.236 874 Planarity : 0.004 0.049 977 Dihedral : 4.126 18.354 834 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.38 % Allowed : 21.94 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 (0.32), residues: 687 helix: 2.85 (0.47), residues: 118 sheet: 0.58 (0.36), residues: 215 loop : -0.95 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 256 HIS 0.012 0.001 HIS B 91 PHE 0.017 0.001 PHE B 228 TYR 0.011 0.001 TYR C 71 ARG 0.007 0.001 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6732 (mp10) REVERT: B 258 TYR cc_start: 0.8775 (m-80) cc_final: 0.8495 (m-80) REVERT: D 128 GLU cc_start: 0.7484 (pp20) cc_final: 0.6809 (pp20) outliers start: 15 outliers final: 12 residues processed: 98 average time/residue: 0.1975 time to fit residues: 24.8899 Evaluate side-chains 101 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 66 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** B 99 HIS ** 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 = 0.3696 r_free = 0.3696 target = 0.154828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117626 restraints weight = 6945.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.119216 restraints weight = 5510.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.120792 restraints weight = 4841.334| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 5704 Z= 0.189 Angle : 0.513 9.524 7721 Z= 0.268 Chirality : 0.040 0.227 874 Planarity : 0.004 0.052 977 Dihedral : 4.056 17.730 834 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.23 % Allowed : 22.42 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.37 (0.32), residues: 687 helix: 2.90 (0.48), residues: 118 sheet: 0.66 (0.36), residues: 210 loop : -0.97 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.012 0.001 HIS B 91 PHE 0.011 0.001 PHE B 228 TYR 0.011 0.001 TYR C 71 ARG 0.006 0.000 ARG D 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6741 (mp10) REVERT: B 114 THR cc_start: 0.8300 (m) cc_final: 0.7904 (p) REVERT: B 258 TYR cc_start: 0.8760 (m-80) cc_final: 0.8477 (m-80) REVERT: D 128 GLU cc_start: 0.7434 (pp20) cc_final: 0.6775 (pp20) outliers start: 14 outliers final: 10 residues processed: 97 average time/residue: 0.1886 time to fit residues: 23.6891 Evaluate side-chains 100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 21 optimal weight: 0.0070 chunk 43 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 48 optimal weight: 4.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** B 99 HIS ** 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 = 0.3692 r_free = 0.3692 target = 0.154311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.117574 restraints weight = 6958.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.119481 restraints weight = 5651.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.120318 restraints weight = 4947.751| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 5704 Z= 0.211 Angle : 0.526 9.807 7721 Z= 0.275 Chirality : 0.040 0.228 874 Planarity : 0.004 0.052 977 Dihedral : 4.071 19.338 834 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.38 % Allowed : 22.73 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.27 (0.32), residues: 687 helix: 2.73 (0.48), residues: 119 sheet: 0.54 (0.36), residues: 210 loop : -0.97 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 256 HIS 0.012 0.001 HIS B 91 PHE 0.014 0.001 PHE B 228 TYR 0.011 0.001 TYR C 71 ARG 0.006 0.000 ARG D 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2111.43 seconds wall clock time: 38 minutes 33.34 seconds (2313.34 seconds total)