Starting phenix.real_space_refine on Wed Sep 17 05:46:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yi7_39311/09_2025/8yi7_39311_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yi7_39311/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yi7_39311/09_2025/8yi7_39311_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yi7_39311/09_2025/8yi7_39311_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yi7_39311/09_2025/8yi7_39311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yi7_39311/09_2025/8yi7_39311.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.50, per 1000 atoms: 0.27 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: 0.49 Conformation dependent library (CDL) restraints added in 219.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.20 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: 0.79 Time building geometry restraints manager: 0.66 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: 1.490 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.780 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.730 ------------------------------------------------------------------------------- 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 0.216 5722 Z= 1.002 Angle : 1.644 29.628 7761 Z= 1.216 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.004 0.001 ARG A 205 TYR 0.025 0.002 TYR B 268 PHE 0.026 0.002 PHE D 99 TRP 0.027 0.003 TRP B 60 HIS 0.004 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.01306 ( 5704) covalent geometry : angle 1.60222 ( 7721) SS BOND : bond 0.05808 ( 14) SS BOND : angle 5.92036 ( 28) hydrogen bonds : bond 0.20263 ( 195) hydrogen bonds : angle 8.79343 ( 543) link_BETA1-4 : bond 0.01249 ( 2) link_BETA1-4 : angle 2.26960 ( 6) link_NAG-ASN : bond 0.01318 ( 2) link_NAG-ASN : angle 5.06095 ( 6) *********************** 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 : 0.227 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: 0.0910 time to fit residues: 21.0216 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 : 0.217 ------------------------------------------------------------------------------- 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 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.0470 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.9080 ------------------------------------------------------------------------------- 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 C 39 HIS D 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.164500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132450 restraints weight = 7013.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132820 restraints weight = 6082.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132948 restraints weight = 5409.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.133481 restraints weight = 5302.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.133631 restraints weight = 5077.921| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5722 Z= 0.169 Angle : 0.636 7.432 7761 Z= 0.339 Chirality : 0.043 0.170 874 Planarity : 0.004 0.042 977 Dihedral : 7.562 61.937 836 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.86 % Allowed : 16.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.32), residues: 687 helix: 3.56 (0.44), residues: 109 sheet: 0.60 (0.35), residues: 226 loop : -0.68 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 75 TYR 0.021 0.002 TYR B 314 PHE 0.017 0.002 PHE B 228 TRP 0.013 0.002 TRP B 60 HIS 0.009 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5704) covalent geometry : angle 0.61078 ( 7721) SS BOND : bond 0.01218 ( 14) SS BOND : angle 2.31469 ( 28) hydrogen bonds : bond 0.06381 ( 195) hydrogen bonds : angle 6.07763 ( 543) link_BETA1-4 : bond 0.00991 ( 2) link_BETA1-4 : angle 2.02208 ( 6) link_NAG-ASN : bond 0.00377 ( 2) link_NAG-ASN : angle 3.77008 ( 6) *********************** 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 127 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6525 (mp10) REVERT: B 114 THR cc_start: 0.8514 (m) cc_final: 0.8141 (p) REVERT: B 288 ARG cc_start: 0.7469 (ptp-170) cc_final: 0.6989 (mtt180) REVERT: D 98 GLN cc_start: 0.8506 (mt0) cc_final: 0.8281 (mt0) REVERT: D 121 ASN cc_start: 0.7401 (m-40) cc_final: 0.7174 (m-40) REVERT: D 122 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7233 (mp10) outliers start: 18 outliers final: 8 residues processed: 120 average time/residue: 0.0791 time to fit residues: 12.2924 Evaluate side-chains 107 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 191 THR 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 135 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 51 optimal weight: 0.1980 chunk 66 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 58 optimal weight: 0.0030 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.0070 overall best weight: 0.3408 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.171386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.144903 restraints weight = 6766.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.145003 restraints weight = 6647.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.145061 restraints weight = 6468.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.145070 restraints weight = 6419.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.145070 restraints weight = 6396.425| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5722 Z= 0.117 Angle : 0.546 6.969 7761 Z= 0.289 Chirality : 0.040 0.181 874 Planarity : 0.004 0.040 977 Dihedral : 5.481 37.346 834 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.86 % Allowed : 18.76 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.32), residues: 687 helix: 3.47 (0.45), residues: 112 sheet: 0.64 (0.34), residues: 226 loop : -0.67 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 48 TYR 0.016 0.001 TYR C 71 PHE 0.019 0.001 PHE C 79 TRP 0.012 0.001 TRP B 60 HIS 0.009 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 5704) covalent geometry : angle 0.52282 ( 7721) SS BOND : bond 0.00540 ( 14) SS BOND : angle 1.93401 ( 28) hydrogen bonds : bond 0.05080 ( 195) hydrogen bonds : angle 5.29111 ( 543) link_BETA1-4 : bond 0.00924 ( 2) link_BETA1-4 : angle 1.83374 ( 6) link_NAG-ASN : bond 0.00273 ( 2) link_NAG-ASN : angle 3.65952 ( 6) *********************** 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 117 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.232 Fit side-chains REVERT: A 157 GLN cc_start: 0.6347 (OUTLIER) cc_final: 0.6098 (mp10) REVERT: B 114 THR cc_start: 0.8412 (m) cc_final: 0.7810 (p) REVERT: B 288 ARG cc_start: 0.7360 (ptp-170) cc_final: 0.7103 (mtt180) outliers start: 18 outliers final: 7 residues processed: 112 average time/residue: 0.0769 time to fit residues: 11.3702 Evaluate side-chains 100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 6 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** B 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.160073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.129159 restraints weight = 6885.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.126691 restraints weight = 6361.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.127106 restraints weight = 6384.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127260 restraints weight = 6023.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.127461 restraints weight = 5773.834| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5722 Z= 0.151 Angle : 0.562 6.586 7761 Z= 0.296 Chirality : 0.041 0.180 874 Planarity : 0.004 0.039 977 Dihedral : 4.390 22.370 834 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.54 % Allowed : 19.08 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.32), residues: 687 helix: 3.29 (0.47), residues: 112 sheet: 0.57 (0.34), residues: 232 loop : -0.75 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 51 TYR 0.015 0.002 TYR C 71 PHE 0.022 0.002 PHE C 79 TRP 0.014 0.001 TRP B 256 HIS 0.011 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5704) covalent geometry : angle 0.54060 ( 7721) SS BOND : bond 0.00308 ( 14) SS BOND : angle 1.78073 ( 28) hydrogen bonds : bond 0.04751 ( 195) hydrogen bonds : angle 4.86163 ( 543) link_BETA1-4 : bond 0.00855 ( 2) link_BETA1-4 : angle 1.69365 ( 6) link_NAG-ASN : bond 0.00205 ( 2) link_NAG-ASN : angle 3.77361 ( 6) *********************** 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 107 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.8842 (t80) cc_final: 0.8541 (t80) REVERT: B 114 THR cc_start: 0.8390 (m) cc_final: 0.8015 (p) REVERT: B 288 ARG cc_start: 0.7678 (ptp-170) cc_final: 0.7355 (mtt180) REVERT: D 48 ARG cc_start: 0.7017 (mpt180) cc_final: 0.6738 (mmt180) outliers start: 16 outliers final: 12 residues processed: 103 average time/residue: 0.0752 time to fit residues: 10.1653 Evaluate side-chains 100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 275 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 111 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 48 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN B 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.157513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124615 restraints weight = 6997.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.122907 restraints weight = 6278.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.123330 restraints weight = 6798.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.123929 restraints weight = 6106.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.124057 restraints weight = 5720.295| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5722 Z= 0.146 Angle : 0.560 10.443 7761 Z= 0.288 Chirality : 0.040 0.185 874 Planarity : 0.004 0.040 977 Dihedral : 4.265 18.203 834 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.54 % Allowed : 19.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.32), residues: 687 helix: 2.92 (0.47), residues: 118 sheet: 0.67 (0.35), residues: 220 loop : -0.86 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.014 0.001 TYR C 71 PHE 0.021 0.002 PHE C 79 TRP 0.012 0.001 TRP B 60 HIS 0.012 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5704) covalent geometry : angle 0.53974 ( 7721) SS BOND : bond 0.00730 ( 14) SS BOND : angle 1.81529 ( 28) hydrogen bonds : bond 0.04506 ( 195) hydrogen bonds : angle 4.68563 ( 543) link_BETA1-4 : bond 0.00793 ( 2) link_BETA1-4 : angle 1.75354 ( 6) link_NAG-ASN : bond 0.00220 ( 2) link_NAG-ASN : angle 3.60838 ( 6) *********************** 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 111 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6641 (mp10) REVERT: A 215 TYR cc_start: 0.8905 (t80) cc_final: 0.8620 (t80) REVERT: B 114 THR cc_start: 0.8344 (m) cc_final: 0.7953 (p) REVERT: B 258 TYR cc_start: 0.8517 (m-80) cc_final: 0.8266 (m-80) REVERT: B 288 ARG cc_start: 0.7768 (ptp-170) cc_final: 0.7487 (mtt180) outliers start: 16 outliers final: 10 residues processed: 107 average time/residue: 0.0788 time to fit residues: 11.0405 Evaluate side-chains 104 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 87 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 50 THR Chi-restraints excluded: chain D residue 95 THR 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 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.0040 chunk 58 optimal weight: 0.0980 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.161375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.135447 restraints weight = 6854.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.132627 restraints weight = 8856.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.133167 restraints weight = 9579.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.133443 restraints weight = 8577.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.133537 restraints weight = 7437.615| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 5722 Z= 0.107 Angle : 0.526 6.083 7761 Z= 0.273 Chirality : 0.039 0.184 874 Planarity : 0.004 0.041 977 Dihedral : 4.106 17.544 834 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.02 % Allowed : 19.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.32), residues: 687 helix: 2.91 (0.47), residues: 118 sheet: 0.76 (0.35), residues: 221 loop : -0.84 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 181 TYR 0.011 0.001 TYR C 71 PHE 0.015 0.001 PHE A 172 TRP 0.011 0.001 TRP B 60 HIS 0.012 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 5704) covalent geometry : angle 0.50627 ( 7721) SS BOND : bond 0.00447 ( 14) SS BOND : angle 1.72619 ( 28) hydrogen bonds : bond 0.04080 ( 195) hydrogen bonds : angle 4.48277 ( 543) link_BETA1-4 : bond 0.00831 ( 2) link_BETA1-4 : angle 1.62269 ( 6) link_NAG-ASN : bond 0.00213 ( 2) link_NAG-ASN : angle 3.33632 ( 6) *********************** 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 107 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.213 Fit side-chains REVERT: A 157 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.6264 (mp10) REVERT: B 114 THR cc_start: 0.8137 (m) cc_final: 0.7768 (p) outliers start: 19 outliers final: 11 residues processed: 103 average time/residue: 0.0884 time to fit residues: 11.7935 Evaluate side-chains 96 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 93 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 135 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 0.0010 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.4926 ------------------------------------------------------------------------------- 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 D 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.159216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127199 restraints weight = 6929.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125848 restraints weight = 7013.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126475 restraints weight = 6715.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.126759 restraints weight = 6163.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126861 restraints weight = 5868.556| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5722 Z= 0.111 Angle : 0.525 6.701 7761 Z= 0.273 Chirality : 0.039 0.223 874 Planarity : 0.004 0.043 977 Dihedral : 4.007 17.715 834 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.23 % Allowed : 21.30 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.32), residues: 687 helix: 2.94 (0.47), residues: 118 sheet: 0.87 (0.36), residues: 218 loop : -0.87 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 51 TYR 0.011 0.001 TYR C 71 PHE 0.011 0.001 PHE A 172 TRP 0.010 0.001 TRP B 60 HIS 0.012 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 5704) covalent geometry : angle 0.50481 ( 7721) SS BOND : bond 0.00528 ( 14) SS BOND : angle 1.86368 ( 28) hydrogen bonds : bond 0.03884 ( 195) hydrogen bonds : angle 4.35214 ( 543) link_BETA1-4 : bond 0.00805 ( 2) link_BETA1-4 : angle 1.56805 ( 6) link_NAG-ASN : bond 0.00195 ( 2) link_NAG-ASN : angle 3.12365 ( 6) *********************** 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 105 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: B 114 THR cc_start: 0.8231 (m) cc_final: 0.7830 (p) REVERT: B 258 TYR cc_start: 0.8522 (m-80) cc_final: 0.8293 (m-80) outliers start: 14 outliers final: 12 residues processed: 101 average time/residue: 0.0749 time to fit residues: 9.9958 Evaluate side-chains 101 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 93 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 0.0060 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.8798 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.155914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.119587 restraints weight = 6828.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121420 restraints weight = 5541.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122359 restraints weight = 4893.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122359 restraints weight = 4554.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122359 restraints weight = 4554.615| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 5722 Z= 0.137 Angle : 0.563 11.017 7761 Z= 0.287 Chirality : 0.040 0.239 874 Planarity : 0.004 0.047 977 Dihedral : 4.031 17.918 834 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.86 % Allowed : 20.67 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.32), residues: 687 helix: 2.88 (0.47), residues: 118 sheet: 0.84 (0.36), residues: 216 loop : -0.94 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 48 TYR 0.012 0.001 TYR C 71 PHE 0.014 0.001 PHE B 228 TRP 0.009 0.001 TRP B 60 HIS 0.011 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5704) covalent geometry : angle 0.54100 ( 7721) SS BOND : bond 0.00598 ( 14) SS BOND : angle 2.11463 ( 28) hydrogen bonds : bond 0.04077 ( 195) hydrogen bonds : angle 4.35766 ( 543) link_BETA1-4 : bond 0.00748 ( 2) link_BETA1-4 : angle 1.57754 ( 6) link_NAG-ASN : bond 0.00182 ( 2) link_NAG-ASN : angle 3.17744 ( 6) *********************** 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 112 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6914 (OUTLIER) cc_final: 0.6639 (mp10) REVERT: B 114 THR cc_start: 0.8270 (m) cc_final: 0.7873 (p) REVERT: B 258 TYR cc_start: 0.8608 (m-80) cc_final: 0.8307 (m-80) REVERT: D 128 GLU cc_start: 0.7722 (pp20) cc_final: 0.7009 (pp20) outliers start: 18 outliers final: 13 residues processed: 106 average time/residue: 0.0874 time to fit residues: 11.9818 Evaluate side-chains 106 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 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 93 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.163816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.139482 restraints weight = 6840.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.137395 restraints weight = 10933.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.138204 restraints weight = 10113.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.138228 restraints weight = 8264.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.138553 restraints weight = 7651.637| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 5722 Z= 0.121 Angle : 0.551 9.625 7761 Z= 0.282 Chirality : 0.040 0.230 874 Planarity : 0.004 0.050 977 Dihedral : 3.987 17.729 834 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.02 % Allowed : 20.19 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.32), residues: 687 helix: 2.94 (0.47), residues: 118 sheet: 0.78 (0.36), residues: 216 loop : -0.97 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 313 TYR 0.010 0.001 TYR C 71 PHE 0.012 0.001 PHE B 140 TRP 0.010 0.001 TRP B 143 HIS 0.012 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5704) covalent geometry : angle 0.52982 ( 7721) SS BOND : bond 0.00574 ( 14) SS BOND : angle 2.03984 ( 28) hydrogen bonds : bond 0.03899 ( 195) hydrogen bonds : angle 4.30876 ( 543) link_BETA1-4 : bond 0.00793 ( 2) link_BETA1-4 : angle 1.56052 ( 6) link_NAG-ASN : bond 0.00191 ( 2) link_NAG-ASN : angle 3.04022 ( 6) *********************** 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 110 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6439 (mp10) REVERT: B 258 TYR cc_start: 0.8629 (m-80) cc_final: 0.8312 (m-80) outliers start: 19 outliers final: 15 residues processed: 104 average time/residue: 0.0877 time to fit residues: 11.8701 Evaluate side-chains 105 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 93 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 135 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 59 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 4 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.156493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.120503 restraints weight = 7017.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.122013 restraints weight = 5584.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.123751 restraints weight = 4918.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124441 restraints weight = 4514.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.124533 restraints weight = 4283.278| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 5722 Z= 0.114 Angle : 0.546 9.680 7761 Z= 0.280 Chirality : 0.039 0.226 874 Planarity : 0.004 0.047 977 Dihedral : 3.947 17.666 834 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.91 % Allowed : 21.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.32), residues: 687 helix: 2.89 (0.47), residues: 118 sheet: 0.72 (0.36), residues: 217 loop : -0.94 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 313 TYR 0.009 0.001 TYR C 71 PHE 0.011 0.001 PHE B 140 TRP 0.009 0.001 TRP B 143 HIS 0.012 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 5704) covalent geometry : angle 0.52632 ( 7721) SS BOND : bond 0.00557 ( 14) SS BOND : angle 2.00662 ( 28) hydrogen bonds : bond 0.03764 ( 195) hydrogen bonds : angle 4.26311 ( 543) link_BETA1-4 : bond 0.00804 ( 2) link_BETA1-4 : angle 1.54232 ( 6) link_NAG-ASN : bond 0.00173 ( 2) link_NAG-ASN : angle 2.94271 ( 6) ********************** 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 97 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 34 MET cc_start: 0.6635 (ppp) cc_final: 0.6421 (ppp) REVERT: A 141 MET cc_start: 0.8026 (ttm) cc_final: 0.7759 (ttm) REVERT: B 258 TYR cc_start: 0.8652 (m-80) cc_final: 0.8346 (m-80) REVERT: D 128 GLU cc_start: 0.7576 (pp20) cc_final: 0.6825 (pp20) outliers start: 12 outliers final: 11 residues processed: 94 average time/residue: 0.0886 time to fit residues: 10.7595 Evaluate side-chains 94 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 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 93 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.152424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.116634 restraints weight = 6935.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.118253 restraints weight = 5695.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.119498 restraints weight = 5048.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.119500 restraints weight = 4708.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.119500 restraints weight = 4706.595| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 5722 Z= 0.166 Angle : 0.582 9.180 7761 Z= 0.298 Chirality : 0.041 0.237 874 Planarity : 0.004 0.050 977 Dihedral : 4.110 18.583 834 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.38 % Allowed : 20.67 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.32), residues: 687 helix: 2.78 (0.47), residues: 119 sheet: 0.41 (0.36), residues: 221 loop : -0.93 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 48 TYR 0.014 0.001 TYR C 71 PHE 0.019 0.002 PHE B 228 TRP 0.011 0.001 TRP B 256 HIS 0.012 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 5704) covalent geometry : angle 0.55994 ( 7721) SS BOND : bond 0.00607 ( 14) SS BOND : angle 2.12736 ( 28) hydrogen bonds : bond 0.04271 ( 195) hydrogen bonds : angle 4.35929 ( 543) link_BETA1-4 : bond 0.00749 ( 2) link_BETA1-4 : angle 1.65050 ( 6) link_NAG-ASN : bond 0.00148 ( 2) link_NAG-ASN : angle 3.17592 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1204.22 seconds wall clock time: 21 minutes 29.46 seconds (1289.46 seconds total)