Starting phenix.real_space_refine on Tue Mar 3 11:16:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x0u_21984/03_2026/6x0u_21984.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x0u_21984/03_2026/6x0u_21984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x0u_21984/03_2026/6x0u_21984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x0u_21984/03_2026/6x0u_21984.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x0u_21984/03_2026/6x0u_21984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x0u_21984/03_2026/6x0u_21984.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 18 5.16 5 C 1942 2.51 5 N 544 2.21 5 O 587 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3091 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 933 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 1 Chain: "D" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1220 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain breaks: 4 Chain: "A" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 484 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 454 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Time building chain proxies: 0.86, per 1000 atoms: 0.28 Number of scatterers: 3091 At special positions: 0 Unit cell: (99.456, 83.916, 81.844, 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 18 16.00 O 587 8.00 N 544 7.00 C 1942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 113.6 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 68.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'B' and resid 8 through 21 removed outlier: 3.826A pdb=" N GLN B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN B 15 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 21 " --> pdb=" O CYS B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 removed outlier: 3.612A pdb=" N ARG B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 65 removed outlier: 3.870A pdb=" N VAL B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 85 removed outlier: 4.061A pdb=" N SER B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS B 82 " --> pdb=" O HIS B 78 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 100 removed outlier: 4.107A pdb=" N ILE B 93 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 99 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 removed outlier: 3.684A pdb=" N PHE D 8 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 13 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 51 removed outlier: 3.902A pdb=" N LYS D 39 " --> pdb=" O ARG D 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.578A pdb=" N LEU D 73 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 removed outlier: 3.642A pdb=" N ALA D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 91 " --> pdb=" O ASP D 87 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 115 removed outlier: 3.537A pdb=" N ASP D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 183 removed outlier: 4.098A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS D 169 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N CYS D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE D 175 " --> pdb=" O CYS D 171 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN D 176 " --> pdb=" O HIS D 172 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR D 178 " --> pdb=" O MET D 174 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.769A pdb=" N THR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 29 " --> pdb=" O MET A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 54 removed outlier: 3.654A pdb=" N SER A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 75 removed outlier: 3.833A pdb=" N SER A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 34 removed outlier: 3.531A pdb=" N MET C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 28 " --> pdb=" O THR C 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 29 " --> pdb=" O MET C 25 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 removed outlier: 3.808A pdb=" N GLY C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 75 removed outlier: 3.862A pdb=" N LEU C 60 " --> pdb=" O ASN C 56 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 408 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: 0.32 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1050 1.34 - 1.46: 519 1.46 - 1.58: 1526 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3121 Sorted by residual: bond pdb=" N ASN D 135 " pdb=" CA ASN D 135 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.60e+00 bond pdb=" N ASN D 136 " pdb=" CA ASN D 136 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.28e-01 bond pdb=" CA VAL B 28 " pdb=" CB VAL B 28 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.11e-02 8.12e+03 6.79e-01 bond pdb=" CA VAL B 86 " pdb=" C VAL B 86 " ideal model delta sigma weight residual 1.525 1.515 0.010 1.29e-02 6.01e+03 6.25e-01 bond pdb=" CG LEU B 96 " pdb=" CD1 LEU B 96 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.13e-01 ... (remaining 3116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 4119 1.77 - 3.53: 76 3.53 - 5.30: 8 5.30 - 7.06: 1 7.06 - 8.83: 1 Bond angle restraints: 4205 Sorted by residual: angle pdb=" C ASN D 135 " pdb=" CA ASN D 135 " pdb=" CB ASN D 135 " ideal model delta sigma weight residual 110.42 115.77 -5.35 1.99e+00 2.53e-01 7.22e+00 angle pdb=" CA LEU D 82 " pdb=" CB LEU D 82 " pdb=" CG LEU D 82 " ideal model delta sigma weight residual 116.30 125.13 -8.83 3.50e+00 8.16e-02 6.36e+00 angle pdb=" N ARG D 141 " pdb=" CA ARG D 141 " pdb=" C ARG D 141 " ideal model delta sigma weight residual 111.96 108.82 3.14 1.41e+00 5.03e-01 4.94e+00 angle pdb=" N ASN D 135 " pdb=" CA ASN D 135 " pdb=" CB ASN D 135 " ideal model delta sigma weight residual 110.49 106.91 3.58 1.69e+00 3.50e-01 4.49e+00 angle pdb=" N ASP A 26 " pdb=" CA ASP A 26 " pdb=" C ASP A 26 " ideal model delta sigma weight residual 113.41 111.00 2.41 1.22e+00 6.72e-01 3.89e+00 ... (remaining 4200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 1738 17.60 - 35.20: 171 35.20 - 52.80: 34 52.80 - 70.39: 5 70.39 - 87.99: 2 Dihedral angle restraints: 1950 sinusoidal: 794 harmonic: 1156 Sorted by residual: dihedral pdb=" CA LEU D 134 " pdb=" C LEU D 134 " pdb=" N ASN D 135 " pdb=" CA ASN D 135 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PHE D 133 " pdb=" C PHE D 133 " pdb=" N LEU D 134 " pdb=" CA LEU D 134 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ASN D 135 " pdb=" C ASN D 135 " pdb=" N ASN D 136 " pdb=" CA ASN D 136 " ideal model delta harmonic sigma weight residual 180.00 163.43 16.57 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 1947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 247 0.024 - 0.048: 175 0.048 - 0.072: 56 0.072 - 0.096: 18 0.096 - 0.120: 9 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA PRO B 123 " pdb=" N PRO B 123 " pdb=" C PRO B 123 " pdb=" CB PRO B 123 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA PRO B 9 " pdb=" N PRO B 9 " pdb=" C PRO B 9 " pdb=" CB PRO B 9 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.09e-01 chirality pdb=" CA VAL D 143 " pdb=" N VAL D 143 " pdb=" C VAL D 143 " pdb=" CB VAL D 143 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 502 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 122 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO B 123 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 185 " -0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO D 186 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 186 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 186 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 8 " 0.016 5.00e-02 4.00e+02 2.42e-02 9.35e-01 pdb=" N PRO B 9 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO B 9 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 9 " 0.014 5.00e-02 4.00e+02 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 872 2.80 - 3.33: 2848 3.33 - 3.85: 4253 3.85 - 4.38: 5348 4.38 - 4.90: 8717 Nonbonded interactions: 22038 Sorted by model distance: nonbonded pdb=" O PRO A 57 " pdb=" OG SER A 61 " model vdw 2.277 3.040 nonbonded pdb=" O ALA C 59 " pdb=" OG SER C 62 " model vdw 2.283 3.040 nonbonded pdb=" OE1 GLN B 84 " pdb=" OG1 THR A 24 " model vdw 2.301 3.040 nonbonded pdb=" O ALA B 115 " pdb=" NE2 GLN B 120 " model vdw 2.310 3.120 nonbonded pdb=" O GLY B 40 " pdb=" OG SER B 41 " model vdw 2.332 3.040 ... (remaining 22033 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 75) selection = chain 'C' } 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: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.650 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.004 0.024 3121 Z= 0.179 Angle : 0.618 8.827 4205 Z= 0.348 Chirality : 0.037 0.120 505 Planarity : 0.003 0.033 540 Dihedral : 14.498 87.993 1190 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.68 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.79 (0.33), residues: 380 helix: -4.35 (0.17), residues: 263 sheet: None (None), residues: 0 loop : -1.86 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 141 TYR 0.012 0.002 TYR B 114 PHE 0.010 0.002 PHE D 156 TRP 0.005 0.002 TRP B 91 HIS 0.002 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 3121) covalent geometry : angle 0.61808 ( 4205) hydrogen bonds : bond 0.32701 ( 136) hydrogen bonds : angle 10.70992 ( 408) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.127 Fit side-chains REVERT: B 88 LYS cc_start: 0.8241 (tppt) cc_final: 0.7685 (tttp) REVERT: D 35 ARG cc_start: 0.5999 (tpt170) cc_final: 0.5711 (tpt170) REVERT: D 69 LYS cc_start: 0.8324 (mttt) cc_final: 0.7534 (tptm) REVERT: D 151 ASP cc_start: 0.8158 (t0) cc_final: 0.7876 (t0) REVERT: D 167 GLU cc_start: 0.8421 (mp0) cc_final: 0.7168 (pt0) REVERT: A 41 MET cc_start: 0.8843 (tpt) cc_final: 0.8513 (tpp) REVERT: C 36 ASN cc_start: 0.7971 (t0) cc_final: 0.7761 (m-40) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1191 time to fit residues: 15.1806 Evaluate side-chains 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.0170 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 82 HIS D 176 GLN C 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.169335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140966 restraints weight = 4288.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.138499 restraints weight = 6328.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139729 restraints weight = 6291.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140023 restraints weight = 4237.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140061 restraints weight = 4304.162| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3121 Z= 0.106 Angle : 0.587 8.375 4205 Z= 0.293 Chirality : 0.036 0.141 505 Planarity : 0.004 0.035 540 Dihedral : 4.361 17.788 423 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.17 % Allowed : 15.79 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.38), residues: 380 helix: -2.30 (0.26), residues: 263 sheet: None (None), residues: 0 loop : -1.68 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.010 0.001 TYR B 95 PHE 0.010 0.001 PHE D 156 TRP 0.009 0.002 TRP B 91 HIS 0.001 0.001 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 3121) covalent geometry : angle 0.58702 ( 4205) hydrogen bonds : bond 0.03411 ( 136) hydrogen bonds : angle 4.42382 ( 408) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.101 Fit side-chains REVERT: B 24 SER cc_start: 0.8184 (m) cc_final: 0.7913 (p) REVERT: B 66 ARG cc_start: 0.7074 (mtm180) cc_final: 0.6796 (mtm-85) REVERT: B 88 LYS cc_start: 0.8046 (tppt) cc_final: 0.7731 (tttp) REVERT: D 42 TYR cc_start: 0.7697 (m-80) cc_final: 0.7072 (m-80) REVERT: D 167 GLU cc_start: 0.8171 (mp0) cc_final: 0.7286 (pt0) REVERT: A 41 MET cc_start: 0.8638 (tpt) cc_final: 0.8410 (tpp) REVERT: A 49 ARG cc_start: 0.7442 (mtt180) cc_final: 0.6142 (mmt180) REVERT: C 36 ASN cc_start: 0.7999 (t0) cc_final: 0.7727 (m-40) outliers start: 4 outliers final: 1 residues processed: 101 average time/residue: 0.1137 time to fit residues: 12.7972 Evaluate side-chains 83 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 25 optimal weight: 0.0170 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 0.0170 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN D 48 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.170899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142412 restraints weight = 4185.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140869 restraints weight = 5657.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141101 restraints weight = 5540.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.141550 restraints weight = 4732.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141397 restraints weight = 4302.987| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3121 Z= 0.097 Angle : 0.536 7.217 4205 Z= 0.264 Chirality : 0.035 0.123 505 Planarity : 0.003 0.035 540 Dihedral : 3.899 17.653 423 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.22 % Allowed : 19.30 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.42), residues: 380 helix: -0.72 (0.31), residues: 264 sheet: None (None), residues: 0 loop : -1.62 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 37 TYR 0.007 0.001 TYR B 95 PHE 0.008 0.001 PHE D 133 TRP 0.010 0.002 TRP B 91 HIS 0.001 0.000 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 3121) covalent geometry : angle 0.53553 ( 4205) hydrogen bonds : bond 0.03200 ( 136) hydrogen bonds : angle 3.63860 ( 408) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.091 Fit side-chains REVERT: B 19 ARG cc_start: 0.7884 (mmm160) cc_final: 0.7574 (mmm160) REVERT: B 24 SER cc_start: 0.8277 (m) cc_final: 0.7929 (p) REVERT: B 50 ASP cc_start: 0.7644 (p0) cc_final: 0.7436 (p0) REVERT: B 66 ARG cc_start: 0.7154 (mtm180) cc_final: 0.6882 (mtm-85) REVERT: B 88 LYS cc_start: 0.8005 (tppt) cc_final: 0.7709 (tttp) REVERT: D 30 ARG cc_start: 0.7505 (tpp80) cc_final: 0.7256 (tpp80) REVERT: D 42 TYR cc_start: 0.7530 (m-80) cc_final: 0.7132 (m-80) REVERT: A 41 MET cc_start: 0.8538 (tpt) cc_final: 0.8325 (tpp) REVERT: A 49 ARG cc_start: 0.7343 (mtt180) cc_final: 0.6008 (mmt180) REVERT: C 30 GLU cc_start: 0.6133 (mm-30) cc_final: 0.5746 (mm-30) outliers start: 11 outliers final: 6 residues processed: 90 average time/residue: 0.1218 time to fit residues: 12.0889 Evaluate side-chains 86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain C residue 32 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.165148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.136346 restraints weight = 4187.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134263 restraints weight = 6169.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.134889 restraints weight = 5838.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135088 restraints weight = 4527.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135238 restraints weight = 4498.184| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3121 Z= 0.100 Angle : 0.534 10.023 4205 Z= 0.260 Chirality : 0.035 0.118 505 Planarity : 0.003 0.034 540 Dihedral : 3.821 17.713 423 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.22 % Allowed : 20.18 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.43), residues: 380 helix: -0.04 (0.32), residues: 272 sheet: None (None), residues: 0 loop : -1.92 (0.54), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 37 TYR 0.010 0.001 TYR B 95 PHE 0.006 0.001 PHE D 133 TRP 0.013 0.003 TRP B 91 HIS 0.001 0.000 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 3121) covalent geometry : angle 0.53435 ( 4205) hydrogen bonds : bond 0.03207 ( 136) hydrogen bonds : angle 3.39723 ( 408) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.120 Fit side-chains REVERT: B 66 ARG cc_start: 0.7221 (mtm180) cc_final: 0.6913 (mtm-85) REVERT: B 88 LYS cc_start: 0.8024 (tppt) cc_final: 0.7706 (tttp) REVERT: B 114 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.5866 (p90) REVERT: D 42 TYR cc_start: 0.7627 (m-80) cc_final: 0.7266 (m-80) REVERT: A 41 MET cc_start: 0.8579 (tpt) cc_final: 0.8217 (tpp) REVERT: A 49 ARG cc_start: 0.7212 (mtt180) cc_final: 0.5909 (mmt180) REVERT: C 30 GLU cc_start: 0.6385 (mm-30) cc_final: 0.5986 (mm-30) outliers start: 11 outliers final: 8 residues processed: 83 average time/residue: 0.1296 time to fit residues: 11.8746 Evaluate side-chains 83 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 50 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.0270 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.162998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135474 restraints weight = 4222.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133362 restraints weight = 5475.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.133931 restraints weight = 5728.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.133789 restraints weight = 4742.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.133924 restraints weight = 4723.025| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3121 Z= 0.136 Angle : 0.567 7.576 4205 Z= 0.281 Chirality : 0.037 0.116 505 Planarity : 0.004 0.034 540 Dihedral : 4.036 17.230 423 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.80 % Allowed : 20.47 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.43), residues: 380 helix: 0.04 (0.32), residues: 280 sheet: None (None), residues: 0 loop : -2.08 (0.57), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 19 TYR 0.012 0.002 TYR B 95 PHE 0.008 0.001 PHE D 8 TRP 0.008 0.002 TRP B 91 HIS 0.001 0.000 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3121) covalent geometry : angle 0.56733 ( 4205) hydrogen bonds : bond 0.03574 ( 136) hydrogen bonds : angle 3.42877 ( 408) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.130 Fit side-chains REVERT: B 19 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7692 (mmm160) REVERT: B 66 ARG cc_start: 0.7210 (mtm180) cc_final: 0.6878 (mtm-85) REVERT: B 88 LYS cc_start: 0.8095 (tppt) cc_final: 0.7728 (tttp) REVERT: B 114 TYR cc_start: 0.7574 (OUTLIER) cc_final: 0.5482 (p90) REVERT: D 134 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7514 (mt) REVERT: D 172 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7767 (t-90) REVERT: A 41 MET cc_start: 0.8681 (tpt) cc_final: 0.8203 (tpp) REVERT: A 49 ARG cc_start: 0.7666 (mtt180) cc_final: 0.6350 (mmt180) outliers start: 13 outliers final: 7 residues processed: 88 average time/residue: 0.1066 time to fit residues: 10.6441 Evaluate side-chains 85 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.164064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136360 restraints weight = 4202.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.134041 restraints weight = 5838.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134833 restraints weight = 5827.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134367 restraints weight = 5076.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134571 restraints weight = 5100.995| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3121 Z= 0.095 Angle : 0.510 6.645 4205 Z= 0.251 Chirality : 0.035 0.118 505 Planarity : 0.003 0.034 540 Dihedral : 3.775 17.802 423 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.09 % Allowed : 21.05 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.44), residues: 380 helix: 0.49 (0.32), residues: 275 sheet: None (None), residues: 0 loop : -1.87 (0.57), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 88 TYR 0.008 0.001 TYR B 95 PHE 0.006 0.001 PHE D 8 TRP 0.006 0.002 TRP B 91 HIS 0.001 0.000 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 3121) covalent geometry : angle 0.51042 ( 4205) hydrogen bonds : bond 0.02943 ( 136) hydrogen bonds : angle 3.18951 ( 408) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.130 Fit side-chains REVERT: B 19 ARG cc_start: 0.7938 (mmm160) cc_final: 0.7616 (mmm160) REVERT: B 66 ARG cc_start: 0.7232 (mtm180) cc_final: 0.6882 (mtm-85) REVERT: B 88 LYS cc_start: 0.8051 (tppt) cc_final: 0.7729 (tttp) REVERT: B 114 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.5485 (p90) REVERT: D 135 ASN cc_start: 0.6476 (OUTLIER) cc_final: 0.6266 (p0) REVERT: D 172 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7811 (t-90) REVERT: A 41 MET cc_start: 0.8675 (tpt) cc_final: 0.8131 (tpp) REVERT: A 49 ARG cc_start: 0.7604 (mtt180) cc_final: 0.6291 (mmt180) outliers start: 14 outliers final: 8 residues processed: 89 average time/residue: 0.1116 time to fit residues: 11.1491 Evaluate side-chains 90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.0270 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.162147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.133719 restraints weight = 4223.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131889 restraints weight = 7070.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.132662 restraints weight = 6374.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.132768 restraints weight = 5157.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.132914 restraints weight = 4689.698| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3121 Z= 0.119 Angle : 0.561 9.669 4205 Z= 0.272 Chirality : 0.036 0.117 505 Planarity : 0.003 0.035 540 Dihedral : 3.842 16.889 423 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.80 % Allowed : 21.35 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.44), residues: 380 helix: 0.58 (0.32), residues: 278 sheet: None (None), residues: 0 loop : -1.89 (0.58), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 88 TYR 0.010 0.001 TYR B 95 PHE 0.006 0.001 PHE B 52 TRP 0.005 0.002 TRP B 91 HIS 0.001 0.000 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3121) covalent geometry : angle 0.56084 ( 4205) hydrogen bonds : bond 0.03258 ( 136) hydrogen bonds : angle 3.22598 ( 408) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.124 Fit side-chains REVERT: B 19 ARG cc_start: 0.8010 (mmm160) cc_final: 0.7728 (mmm160) REVERT: B 66 ARG cc_start: 0.7280 (mtm180) cc_final: 0.6919 (mtm-85) REVERT: B 88 LYS cc_start: 0.8118 (tppt) cc_final: 0.7740 (tttp) REVERT: B 114 TYR cc_start: 0.7621 (OUTLIER) cc_final: 0.5804 (p90) REVERT: D 135 ASN cc_start: 0.6561 (OUTLIER) cc_final: 0.6302 (p0) REVERT: D 172 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7874 (t-90) REVERT: A 41 MET cc_start: 0.8707 (tpt) cc_final: 0.8140 (tpp) REVERT: A 49 ARG cc_start: 0.7623 (mtt180) cc_final: 0.6349 (mmt180) outliers start: 13 outliers final: 7 residues processed: 85 average time/residue: 0.1191 time to fit residues: 11.2980 Evaluate side-chains 84 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 50 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 0.0770 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.168353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 156)---------------| | r_work = 0.3617 r_free = 0.3617 target = 0.140134 restraints weight = 4222.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137789 restraints weight = 5711.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139082 restraints weight = 4779.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137620 restraints weight = 5742.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137580 restraints weight = 5320.034| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3121 Z= 0.089 Angle : 0.529 8.028 4205 Z= 0.255 Chirality : 0.035 0.119 505 Planarity : 0.003 0.033 540 Dihedral : 3.602 17.600 423 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.22 % Allowed : 21.64 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.44), residues: 380 helix: 0.94 (0.33), residues: 278 sheet: None (None), residues: 0 loop : -1.66 (0.59), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 88 TYR 0.006 0.001 TYR B 95 PHE 0.006 0.001 PHE D 133 TRP 0.005 0.001 TRP B 91 HIS 0.001 0.000 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 3121) covalent geometry : angle 0.52922 ( 4205) hydrogen bonds : bond 0.02685 ( 136) hydrogen bonds : angle 3.10891 ( 408) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.128 Fit side-chains REVERT: B 66 ARG cc_start: 0.7177 (mtm180) cc_final: 0.6842 (mtm-85) REVERT: B 88 LYS cc_start: 0.8055 (tppt) cc_final: 0.7712 (tttp) REVERT: B 114 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.5801 (p90) REVERT: D 135 ASN cc_start: 0.6419 (OUTLIER) cc_final: 0.6198 (p0) REVERT: D 172 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7884 (t-90) REVERT: A 49 ARG cc_start: 0.7502 (mtt180) cc_final: 0.6218 (mmt180) outliers start: 11 outliers final: 7 residues processed: 87 average time/residue: 0.1181 time to fit residues: 11.4740 Evaluate side-chains 86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.163520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135042 restraints weight = 4231.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133838 restraints weight = 6643.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.133987 restraints weight = 5985.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134524 restraints weight = 5014.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134455 restraints weight = 4996.218| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3121 Z= 0.118 Angle : 0.570 7.822 4205 Z= 0.274 Chirality : 0.036 0.117 505 Planarity : 0.004 0.037 540 Dihedral : 3.729 16.580 423 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.22 % Allowed : 22.22 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.44), residues: 380 helix: 0.99 (0.32), residues: 278 sheet: None (None), residues: 0 loop : -1.70 (0.57), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 88 TYR 0.010 0.001 TYR B 95 PHE 0.007 0.001 PHE B 52 TRP 0.004 0.002 TRP B 91 HIS 0.001 0.000 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3121) covalent geometry : angle 0.56956 ( 4205) hydrogen bonds : bond 0.03130 ( 136) hydrogen bonds : angle 3.21770 ( 408) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.072 Fit side-chains REVERT: B 66 ARG cc_start: 0.7291 (mtm180) cc_final: 0.6932 (mtm-85) REVERT: B 88 LYS cc_start: 0.8163 (tppt) cc_final: 0.7768 (tttp) REVERT: B 114 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.5831 (p90) REVERT: D 172 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.7815 (t-90) REVERT: A 49 ARG cc_start: 0.7560 (mtt180) cc_final: 0.6341 (mmt180) outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 0.0941 time to fit residues: 8.7093 Evaluate side-chains 84 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.164746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137431 restraints weight = 4186.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.135225 restraints weight = 5981.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136118 restraints weight = 5878.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135737 restraints weight = 4651.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.136025 restraints weight = 4532.115| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3121 Z= 0.097 Angle : 0.561 10.230 4205 Z= 0.263 Chirality : 0.036 0.118 505 Planarity : 0.003 0.036 540 Dihedral : 3.629 17.262 423 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.63 % Allowed : 23.10 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.44), residues: 380 helix: 1.15 (0.32), residues: 278 sheet: None (None), residues: 0 loop : -1.60 (0.58), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 88 TYR 0.008 0.001 TYR B 95 PHE 0.006 0.001 PHE D 8 TRP 0.004 0.001 TRP B 91 HIS 0.001 0.000 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 3121) covalent geometry : angle 0.56096 ( 4205) hydrogen bonds : bond 0.02839 ( 136) hydrogen bonds : angle 3.17178 ( 408) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.132 Fit side-chains REVERT: B 66 ARG cc_start: 0.7189 (mtm180) cc_final: 0.6841 (mtm-85) REVERT: B 88 LYS cc_start: 0.8179 (tppt) cc_final: 0.7791 (tttp) REVERT: B 114 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.5913 (p90) REVERT: D 172 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7815 (t-90) REVERT: A 49 ARG cc_start: 0.7548 (mtt180) cc_final: 0.6273 (mmt180) outliers start: 9 outliers final: 6 residues processed: 82 average time/residue: 0.1091 time to fit residues: 10.0172 Evaluate side-chains 82 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.165866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139436 restraints weight = 4304.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137262 restraints weight = 5593.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137806 restraints weight = 5701.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137867 restraints weight = 4724.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137783 restraints weight = 4713.094| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3121 Z= 0.094 Angle : 0.550 8.731 4205 Z= 0.261 Chirality : 0.035 0.118 505 Planarity : 0.003 0.035 540 Dihedral : 3.525 15.316 423 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.92 % Allowed : 23.10 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.45), residues: 380 helix: 1.30 (0.32), residues: 278 sheet: None (None), residues: 0 loop : -1.39 (0.60), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 88 TYR 0.008 0.001 TYR B 95 PHE 0.006 0.001 PHE D 133 TRP 0.004 0.001 TRP B 91 HIS 0.001 0.000 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 3121) covalent geometry : angle 0.55022 ( 4205) hydrogen bonds : bond 0.02752 ( 136) hydrogen bonds : angle 3.09305 ( 408) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 870.73 seconds wall clock time: 15 minutes 31.38 seconds (931.38 seconds total)