Starting phenix.real_space_refine on Wed Sep 17 04:29:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yvu_39614/09_2025/8yvu_39614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yvu_39614/09_2025/8yvu_39614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yvu_39614/09_2025/8yvu_39614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yvu_39614/09_2025/8yvu_39614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yvu_39614/09_2025/8yvu_39614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yvu_39614/09_2025/8yvu_39614.map" } resolution = 3.9 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= 0.008 sd= 0.202 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 30 5.16 5 C 2828 2.51 5 N 646 2.21 5 O 712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s 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: 4216 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 311 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "B" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1211 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 239 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "D" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 319 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "E" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 311 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "F" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1211 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "G" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 239 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "H" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 319 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.33, per 1000 atoms: 0.32 Number of scatterers: 4216 At special positions: 0 Unit cell: (71.742, 99.4605, 89.6775, 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 30 16.00 O 712 8.00 N 646 7.00 C 2828 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: 0.40 Conformation dependent library (CDL) restraints added in 156.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 988 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 84.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 206 through 235 removed outlier: 3.783A pdb=" N ILE A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 235 " --> pdb=" O THR A 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 58 through 83 removed outlier: 3.605A pdb=" N GLY B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS B 74 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 75 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 104 through 121 removed outlier: 3.590A pdb=" N PHE B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 161 removed outlier: 3.603A pdb=" N LEU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 205 removed outlier: 3.565A pdb=" N SER B 176 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 34 removed outlier: 3.532A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 53 Processing helix chain 'D' and resid 25 through 59 removed outlier: 4.189A pdb=" N ILE D 31 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU D 32 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N CYS D 44 " --> pdb=" O THR D 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 234 removed outlier: 3.524A pdb=" N LEU E 210 " --> pdb=" O PHE E 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE E 214 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 57 Processing helix chain 'F' and resid 58 through 83 removed outlier: 3.669A pdb=" N GLY F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS F 74 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE F 75 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY F 76 " --> pdb=" O CYS F 72 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU F 83 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 121 removed outlier: 4.243A pdb=" N ILE F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE F 107 " --> pdb=" O TRP F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 161 removed outlier: 3.725A pdb=" N THR F 146 " --> pdb=" O GLY F 142 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA F 157 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR F 158 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE F 159 " --> pdb=" O SER F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 205 removed outlier: 3.581A pdb=" N SER F 176 " --> pdb=" O CYS F 172 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER F 195 " --> pdb=" O LEU F 191 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY F 205 " --> pdb=" O ILE F 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 53 removed outlier: 3.683A pdb=" N ILE G 31 " --> pdb=" O ILE G 27 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU G 32 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR G 35 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY G 36 " --> pdb=" O LEU G 32 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE G 37 " --> pdb=" O PHE G 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 59 removed outlier: 3.879A pdb=" N ILE H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU H 32 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU H 59 " --> pdb=" O ILE H 55 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 954 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: 0.70 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1216 1.34 - 1.46: 1021 1.46 - 1.58: 2021 1.58 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 4298 Sorted by residual: bond pdb=" C13 CLR F 301 " pdb=" C17 CLR F 301 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" C13 CLR A 301 " pdb=" C17 CLR A 301 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.68e+00 bond pdb=" C13 CLR F 301 " pdb=" C14 CLR F 301 " ideal model delta sigma weight residual 1.537 1.505 0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C13 CLR A 301 " pdb=" C14 CLR A 301 " ideal model delta sigma weight residual 1.537 1.505 0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" CA LYS A 235 " pdb=" CB LYS A 235 " ideal model delta sigma weight residual 1.524 1.545 -0.022 1.41e-02 5.03e+03 2.37e+00 ... (remaining 4293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 5595 1.59 - 3.17: 161 3.17 - 4.76: 45 4.76 - 6.35: 13 6.35 - 7.93: 4 Bond angle restraints: 5818 Sorted by residual: angle pdb=" N ILE B 106 " pdb=" CA ILE B 106 " pdb=" C ILE B 106 " ideal model delta sigma weight residual 111.91 106.11 5.80 8.90e-01 1.26e+00 4.25e+01 angle pdb=" N PHE B 107 " pdb=" CA PHE B 107 " pdb=" C PHE B 107 " ideal model delta sigma weight residual 112.93 106.87 6.06 1.33e+00 5.65e-01 2.08e+01 angle pdb=" C LEU D 24 " pdb=" N CYS D 25 " pdb=" CA CYS D 25 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C LYS F 166 " pdb=" CA LYS F 166 " pdb=" CB LYS F 166 " ideal model delta sigma weight residual 116.34 110.97 5.37 1.40e+00 5.10e-01 1.47e+01 angle pdb=" CA LYS A 235 " pdb=" CB LYS A 235 " pdb=" CG LYS A 235 " ideal model delta sigma weight residual 114.10 120.55 -6.45 2.00e+00 2.50e-01 1.04e+01 ... (remaining 5813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 2339 15.97 - 31.93: 195 31.93 - 47.90: 58 47.90 - 63.86: 10 63.86 - 79.83: 6 Dihedral angle restraints: 2608 sinusoidal: 1076 harmonic: 1532 Sorted by residual: dihedral pdb=" CA ILE F 161 " pdb=" C ILE F 161 " pdb=" N HIS F 162 " pdb=" CA HIS F 162 " ideal model delta harmonic sigma weight residual 180.00 159.32 20.68 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ILE B 161 " pdb=" C ILE B 161 " pdb=" N HIS B 162 " pdb=" CA HIS B 162 " ideal model delta harmonic sigma weight residual 180.00 162.30 17.70 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CB ARG B 121 " pdb=" CG ARG B 121 " pdb=" CD ARG B 121 " pdb=" NE ARG B 121 " ideal model delta sinusoidal sigma weight residual -60.00 -110.72 50.72 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 2605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 612 0.054 - 0.107: 98 0.107 - 0.161: 10 0.161 - 0.215: 4 0.215 - 0.268: 2 Chirality restraints: 726 Sorted by residual: chirality pdb=" C13 CLR F 301 " pdb=" C12 CLR F 301 " pdb=" C14 CLR F 301 " pdb=" C17 CLR F 301 " both_signs ideal model delta sigma weight residual False -2.93 -2.66 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C13 CLR A 301 " pdb=" C12 CLR A 301 " pdb=" C14 CLR A 301 " pdb=" C17 CLR A 301 " both_signs ideal model delta sigma weight residual False -2.93 -2.67 -0.26 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C10 CLR A 301 " pdb=" C1 CLR A 301 " pdb=" C5 CLR A 301 " pdb=" C9 CLR A 301 " both_signs ideal model delta sigma weight residual False -2.85 -2.65 -0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 723 not shown) Planarity restraints: 666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 227 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C GLN A 227 " 0.022 2.00e-02 2.50e+03 pdb=" O GLN A 227 " -0.008 2.00e-02 2.50e+03 pdb=" N GLN A 228 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 168 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C PHE F 168 " 0.022 2.00e-02 2.50e+03 pdb=" O PHE F 168 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU F 169 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 33 " -0.011 2.00e-02 2.50e+03 8.20e-03 1.18e+00 pdb=" CG PHE H 33 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE H 33 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE H 33 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE H 33 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE H 33 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 33 " -0.004 2.00e-02 2.50e+03 ... (remaining 663 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1046 2.80 - 3.33: 4602 3.33 - 3.85: 6699 3.85 - 4.38: 7061 4.38 - 4.90: 12096 Nonbonded interactions: 31504 Sorted by model distance: nonbonded pdb=" OG SER B 155 " pdb=" OG1 THR B 179 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLN A 227 " pdb=" NH2 ARG C 45 " model vdw 2.339 3.120 nonbonded pdb=" CD1 LEU E 211 " pdb=" C26 CLR F 301 " model vdw 2.356 3.880 nonbonded pdb=" O SER B 115 " pdb=" OG SER B 118 " model vdw 2.371 3.040 nonbonded pdb=" NZ LYS B 55 " pdb=" O CYS B 202 " model vdw 2.412 3.120 ... (remaining 31499 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 201 through 237) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 49 through 208) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 6.130 Find NCS groups from input model: 0.040 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 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 : 0.003 0.054 4298 Z= 0.158 Angle : 0.712 7.933 5818 Z= 0.380 Chirality : 0.043 0.268 726 Planarity : 0.003 0.022 666 Dihedral : 13.757 79.831 1620 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.09 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.38), residues: 514 helix: 1.80 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -2.79 (0.57), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 51 TYR 0.012 0.002 TYR H 43 PHE 0.018 0.001 PHE H 33 TRP 0.010 0.001 TRP B 103 HIS 0.002 0.000 HIS F 87 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4298) covalent geometry : angle 0.71170 ( 5818) hydrogen bonds : bond 0.12977 ( 319) hydrogen bonds : angle 4.06686 ( 954) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.158 Fit side-chains REVERT: D 49 GLN cc_start: 0.8571 (tm-30) cc_final: 0.7998 (tm-30) REVERT: E 214 ILE cc_start: 0.8801 (pt) cc_final: 0.8557 (pt) REVERT: F 96 PHE cc_start: 0.8878 (m-80) cc_final: 0.8666 (m-80) REVERT: F 158 TYR cc_start: 0.8155 (t80) cc_final: 0.7819 (t80) REVERT: F 181 ILE cc_start: 0.9061 (mm) cc_final: 0.8781 (mm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0680 time to fit residues: 11.2946 Evaluate side-chains 108 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 0.0070 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.0020 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 overall best weight: 0.5006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 228 GLN G 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.257115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.205194 restraints weight = 5216.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.211298 restraints weight = 2741.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.215278 restraints weight = 1821.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.217551 restraints weight = 1410.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.219034 restraints weight = 1207.667| |-----------------------------------------------------------------------------| r_work (final): 0.4593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4298 Z= 0.136 Angle : 0.664 7.694 5818 Z= 0.337 Chirality : 0.038 0.129 726 Planarity : 0.003 0.025 666 Dihedral : 4.839 22.254 688 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.47 % Favored : 95.14 % Rotamer: Outliers : 2.61 % Allowed : 12.61 % Favored : 84.78 % 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 aren not related in a simple way. whole: 1.49 (0.38), residues: 514 helix: 1.73 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -2.42 (0.64), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 51 TYR 0.024 0.002 TYR G 43 PHE 0.019 0.001 PHE F 60 TRP 0.019 0.001 TRP B 103 HIS 0.002 0.000 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4298) covalent geometry : angle 0.66396 ( 5818) hydrogen bonds : bond 0.04625 ( 319) hydrogen bonds : angle 3.57351 ( 954) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.150 Fit side-chains REVERT: B 146 THR cc_start: 0.6701 (t) cc_final: 0.6478 (m) REVERT: D 49 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8025 (tm-30) REVERT: E 214 ILE cc_start: 0.8782 (pt) cc_final: 0.8510 (pt) REVERT: E 227 GLN cc_start: 0.8381 (tm-30) cc_final: 0.7934 (tp-100) REVERT: F 70 MET cc_start: 0.6986 (tpp) cc_final: 0.6712 (tpp) REVERT: F 158 TYR cc_start: 0.8034 (t80) cc_final: 0.7803 (t80) REVERT: F 188 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8703 (pp) outliers start: 12 outliers final: 7 residues processed: 122 average time/residue: 0.0622 time to fit residues: 9.6101 Evaluate side-chains 112 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain H residue 50 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 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 = 0.4843 r_free = 0.4843 target = 0.250737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.201821 restraints weight = 4891.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.207105 restraints weight = 2629.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.210476 restraints weight = 1760.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.212481 restraints weight = 1374.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.213849 restraints weight = 1173.330| |-----------------------------------------------------------------------------| r_work (final): 0.4557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4298 Z= 0.142 Angle : 0.629 8.515 5818 Z= 0.326 Chirality : 0.037 0.128 726 Planarity : 0.003 0.024 666 Dihedral : 5.028 42.378 688 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.89 % Favored : 95.72 % Rotamer: Outliers : 3.70 % Allowed : 15.87 % Favored : 80.43 % 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 aren not related in a simple way. whole: 1.39 (0.38), residues: 514 helix: 1.68 (0.25), residues: 420 sheet: None (None), residues: 0 loop : -2.66 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 51 TYR 0.022 0.002 TYR F 100 PHE 0.019 0.002 PHE F 177 TRP 0.018 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4298) covalent geometry : angle 0.62902 ( 5818) hydrogen bonds : bond 0.04464 ( 319) hydrogen bonds : angle 3.59732 ( 954) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.144 Fit side-chains REVERT: D 49 GLN cc_start: 0.8648 (tm-30) cc_final: 0.7976 (tm-30) REVERT: E 214 ILE cc_start: 0.8745 (pt) cc_final: 0.8422 (pt) REVERT: F 70 MET cc_start: 0.6997 (tpp) cc_final: 0.6655 (tpp) REVERT: F 75 PHE cc_start: 0.8483 (m-80) cc_final: 0.7892 (m-80) REVERT: F 158 TYR cc_start: 0.8009 (t80) cc_final: 0.7804 (t80) REVERT: F 188 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8696 (pp) REVERT: H 49 GLN cc_start: 0.8398 (tp-100) cc_final: 0.8193 (tp-100) outliers start: 17 outliers final: 12 residues processed: 123 average time/residue: 0.0719 time to fit residues: 11.0118 Evaluate side-chains 118 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain H residue 50 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 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 = 0.4820 r_free = 0.4820 target = 0.248191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.198638 restraints weight = 4949.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.203788 restraints weight = 2684.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.207149 restraints weight = 1811.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.208852 restraints weight = 1407.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.210362 restraints weight = 1217.575| |-----------------------------------------------------------------------------| r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4298 Z= 0.145 Angle : 0.642 8.758 5818 Z= 0.333 Chirality : 0.037 0.143 726 Planarity : 0.003 0.022 666 Dihedral : 4.810 33.940 688 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.09 % Favored : 95.53 % Rotamer: Outliers : 4.13 % Allowed : 20.65 % Favored : 75.22 % 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 aren not related in a simple way. whole: 1.35 (0.38), residues: 514 helix: 1.65 (0.25), residues: 420 sheet: None (None), residues: 0 loop : -2.66 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 51 TYR 0.023 0.002 TYR F 100 PHE 0.014 0.001 PHE H 33 TRP 0.017 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4298) covalent geometry : angle 0.64176 ( 5818) hydrogen bonds : bond 0.04422 ( 319) hydrogen bonds : angle 3.59682 ( 954) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: B 58 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7623 (tm-30) REVERT: C 41 LEU cc_start: 0.7437 (tt) cc_final: 0.7231 (tt) REVERT: D 49 GLN cc_start: 0.8678 (tm-30) cc_final: 0.7997 (tm-30) REVERT: E 214 ILE cc_start: 0.8762 (pt) cc_final: 0.8431 (pt) REVERT: F 70 MET cc_start: 0.7005 (tpp) cc_final: 0.6616 (tpp) REVERT: F 75 PHE cc_start: 0.8513 (m-80) cc_final: 0.7859 (m-80) REVERT: F 177 PHE cc_start: 0.9101 (t80) cc_final: 0.8762 (t80) REVERT: F 188 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8689 (pp) REVERT: H 49 GLN cc_start: 0.8326 (tp-100) cc_final: 0.8077 (tp-100) outliers start: 19 outliers final: 9 residues processed: 124 average time/residue: 0.0700 time to fit residues: 10.9116 Evaluate side-chains 120 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain H residue 50 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 229 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.250295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.195579 restraints weight = 5260.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.201181 restraints weight = 2918.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.204042 restraints weight = 2012.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.206686 restraints weight = 1618.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.207709 restraints weight = 1403.823| |-----------------------------------------------------------------------------| r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4298 Z= 0.152 Angle : 0.647 9.337 5818 Z= 0.336 Chirality : 0.037 0.136 726 Planarity : 0.003 0.022 666 Dihedral : 4.709 26.151 688 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.47 % Favored : 95.14 % Rotamer: Outliers : 5.22 % Allowed : 21.30 % Favored : 73.48 % 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 aren not related in a simple way. whole: 1.44 (0.38), residues: 514 helix: 1.75 (0.25), residues: 408 sheet: None (None), residues: 0 loop : -2.30 (0.59), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 51 TYR 0.023 0.002 TYR F 100 PHE 0.017 0.001 PHE H 33 TRP 0.018 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 4298) covalent geometry : angle 0.64664 ( 5818) hydrogen bonds : bond 0.04435 ( 319) hydrogen bonds : angle 3.65801 ( 954) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.160 Fit side-chains REVERT: C 41 LEU cc_start: 0.7661 (tt) cc_final: 0.7444 (tt) REVERT: D 49 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8008 (tm-30) REVERT: E 214 ILE cc_start: 0.8758 (pt) cc_final: 0.8449 (pt) REVERT: E 227 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8087 (tp-100) REVERT: F 70 MET cc_start: 0.7036 (tpp) cc_final: 0.6657 (tpp) REVERT: F 75 PHE cc_start: 0.8552 (m-80) cc_final: 0.7825 (m-80) REVERT: F 188 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8685 (pp) REVERT: H 49 GLN cc_start: 0.8367 (tp-100) cc_final: 0.8105 (tp-100) REVERT: H 52 LYS cc_start: 0.8568 (mmtp) cc_final: 0.8214 (mmtp) outliers start: 24 outliers final: 13 residues processed: 125 average time/residue: 0.0594 time to fit residues: 9.4852 Evaluate side-chains 123 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain H residue 50 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.246581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.195077 restraints weight = 5083.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.200326 restraints weight = 2835.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.203626 restraints weight = 1938.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.205309 restraints weight = 1535.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.206924 restraints weight = 1336.503| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4298 Z= 0.146 Angle : 0.650 9.550 5818 Z= 0.336 Chirality : 0.037 0.136 726 Planarity : 0.003 0.022 666 Dihedral : 4.623 22.967 688 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.09 % Favored : 95.53 % Rotamer: Outliers : 5.22 % Allowed : 22.17 % Favored : 72.61 % 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 aren not related in a simple way. whole: 1.54 (0.37), residues: 514 helix: 1.87 (0.25), residues: 406 sheet: None (None), residues: 0 loop : -2.41 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 51 TYR 0.025 0.002 TYR F 100 PHE 0.016 0.001 PHE H 33 TRP 0.019 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4298) covalent geometry : angle 0.65026 ( 5818) hydrogen bonds : bond 0.04403 ( 319) hydrogen bonds : angle 3.62368 ( 954) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: B 58 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: D 49 GLN cc_start: 0.8440 (tm-30) cc_final: 0.7829 (tm-30) REVERT: E 214 ILE cc_start: 0.8757 (pt) cc_final: 0.8416 (pt) REVERT: F 58 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7264 (mp10) REVERT: F 70 MET cc_start: 0.6980 (tpp) cc_final: 0.6567 (tpp) REVERT: F 75 PHE cc_start: 0.8507 (m-80) cc_final: 0.7782 (m-80) REVERT: F 188 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8689 (pp) REVERT: H 49 GLN cc_start: 0.8247 (tp-100) cc_final: 0.7992 (tp-100) REVERT: H 50 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8374 (p) REVERT: H 52 LYS cc_start: 0.8513 (mmtp) cc_final: 0.8103 (mmtp) outliers start: 24 outliers final: 14 residues processed: 130 average time/residue: 0.0606 time to fit residues: 10.2484 Evaluate side-chains 129 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain H residue 50 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 49 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 = 0.4812 r_free = 0.4812 target = 0.244966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.194992 restraints weight = 5052.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.199857 restraints weight = 2871.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.203141 restraints weight = 1994.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.204798 restraints weight = 1573.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.206368 restraints weight = 1367.770| |-----------------------------------------------------------------------------| r_work (final): 0.4517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4298 Z= 0.141 Angle : 0.666 9.078 5818 Z= 0.341 Chirality : 0.037 0.144 726 Planarity : 0.003 0.022 666 Dihedral : 4.578 23.860 688 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.47 % Favored : 95.14 % Rotamer: Outliers : 4.78 % Allowed : 23.91 % Favored : 71.30 % 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 aren not related in a simple way. whole: 1.55 (0.37), residues: 514 helix: 1.87 (0.25), residues: 408 sheet: None (None), residues: 0 loop : -2.43 (0.58), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 51 TYR 0.030 0.002 TYR G 43 PHE 0.015 0.001 PHE F 60 TRP 0.018 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4298) covalent geometry : angle 0.66578 ( 5818) hydrogen bonds : bond 0.04351 ( 319) hydrogen bonds : angle 3.62679 ( 954) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.180 Fit side-chains REVERT: D 49 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7835 (tm-30) REVERT: E 214 ILE cc_start: 0.8799 (pt) cc_final: 0.8478 (pt) REVERT: E 227 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8115 (tp-100) REVERT: E 228 GLN cc_start: 0.7033 (tm-30) cc_final: 0.6459 (tm-30) REVERT: F 58 GLN cc_start: 0.7578 (mt0) cc_final: 0.7281 (pm20) REVERT: F 70 MET cc_start: 0.6974 (tpp) cc_final: 0.6535 (tpp) REVERT: F 75 PHE cc_start: 0.8618 (m-80) cc_final: 0.8051 (m-80) REVERT: F 188 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8681 (pp) REVERT: H 49 GLN cc_start: 0.8240 (tp-100) cc_final: 0.7986 (tp-100) REVERT: H 50 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8357 (p) REVERT: H 52 LYS cc_start: 0.8436 (mmtp) cc_final: 0.8213 (mmtp) outliers start: 22 outliers final: 17 residues processed: 123 average time/residue: 0.0612 time to fit residues: 9.7091 Evaluate side-chains 130 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 50 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 38 optimal weight: 0.0670 chunk 12 optimal weight: 0.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 49 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 = 0.4833 r_free = 0.4833 target = 0.248451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.197612 restraints weight = 5006.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.202984 restraints weight = 2780.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.206131 restraints weight = 1891.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.208531 restraints weight = 1489.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.209634 restraints weight = 1279.709| |-----------------------------------------------------------------------------| r_work (final): 0.4536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4298 Z= 0.134 Angle : 0.668 9.044 5818 Z= 0.338 Chirality : 0.037 0.132 726 Planarity : 0.003 0.020 666 Dihedral : 4.494 25.686 688 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.28 % Favored : 95.33 % Rotamer: Outliers : 4.78 % Allowed : 25.00 % Favored : 70.22 % 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 aren not related in a simple way. whole: 1.46 (0.37), residues: 514 helix: 1.84 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.87 (0.53), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 51 TYR 0.031 0.002 TYR G 43 PHE 0.020 0.001 PHE F 102 TRP 0.017 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4298) covalent geometry : angle 0.66789 ( 5818) hydrogen bonds : bond 0.04284 ( 319) hydrogen bonds : angle 3.57962 ( 954) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: D 49 GLN cc_start: 0.8431 (tm-30) cc_final: 0.7842 (tm-30) REVERT: E 214 ILE cc_start: 0.8780 (pt) cc_final: 0.8452 (pt) REVERT: E 227 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8220 (tp-100) REVERT: E 228 GLN cc_start: 0.6958 (tm-30) cc_final: 0.6371 (tm-30) REVERT: F 58 GLN cc_start: 0.7558 (mt0) cc_final: 0.7221 (pm20) REVERT: F 70 MET cc_start: 0.7416 (tpp) cc_final: 0.6798 (tpp) REVERT: F 75 PHE cc_start: 0.8645 (m-80) cc_final: 0.8088 (m-80) REVERT: F 188 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8682 (pp) REVERT: H 49 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7982 (tp-100) REVERT: H 50 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8341 (p) REVERT: H 52 LYS cc_start: 0.8537 (mmtp) cc_final: 0.8237 (mmtp) outliers start: 22 outliers final: 13 residues processed: 125 average time/residue: 0.0658 time to fit residues: 10.6203 Evaluate side-chains 124 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain H residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 49 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 = 0.4834 r_free = 0.4834 target = 0.247279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.198034 restraints weight = 5179.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.203363 restraints weight = 2837.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.206704 restraints weight = 1918.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.208798 restraints weight = 1507.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.209910 restraints weight = 1302.801| |-----------------------------------------------------------------------------| r_work (final): 0.4546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4298 Z= 0.133 Angle : 0.676 9.389 5818 Z= 0.341 Chirality : 0.037 0.137 726 Planarity : 0.003 0.019 666 Dihedral : 4.467 25.973 688 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.09 % Favored : 95.53 % Rotamer: Outliers : 3.91 % Allowed : 25.87 % Favored : 70.22 % 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 aren not related in a simple way. whole: 1.46 (0.37), residues: 514 helix: 1.85 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.86 (0.53), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 51 TYR 0.024 0.002 TYR F 100 PHE 0.015 0.001 PHE H 33 TRP 0.015 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4298) covalent geometry : angle 0.67608 ( 5818) hydrogen bonds : bond 0.04215 ( 319) hydrogen bonds : angle 3.56291 ( 954) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: B 188 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7243 (mt) REVERT: C 52 LYS cc_start: 0.8456 (tptt) cc_final: 0.7271 (mttp) REVERT: D 49 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7840 (tm-30) REVERT: E 214 ILE cc_start: 0.8771 (pt) cc_final: 0.8453 (pt) REVERT: E 227 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8228 (tp-100) REVERT: E 228 GLN cc_start: 0.6970 (tm-30) cc_final: 0.6441 (tm-30) REVERT: F 70 MET cc_start: 0.7474 (tpp) cc_final: 0.6851 (tpp) REVERT: F 75 PHE cc_start: 0.8647 (m-80) cc_final: 0.8080 (m-80) REVERT: F 188 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8688 (pp) REVERT: H 49 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7986 (tp-100) REVERT: H 50 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8323 (p) REVERT: H 52 LYS cc_start: 0.8586 (mmtp) cc_final: 0.8236 (mmtp) outliers start: 18 outliers final: 14 residues processed: 121 average time/residue: 0.0658 time to fit residues: 10.2193 Evaluate side-chains 125 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain H residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.247801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.200775 restraints weight = 4976.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.207808 restraints weight = 3291.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.208801 restraints weight = 1887.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.208907 restraints weight = 1601.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.209168 restraints weight = 1510.557| |-----------------------------------------------------------------------------| r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4298 Z= 0.140 Angle : 0.695 9.189 5818 Z= 0.350 Chirality : 0.037 0.134 726 Planarity : 0.003 0.020 666 Dihedral : 4.469 25.227 688 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.28 % Favored : 95.53 % Rotamer: Outliers : 4.35 % Allowed : 25.87 % Favored : 69.78 % 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 aren not related in a simple way. whole: 1.40 (0.37), residues: 514 helix: 1.80 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.84 (0.54), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 51 TYR 0.022 0.002 TYR F 100 PHE 0.015 0.001 PHE H 33 TRP 0.015 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4298) covalent geometry : angle 0.69540 ( 5818) hydrogen bonds : bond 0.04272 ( 319) hydrogen bonds : angle 3.59863 ( 954) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.157 Fit side-chains REVERT: B 188 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7299 (mt) REVERT: D 49 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7859 (tm-30) REVERT: E 214 ILE cc_start: 0.8784 (pt) cc_final: 0.8428 (pt) REVERT: E 227 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8236 (tp-100) REVERT: E 228 GLN cc_start: 0.6942 (tm-30) cc_final: 0.6471 (tm-30) REVERT: F 70 MET cc_start: 0.7313 (tpp) cc_final: 0.6670 (tpp) REVERT: F 75 PHE cc_start: 0.8591 (m-80) cc_final: 0.8090 (m-80) REVERT: F 188 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8668 (pp) REVERT: H 49 GLN cc_start: 0.8094 (tp-100) cc_final: 0.7884 (tp-100) REVERT: H 50 VAL cc_start: 0.8636 (p) cc_final: 0.8254 (p) REVERT: H 52 LYS cc_start: 0.8521 (mmtp) cc_final: 0.8145 (mmtp) outliers start: 20 outliers final: 16 residues processed: 126 average time/residue: 0.0668 time to fit residues: 10.7278 Evaluate side-chains 128 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 188 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.246392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.200554 restraints weight = 5312.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.202001 restraints weight = 3353.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.204281 restraints weight = 2651.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.204534 restraints weight = 2107.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.204770 restraints weight = 2001.872| |-----------------------------------------------------------------------------| r_work (final): 0.4489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 4298 Z= 0.219 Angle : 1.216 59.191 5818 Z= 0.706 Chirality : 0.047 0.691 726 Planarity : 0.003 0.027 666 Dihedral : 4.668 35.359 688 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.28 % Favored : 95.33 % Rotamer: Outliers : 3.91 % Allowed : 26.52 % Favored : 69.57 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.41 (0.37), residues: 514 helix: 1.80 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.85 (0.54), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 121 TYR 0.019 0.002 TYR F 100 PHE 0.018 0.001 PHE H 33 TRP 0.015 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 4298) covalent geometry : angle 1.21576 ( 5818) hydrogen bonds : bond 0.04292 ( 319) hydrogen bonds : angle 3.62922 ( 954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 916.99 seconds wall clock time: 16 minutes 32.94 seconds (992.94 seconds total)