Starting phenix.real_space_refine on Mon Jan 13 21:37:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yvu_39614/01_2025/8yvu_39614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yvu_39614/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yvu_39614/01_2025/8yvu_39614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yvu_39614/01_2025/8yvu_39614.map" model { file = "/net/cci-nas-00/data/ceres_data/8yvu_39614/01_2025/8yvu_39614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yvu_39614/01_2025/8yvu_39614.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 3.28, per 1000 atoms: 0.78 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: 1.18 Conformation dependent library (CDL) restraints added in 472.9 milliseconds 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: 0.27 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: 1.09 Time building geometry restraints manager: 1.33 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: 0.150 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.170 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.730 ------------------------------------------------------------------------------- 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= 0.206 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (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 TRP 0.010 0.001 TRP B 103 HIS 0.002 0.000 HIS F 87 PHE 0.018 0.001 PHE H 33 TYR 0.012 0.002 TYR H 43 ARG 0.007 0.000 ARG D 51 *********************** 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 : 0.503 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: 0.1626 time to fit residues: 26.7705 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 : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4867 r_free = 0.4867 target = 0.254567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.200615 restraints weight = 5253.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.206723 restraints weight = 2829.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.210404 restraints weight = 1894.378| |-----------------------------------------------------------------------------| r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4298 Z= 0.215 Angle : 0.674 7.625 5818 Z= 0.345 Chirality : 0.039 0.133 726 Planarity : 0.003 0.026 666 Dihedral : 4.889 23.974 688 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.47 % Favored : 95.14 % Rotamer: Outliers : 3.48 % Allowed : 12.39 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.38), residues: 514 helix: 1.71 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -2.38 (0.65), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.002 0.000 HIS B 160 PHE 0.018 0.002 PHE F 60 TYR 0.018 0.002 TYR G 43 ARG 0.003 0.000 ARG D 51 *********************** 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 130 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.457 Fit side-chains REVERT: D 49 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8024 (tm-30) REVERT: E 214 ILE cc_start: 0.8773 (pt) cc_final: 0.8489 (pt) REVERT: E 227 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7992 (tp-100) REVERT: E 228 GLN cc_start: 0.7196 (tm-30) cc_final: 0.6762 (tm-30) REVERT: F 70 MET cc_start: 0.7022 (tpp) cc_final: 0.6762 (tpp) REVERT: F 75 PHE cc_start: 0.8515 (m-80) cc_final: 0.7882 (m-80) REVERT: F 158 TYR cc_start: 0.8181 (t80) cc_final: 0.7905 (t80) REVERT: F 185 MET cc_start: 0.7497 (tpt) cc_final: 0.7262 (tpt) REVERT: F 188 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8694 (pp) REVERT: H 41 LEU cc_start: 0.7411 (tp) cc_final: 0.7186 (tp) outliers start: 16 outliers final: 11 residues processed: 118 average time/residue: 0.1689 time to fit residues: 24.7818 Evaluate side-chains 113 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 B residue 183 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 ASP 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 0 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4853 r_free = 0.4853 target = 0.250452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.201996 restraints weight = 4893.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.207267 restraints weight = 2621.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.210770 restraints weight = 1761.277| |-----------------------------------------------------------------------------| r_work (final): 0.4557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.1859 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= 0.179 Angle : 0.623 8.495 5818 Z= 0.322 Chirality : 0.037 0.130 726 Planarity : 0.003 0.022 666 Dihedral : 4.825 34.729 688 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.09 % Favored : 95.53 % Rotamer: Outliers : 2.61 % Allowed : 16.30 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.38), residues: 514 helix: 1.68 (0.25), residues: 420 sheet: None (None), residues: 0 loop : -2.61 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 PHE 0.020 0.001 PHE F 177 TYR 0.022 0.002 TYR F 100 ARG 0.005 0.000 ARG D 51 *********************** 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 126 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.502 Fit side-chains REVERT: D 49 GLN cc_start: 0.8619 (tm-30) cc_final: 0.7969 (tm-30) REVERT: E 214 ILE cc_start: 0.8737 (pt) cc_final: 0.8413 (pt) REVERT: F 70 MET cc_start: 0.6989 (tpp) cc_final: 0.6648 (tpp) REVERT: F 75 PHE cc_start: 0.8440 (m-80) cc_final: 0.7534 (m-80) REVERT: F 158 TYR cc_start: 0.8094 (t80) cc_final: 0.7889 (t80) REVERT: F 185 MET cc_start: 0.7349 (tpt) cc_final: 0.7073 (tpt) REVERT: F 188 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8683 (pp) REVERT: H 41 LEU cc_start: 0.7449 (tp) cc_final: 0.7228 (tp) outliers start: 12 outliers final: 8 residues processed: 119 average time/residue: 0.1633 time to fit residues: 24.4003 Evaluate side-chains 110 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain D residue 31 ILE 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 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 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 chunk 24 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4814 r_free = 0.4814 target = 0.245293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.195857 restraints weight = 5044.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.200830 restraints weight = 2766.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.204087 restraints weight = 1893.409| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4298 Z= 0.211 Angle : 0.642 8.764 5818 Z= 0.332 Chirality : 0.038 0.136 726 Planarity : 0.003 0.023 666 Dihedral : 4.704 27.352 688 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.47 % Favored : 95.14 % Rotamer: Outliers : 5.00 % Allowed : 19.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.38), residues: 514 helix: 1.69 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -2.72 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 PHE 0.014 0.001 PHE F 177 TYR 0.023 0.002 TYR F 100 ARG 0.005 0.000 ARG D 51 *********************** 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 137 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.452 Fit side-chains REVERT: B 58 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7625 (tm-30) REVERT: C 41 LEU cc_start: 0.7542 (tt) cc_final: 0.7292 (tt) REVERT: D 49 GLN cc_start: 0.8660 (tm-30) cc_final: 0.7973 (tm-30) REVERT: E 214 ILE cc_start: 0.8770 (pt) cc_final: 0.8428 (pt) REVERT: F 70 MET cc_start: 0.7012 (tpp) cc_final: 0.6643 (tpp) REVERT: F 75 PHE cc_start: 0.8495 (m-80) cc_final: 0.7554 (m-80) REVERT: F 158 TYR cc_start: 0.8142 (t80) cc_final: 0.7935 (t80) REVERT: F 177 PHE cc_start: 0.9080 (t80) cc_final: 0.8742 (t80) REVERT: F 185 MET cc_start: 0.7345 (tpt) cc_final: 0.7141 (tpt) REVERT: F 188 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8677 (pp) REVERT: H 37 ILE cc_start: 0.8171 (mt) cc_final: 0.7961 (tp) REVERT: H 41 LEU cc_start: 0.7651 (tp) cc_final: 0.7431 (tp) REVERT: H 49 GLN cc_start: 0.8350 (tp-100) cc_final: 0.8093 (tp-100) REVERT: H 52 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8238 (mmtp) REVERT: H 59 GLU cc_start: 0.6101 (pp20) cc_final: 0.5699 (tm-30) outliers start: 23 outliers final: 11 residues processed: 129 average time/residue: 0.1602 time to fit residues: 25.8129 Evaluate side-chains 124 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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 186 LEU 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 12 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 31 optimal weight: 0.2980 chunk 47 optimal weight: 0.4980 chunk 25 optimal weight: 0.2980 chunk 18 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** E 228 GLN E 229 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.245666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.194463 restraints weight = 5467.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.199872 restraints weight = 3039.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.203117 restraints weight = 2070.896| |-----------------------------------------------------------------------------| r_work (final): 0.4475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4298 Z= 0.208 Angle : 0.646 9.182 5818 Z= 0.334 Chirality : 0.037 0.136 726 Planarity : 0.003 0.022 666 Dihedral : 4.600 22.345 688 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.47 % Favored : 95.14 % Rotamer: Outliers : 5.00 % Allowed : 21.30 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.38), residues: 514 helix: 1.70 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -2.72 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 PHE 0.012 0.001 PHE F 177 TYR 0.024 0.002 TYR F 100 ARG 0.005 0.000 ARG D 51 *********************** 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 138 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.486 Fit side-chains REVERT: C 41 LEU cc_start: 0.7564 (tt) cc_final: 0.7360 (tt) REVERT: D 49 GLN cc_start: 0.8668 (tm-30) cc_final: 0.7996 (tm-30) REVERT: E 214 ILE cc_start: 0.8763 (pt) cc_final: 0.8443 (pt) REVERT: E 227 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8064 (tp-100) REVERT: F 70 MET cc_start: 0.7092 (tpp) cc_final: 0.6693 (tpp) REVERT: F 75 PHE cc_start: 0.8551 (m-80) cc_final: 0.8078 (m-80) REVERT: F 158 TYR cc_start: 0.8344 (t80) cc_final: 0.8048 (t80) REVERT: F 185 MET cc_start: 0.7345 (tpt) cc_final: 0.7056 (tpt) REVERT: F 188 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8679 (pp) REVERT: H 41 LEU cc_start: 0.7655 (tp) cc_final: 0.7437 (tp) REVERT: H 49 GLN cc_start: 0.8458 (tp-100) cc_final: 0.8188 (tp-100) REVERT: H 50 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8434 (p) outliers start: 23 outliers final: 14 residues processed: 128 average time/residue: 0.1520 time to fit residues: 24.4587 Evaluate side-chains 130 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.4847 r_free = 0.4847 target = 0.251634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.198802 restraints weight = 5310.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.204353 restraints weight = 2906.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.208141 restraints weight = 1993.960| |-----------------------------------------------------------------------------| r_work (final): 0.4505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4298 Z= 0.177 Angle : 0.641 9.190 5818 Z= 0.327 Chirality : 0.037 0.136 726 Planarity : 0.003 0.019 666 Dihedral : 4.467 24.345 688 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.47 % Favored : 95.14 % Rotamer: Outliers : 4.35 % Allowed : 21.74 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.38), residues: 514 helix: 1.75 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -2.82 (0.59), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 PHE 0.010 0.001 PHE F 177 TYR 0.029 0.002 TYR G 43 ARG 0.005 0.000 ARG D 51 *********************** 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 138 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: C 41 LEU cc_start: 0.7535 (tt) cc_final: 0.7322 (tt) REVERT: D 49 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7814 (tm-30) REVERT: E 214 ILE cc_start: 0.8734 (pt) cc_final: 0.8407 (pt) REVERT: F 70 MET cc_start: 0.7625 (tpp) cc_final: 0.7043 (tpp) REVERT: F 75 PHE cc_start: 0.8615 (m-80) cc_final: 0.8274 (m-80) REVERT: F 158 TYR cc_start: 0.8360 (t80) cc_final: 0.8059 (t80) REVERT: F 185 MET cc_start: 0.7362 (tpt) cc_final: 0.7031 (tpt) REVERT: F 188 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8677 (pp) REVERT: H 49 GLN cc_start: 0.8456 (tp-100) cc_final: 0.8233 (tp-100) REVERT: H 50 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8378 (p) REVERT: H 52 LYS cc_start: 0.8659 (mmtp) cc_final: 0.8291 (mmtp) outliers start: 20 outliers final: 11 residues processed: 131 average time/residue: 0.1468 time to fit residues: 24.3429 Evaluate side-chains 127 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 8 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 10.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.3964 ------------------------------------------------------------------------------- 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 = 0.4788 r_free = 0.4788 target = 0.243216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.191474 restraints weight = 5070.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.196385 restraints weight = 2878.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.199441 restraints weight = 2001.650| |-----------------------------------------------------------------------------| r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4298 Z= 0.251 Angle : 0.712 9.904 5818 Z= 0.364 Chirality : 0.039 0.146 726 Planarity : 0.003 0.023 666 Dihedral : 4.694 20.381 688 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.06 % Favored : 94.55 % Rotamer: Outliers : 5.00 % Allowed : 23.04 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.37), residues: 514 helix: 1.74 (0.25), residues: 406 sheet: None (None), residues: 0 loop : -2.40 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 PHE 0.024 0.002 PHE F 60 TYR 0.025 0.002 TYR F 100 ARG 0.005 0.000 ARG D 51 *********************** 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 143 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.462 Fit side-chains REVERT: B 58 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: D 49 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8024 (tm-30) REVERT: E 214 ILE cc_start: 0.8836 (pt) cc_final: 0.8502 (pt) REVERT: E 227 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8104 (tp-100) REVERT: F 58 GLN cc_start: 0.7889 (mt0) cc_final: 0.7129 (pm20) REVERT: F 70 MET cc_start: 0.7080 (tpp) cc_final: 0.6662 (tpp) REVERT: F 75 PHE cc_start: 0.8634 (m-80) cc_final: 0.8326 (m-80) REVERT: F 158 TYR cc_start: 0.8277 (t80) cc_final: 0.7998 (t80) REVERT: F 185 MET cc_start: 0.7337 (tpt) cc_final: 0.7000 (tpt) REVERT: F 188 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8691 (pp) REVERT: H 49 GLN cc_start: 0.8380 (tp-100) cc_final: 0.8126 (tp-100) REVERT: H 52 LYS cc_start: 0.8664 (mmtp) cc_final: 0.8231 (mmtp) outliers start: 23 outliers final: 19 residues processed: 135 average time/residue: 0.1549 time to fit residues: 26.2860 Evaluate side-chains 135 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 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 F residue 190 ILE Chi-restraints excluded: chain F residue 191 LEU 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 24 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 31 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** 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 = 0.4795 r_free = 0.4795 target = 0.243218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.197335 restraints weight = 4983.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.200640 restraints weight = 3644.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.203743 restraints weight = 2048.871| |-----------------------------------------------------------------------------| r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4298 Z= 0.220 Angle : 0.694 9.024 5818 Z= 0.352 Chirality : 0.038 0.136 726 Planarity : 0.003 0.022 666 Dihedral : 4.572 22.652 688 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.28 % Favored : 95.33 % Rotamer: Outliers : 5.00 % Allowed : 24.57 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.37), residues: 514 helix: 1.68 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.79 (0.56), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 PHE 0.022 0.001 PHE F 60 TYR 0.027 0.002 TYR F 100 ARG 0.005 0.000 ARG D 51 *********************** 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 138 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: D 49 GLN cc_start: 0.8434 (tm-30) cc_final: 0.7830 (tm-30) REVERT: E 214 ILE cc_start: 0.8798 (pt) cc_final: 0.8424 (pt) REVERT: E 227 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8228 (tp-100) REVERT: E 228 GLN cc_start: 0.7023 (tm-30) cc_final: 0.6493 (tm-30) REVERT: F 58 GLN cc_start: 0.7621 (mt0) cc_final: 0.7059 (pm20) REVERT: F 70 MET cc_start: 0.7335 (tpp) cc_final: 0.6680 (tpp) REVERT: F 75 PHE cc_start: 0.8598 (m-80) cc_final: 0.8348 (m-80) REVERT: F 188 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8634 (pp) REVERT: H 49 GLN cc_start: 0.8207 (tp-100) cc_final: 0.7941 (tp-100) REVERT: H 50 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8377 (p) REVERT: H 52 LYS cc_start: 0.8558 (mmtp) cc_final: 0.8067 (mmtp) outliers start: 23 outliers final: 17 residues processed: 128 average time/residue: 0.1480 time to fit residues: 24.1664 Evaluate side-chains 131 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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 177 PHE Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain H residue 27 ILE 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 26 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 22 optimal weight: 0.3980 chunk 43 optimal weight: 0.3980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4816 r_free = 0.4816 target = 0.245825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.193413 restraints weight = 5096.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.198597 restraints weight = 2856.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.201938 restraints weight = 1981.577| |-----------------------------------------------------------------------------| r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4298 Z= 0.216 Angle : 0.706 9.244 5818 Z= 0.355 Chirality : 0.038 0.144 726 Planarity : 0.003 0.021 666 Dihedral : 4.585 24.171 688 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.67 % Favored : 95.14 % Rotamer: Outliers : 4.57 % Allowed : 26.30 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.37), residues: 514 helix: 1.70 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.84 (0.55), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 PHE 0.021 0.001 PHE F 102 TYR 0.025 0.002 TYR F 100 ARG 0.005 0.000 ARG D 51 *********************** 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 133 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: D 49 GLN cc_start: 0.8453 (tm-30) cc_final: 0.7863 (tm-30) REVERT: E 214 ILE cc_start: 0.8811 (pt) cc_final: 0.8486 (pt) REVERT: E 227 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8257 (tp-100) REVERT: E 228 GLN cc_start: 0.7081 (tm-30) cc_final: 0.6539 (tm-30) REVERT: F 58 GLN cc_start: 0.7854 (mt0) cc_final: 0.7097 (pm20) REVERT: F 70 MET cc_start: 0.7516 (tpp) cc_final: 0.6956 (tpp) REVERT: F 75 PHE cc_start: 0.8588 (m-80) cc_final: 0.7933 (m-80) REVERT: F 188 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8685 (pp) REVERT: H 49 GLN cc_start: 0.8356 (tp-100) cc_final: 0.8074 (tp-100) REVERT: H 50 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8454 (p) REVERT: H 52 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8279 (mmtp) outliers start: 21 outliers final: 16 residues processed: 124 average time/residue: 0.1534 time to fit residues: 24.1512 Evaluate side-chains 130 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 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 177 PHE Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 191 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 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4834 r_free = 0.4834 target = 0.248319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.200145 restraints weight = 5006.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.204521 restraints weight = 3614.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.206552 restraints weight = 2142.211| |-----------------------------------------------------------------------------| r_work (final): 0.4505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4298 Z= 0.188 Angle : 0.694 9.626 5818 Z= 0.346 Chirality : 0.037 0.141 726 Planarity : 0.003 0.020 666 Dihedral : 4.427 26.274 688 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.28 % Favored : 95.53 % Rotamer: Outliers : 3.04 % Allowed : 27.83 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.37), residues: 514 helix: 1.79 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.85 (0.54), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 PHE 0.020 0.001 PHE F 60 TYR 0.025 0.002 TYR F 100 ARG 0.007 0.000 ARG D 51 ********************** 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 124 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: C 52 LYS cc_start: 0.8321 (tptp) cc_final: 0.7069 (mttp) REVERT: D 49 GLN cc_start: 0.8487 (tm-30) cc_final: 0.7888 (tm-30) REVERT: E 214 ILE cc_start: 0.8789 (pt) cc_final: 0.8435 (pt) REVERT: E 227 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8220 (tp-100) REVERT: E 228 GLN cc_start: 0.7140 (tm-30) cc_final: 0.6906 (tm-30) REVERT: F 58 GLN cc_start: 0.7613 (mt0) cc_final: 0.7187 (pm20) REVERT: F 70 MET cc_start: 0.7479 (tpp) cc_final: 0.7117 (tpp) REVERT: F 188 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8643 (pp) REVERT: H 49 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7991 (tp-100) REVERT: H 52 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8321 (mmtp) outliers start: 14 outliers final: 11 residues processed: 118 average time/residue: 0.1466 time to fit residues: 21.8583 Evaluate side-chains 119 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 D residue 31 ILE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 64 THR 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 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.0670 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 0.0470 chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 = 0.4860 r_free = 0.4860 target = 0.251123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.203596 restraints weight = 4979.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.210229 restraints weight = 3316.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.210954 restraints weight = 1906.881| |-----------------------------------------------------------------------------| r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.3186 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= 0.180 Angle : 0.695 9.264 5818 Z= 0.344 Chirality : 0.037 0.138 726 Planarity : 0.003 0.020 666 Dihedral : 4.444 26.330 688 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.28 % Favored : 95.53 % Rotamer: Outliers : 2.83 % Allowed : 28.04 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.37), residues: 514 helix: 1.90 (0.25), residues: 408 sheet: None (None), residues: 0 loop : -2.58 (0.56), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 PHE 0.019 0.001 PHE F 60 TYR 0.022 0.002 TYR F 100 ARG 0.006 0.000 ARG D 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1620.34 seconds wall clock time: 29 minutes 48.35 seconds (1788.35 seconds total)