Starting phenix.real_space_refine on Thu Mar 6 00:04:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yvu_39614/03_2025/8yvu_39614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yvu_39614/03_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_39614/03_2025/8yvu_39614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yvu_39614/03_2025/8yvu_39614.map" model { file = "/net/cci-nas-00/data/ceres_data/8yvu_39614/03_2025/8yvu_39614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yvu_39614/03_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-5624/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: 3.05, per 1000 atoms: 0.72 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: 1.00 Conformation dependent library (CDL) restraints added in 471.5 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: 0.33 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: 0.98 Time building geometry restraints manager: 1.19 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: 2.120 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.350 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.590 ------------------------------------------------------------------------------- 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 : 0.479 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: 0.1526 time to fit residues: 25.1752 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 : 0.418 ------------------------------------------------------------------------------- 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 = 59)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.200717 restraints weight = 5253.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.206709 restraints weight = 2818.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.210438 restraints weight = 1900.677| |-----------------------------------------------------------------------------| r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 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 23.973 688 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 : 0.459 Fit side-chains REVERT: D 49 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8029 (tm-30) REVERT: E 214 ILE cc_start: 0.8778 (pt) cc_final: 0.8495 (pt) REVERT: E 227 GLN cc_start: 0.8460 (tm-30) cc_final: 0.7993 (tp-100) REVERT: E 228 GLN cc_start: 0.7197 (tm-30) cc_final: 0.6762 (tm-30) REVERT: F 70 MET cc_start: 0.7024 (tpp) cc_final: 0.6766 (tpp) REVERT: F 75 PHE cc_start: 0.8517 (m-80) cc_final: 0.7884 (m-80) REVERT: F 158 TYR cc_start: 0.8178 (t80) cc_final: 0.7902 (t80) REVERT: F 185 MET cc_start: 0.7504 (tpt) cc_final: 0.7265 (tpt) REVERT: F 188 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8694 (pp) REVERT: H 41 LEU cc_start: 0.7408 (tp) cc_final: 0.7183 (tp) outliers start: 16 outliers final: 11 residues processed: 118 average time/residue: 0.2265 time to fit residues: 33.4113 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 : 0.909 ------------------------------------------------------------------------------- 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: 4.9990 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4833 r_free = 0.4833 target = 0.248105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.199097 restraints weight = 4901.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.204243 restraints weight = 2659.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.207268 restraints weight = 1793.783| |-----------------------------------------------------------------------------| r_work (final): 0.4518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4298 Z= 0.201 Angle : 0.638 8.433 5818 Z= 0.331 Chirality : 0.037 0.131 726 Planarity : 0.003 0.024 666 Dihedral : 4.804 32.255 688 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.09 % Favored : 95.53 % Rotamer: Outliers : 3.04 % Allowed : 16.74 % Favored : 80.22 % 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: 1.64 (0.25), residues: 420 sheet: None (None), residues: 0 loop : -2.58 (0.64), residues: 94 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 0.019 0.002 PHE F 177 TYR 0.022 0.002 TYR F 100 ARG 0.004 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 128 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.467 Fit side-chains REVERT: D 49 GLN cc_start: 0.8633 (tm-30) cc_final: 0.7983 (tm-30) REVERT: E 214 ILE cc_start: 0.8755 (pt) cc_final: 0.8420 (pt) REVERT: F 70 MET cc_start: 0.6995 (tpp) cc_final: 0.6640 (tpp) REVERT: F 75 PHE cc_start: 0.8448 (m-80) cc_final: 0.8056 (m-80) REVERT: F 158 TYR cc_start: 0.8076 (t80) cc_final: 0.7848 (t80) REVERT: F 188 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8695 (pp) REVERT: H 41 LEU cc_start: 0.7451 (tp) cc_final: 0.7217 (tp) outliers start: 14 outliers final: 10 residues processed: 120 average time/residue: 0.2446 time to fit residues: 36.5216 Evaluate side-chains 112 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 24 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4796 r_free = 0.4796 target = 0.243869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.193551 restraints weight = 4981.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.198352 restraints weight = 2798.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.201396 restraints weight = 1921.941| |-----------------------------------------------------------------------------| r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4298 Z= 0.277 Angle : 0.680 8.791 5818 Z= 0.357 Chirality : 0.039 0.148 726 Planarity : 0.003 0.027 666 Dihedral : 4.827 21.137 688 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.25 % Favored : 94.36 % Rotamer: Outliers : 5.65 % Allowed : 21.09 % Favored : 73.26 % 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: 1.19 (0.37), residues: 514 helix: 1.62 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -3.07 (0.56), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 PHE 0.017 0.002 PHE D 33 TYR 0.022 0.002 TYR F 100 ARG 0.004 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 139 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.499 Fit side-chains REVERT: D 49 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8017 (tm-30) REVERT: E 214 ILE cc_start: 0.8808 (pt) cc_final: 0.8467 (pt) REVERT: F 70 MET cc_start: 0.7025 (tpp) cc_final: 0.6654 (tpp) REVERT: F 75 PHE cc_start: 0.8375 (m-80) cc_final: 0.8093 (m-80) REVERT: F 158 TYR cc_start: 0.8140 (t80) cc_final: 0.7887 (t80) REVERT: F 177 PHE cc_start: 0.8907 (t80) cc_final: 0.8523 (t80) REVERT: F 188 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8691 (pp) REVERT: H 41 LEU cc_start: 0.7642 (tp) cc_final: 0.7389 (tp) REVERT: H 49 GLN cc_start: 0.8358 (tp-100) cc_final: 0.8106 (tp-100) REVERT: H 52 LYS cc_start: 0.8536 (mmtp) cc_final: 0.8229 (mmtp) REVERT: H 59 GLU cc_start: 0.5859 (pp20) cc_final: 0.5638 (tm-30) outliers start: 26 outliers final: 11 residues processed: 129 average time/residue: 0.2410 time to fit residues: 39.2132 Evaluate side-chains 121 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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: 5.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 18 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.4835 r_free = 0.4835 target = 0.246475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.195359 restraints weight = 5428.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.200798 restraints weight = 3017.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.204045 restraints weight = 2076.553| |-----------------------------------------------------------------------------| r_work (final): 0.4489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4298 Z= 0.195 Angle : 0.634 9.473 5818 Z= 0.329 Chirality : 0.037 0.138 726 Planarity : 0.003 0.020 666 Dihedral : 4.537 22.625 688 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.89 % Favored : 95.72 % Rotamer: Outliers : 5.22 % Allowed : 20.65 % Favored : 74.13 % 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: 1.86 (0.25), residues: 406 sheet: None (None), residues: 0 loop : -2.33 (0.58), residues: 108 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 0.013 0.001 PHE F 177 TYR 0.025 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: 24 poor density : 114 time to evaluate : 0.509 Fit side-chains REVERT: B 58 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: D 49 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7794 (tm-30) REVERT: E 214 ILE cc_start: 0.8759 (pt) cc_final: 0.8441 (pt) REVERT: E 227 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8078 (tp-100) REVERT: F 58 GLN cc_start: 0.7956 (mt0) cc_final: 0.7680 (mt0) REVERT: F 70 MET cc_start: 0.7077 (tpp) cc_final: 0.6679 (tpp) REVERT: F 75 PHE cc_start: 0.8447 (m-80) cc_final: 0.8101 (m-80) REVERT: F 158 TYR cc_start: 0.8354 (t80) cc_final: 0.8060 (t80) REVERT: F 177 PHE cc_start: 0.8881 (t80) cc_final: 0.8671 (t80) REVERT: F 188 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8682 (pp) REVERT: H 41 LEU cc_start: 0.7620 (tp) cc_final: 0.7390 (tp) REVERT: H 49 GLN cc_start: 0.8423 (tp-100) cc_final: 0.8137 (tp-100) REVERT: H 50 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8428 (p) outliers start: 24 outliers final: 13 residues processed: 129 average time/residue: 0.1865 time to fit residues: 30.0323 Evaluate side-chains 126 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 4 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4837 r_free = 0.4837 target = 0.248708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.197932 restraints weight = 4990.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.203146 restraints weight = 2756.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.206535 restraints weight = 1887.561| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4298 Z= 0.200 Angle : 0.647 9.379 5818 Z= 0.332 Chirality : 0.037 0.136 726 Planarity : 0.003 0.019 666 Dihedral : 4.492 23.441 688 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.47 % Favored : 95.14 % Rotamer: Outliers : 4.78 % Allowed : 22.61 % 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 (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: 1.41 (0.37), residues: 514 helix: 1.73 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -2.73 (0.60), residues: 96 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 0.018 0.001 PHE H 33 TYR 0.025 0.002 TYR F 100 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 137 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.436 Fit side-chains REVERT: D 49 GLN cc_start: 0.8410 (tm-30) cc_final: 0.7817 (tm-30) REVERT: E 214 ILE cc_start: 0.8753 (pt) cc_final: 0.8418 (pt) REVERT: F 70 MET cc_start: 0.7039 (tpp) cc_final: 0.6630 (tpp) REVERT: F 75 PHE cc_start: 0.8497 (m-80) cc_final: 0.8253 (m-80) REVERT: F 158 TYR cc_start: 0.8227 (t80) cc_final: 0.7969 (t80) REVERT: F 188 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8692 (pp) REVERT: H 41 LEU cc_start: 0.7650 (tp) cc_final: 0.7421 (tp) REVERT: H 49 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8175 (tp-100) REVERT: H 50 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8394 (p) REVERT: H 52 LYS cc_start: 0.8632 (mmtp) cc_final: 0.8273 (mmtp) outliers start: 22 outliers final: 13 residues processed: 128 average time/residue: 0.1596 time to fit residues: 25.8514 Evaluate side-chains 128 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4792 r_free = 0.4792 target = 0.242996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.190613 restraints weight = 5093.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.195605 restraints weight = 2891.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.198738 restraints weight = 2017.016| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 4298 Z= 0.286 Angle : 0.703 9.014 5818 Z= 0.364 Chirality : 0.039 0.149 726 Planarity : 0.003 0.024 666 Dihedral : 4.755 19.553 688 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.06 % Favored : 94.55 % Rotamer: Outliers : 5.65 % Allowed : 23.70 % Favored : 70.65 % 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: 1.16 (0.37), residues: 514 helix: 1.61 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -3.12 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 PHE 0.022 0.002 PHE H 33 TYR 0.029 0.002 TYR G 43 ARG 0.004 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 142 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: D 49 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8030 (tm-30) REVERT: E 214 ILE cc_start: 0.8842 (pt) cc_final: 0.8526 (pt) REVERT: E 227 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8248 (tp-100) REVERT: F 58 GLN cc_start: 0.7961 (mt0) cc_final: 0.7200 (pm20) REVERT: F 70 MET cc_start: 0.7009 (tpp) cc_final: 0.6615 (tpp) REVERT: F 75 PHE cc_start: 0.8510 (m-80) cc_final: 0.7758 (m-80) REVERT: F 158 TYR cc_start: 0.8297 (t80) cc_final: 0.7980 (t80) REVERT: F 188 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8698 (pp) REVERT: H 41 LEU cc_start: 0.7655 (tp) cc_final: 0.7408 (tp) REVERT: H 49 GLN cc_start: 0.8372 (tp-100) cc_final: 0.8128 (tp-100) REVERT: H 52 LYS cc_start: 0.8697 (mmtp) cc_final: 0.8242 (mmtp) outliers start: 26 outliers final: 22 residues processed: 131 average time/residue: 0.1752 time to fit residues: 28.8819 Evaluate side-chains 132 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU 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 189 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 224 ILE 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 191 LEU Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 37 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 24 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.0040 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.0970 chunk 23 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.4824 r_free = 0.4824 target = 0.247257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.196928 restraints weight = 4943.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.202112 restraints weight = 2738.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.205486 restraints weight = 1887.792| |-----------------------------------------------------------------------------| r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4298 Z= 0.209 Angle : 0.672 9.213 5818 Z= 0.341 Chirality : 0.037 0.134 726 Planarity : 0.003 0.020 666 Dihedral : 4.498 23.645 688 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.09 % Favored : 95.53 % Rotamer: Outliers : 3.91 % Allowed : 26.30 % 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 (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: 1.31 (0.37), residues: 514 helix: 1.72 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.79 (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 0.025 0.001 PHE H 33 TYR 0.027 0.002 TYR F 100 ARG 0.007 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 133 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: D 49 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7801 (tm-30) REVERT: E 214 ILE cc_start: 0.8794 (pt) cc_final: 0.8482 (pt) REVERT: E 227 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8239 (tp-100) REVERT: E 228 GLN cc_start: 0.7061 (tm-30) cc_final: 0.6512 (tm-30) REVERT: F 58 GLN cc_start: 0.7900 (mt0) cc_final: 0.7161 (pm20) REVERT: F 70 MET cc_start: 0.7479 (tpp) cc_final: 0.6936 (tpp) REVERT: F 75 PHE cc_start: 0.8444 (m-80) cc_final: 0.8176 (m-80) REVERT: F 158 TYR cc_start: 0.8222 (t80) cc_final: 0.7944 (t80) REVERT: F 188 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8689 (pp) REVERT: H 49 GLN cc_start: 0.8375 (tp-100) cc_final: 0.8072 (tp-100) REVERT: H 50 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8408 (p) REVERT: H 52 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8315 (mmtp) outliers start: 18 outliers final: 9 residues processed: 127 average time/residue: 0.1715 time to fit residues: 27.1842 Evaluate side-chains 122 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 C residue 32 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain E residue 218 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 overall best weight: 0.7542 ------------------------------------------------------------------------------- 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 = 0.4805 r_free = 0.4805 target = 0.244054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.194450 restraints weight = 5037.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.199397 restraints weight = 2833.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.202529 restraints weight = 1965.749| |-----------------------------------------------------------------------------| r_work (final): 0.4492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4298 Z= 0.215 Angle : 0.692 10.203 5818 Z= 0.350 Chirality : 0.037 0.141 726 Planarity : 0.003 0.020 666 Dihedral : 4.517 23.889 688 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.67 % Favored : 95.14 % Rotamer: Outliers : 4.35 % Allowed : 26.09 % Favored : 69.57 % 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: 1.35 (0.37), residues: 514 helix: 1.75 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.78 (0.56), 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 0.028 0.001 PHE F 60 TYR 0.026 0.002 TYR F 100 ARG 0.006 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 131 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.506 Fit side-chains REVERT: D 49 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7845 (tm-30) REVERT: E 214 ILE cc_start: 0.8802 (pt) cc_final: 0.8475 (pt) REVERT: E 227 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8257 (tp-100) REVERT: E 228 GLN cc_start: 0.7082 (tm-30) cc_final: 0.6519 (tm-30) REVERT: F 58 GLN cc_start: 0.7854 (mt0) cc_final: 0.7101 (pm20) REVERT: F 70 MET cc_start: 0.7463 (tpp) cc_final: 0.6919 (tpp) REVERT: F 75 PHE cc_start: 0.8435 (m-80) cc_final: 0.7722 (m-80) REVERT: F 158 TYR cc_start: 0.8183 (t80) cc_final: 0.7899 (t80) REVERT: F 188 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8684 (pp) REVERT: H 49 GLN cc_start: 0.8329 (tp-100) cc_final: 0.8033 (tp-100) REVERT: H 50 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8399 (p) REVERT: H 52 LYS cc_start: 0.8644 (mmtp) cc_final: 0.8298 (mmtp) outliers start: 20 outliers final: 13 residues processed: 122 average time/residue: 0.1470 time to fit residues: 22.7792 Evaluate side-chains 126 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 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 = 0.4802 r_free = 0.4802 target = 0.243697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.193756 restraints weight = 5069.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.198685 restraints weight = 2910.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.201736 restraints weight = 2031.754| |-----------------------------------------------------------------------------| r_work (final): 0.4480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.3049 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= 0.217 Angle : 0.702 9.313 5818 Z= 0.355 Chirality : 0.038 0.137 726 Planarity : 0.003 0.021 666 Dihedral : 4.514 24.252 688 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.47 % Favored : 95.33 % Rotamer: Outliers : 3.04 % Allowed : 27.61 % Favored : 69.35 % 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: 1.32 (0.37), residues: 514 helix: 1.72 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.76 (0.56), 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 0.028 0.001 PHE H 33 TYR 0.025 0.002 TYR F 100 ARG 0.006 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 127 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: B 188 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7246 (mt) REVERT: C 52 LYS cc_start: 0.8370 (tptp) cc_final: 0.7093 (mttp) REVERT: D 49 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7849 (tm-30) REVERT: E 214 ILE cc_start: 0.8802 (pt) cc_final: 0.8481 (pt) REVERT: E 227 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8261 (tp-100) REVERT: E 228 GLN cc_start: 0.7175 (tm-30) cc_final: 0.6890 (tm-30) REVERT: F 58 GLN cc_start: 0.7842 (mt0) cc_final: 0.7088 (pm20) REVERT: F 70 MET cc_start: 0.7476 (tpp) cc_final: 0.6927 (tpp) REVERT: F 75 PHE cc_start: 0.8442 (m-80) cc_final: 0.7792 (m-80) REVERT: F 158 TYR cc_start: 0.8229 (t80) cc_final: 0.7926 (t80) REVERT: F 188 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8681 (pp) REVERT: H 49 GLN cc_start: 0.8354 (tp-100) cc_final: 0.8052 (tp-100) REVERT: H 50 VAL cc_start: 0.8675 (p) cc_final: 0.8398 (p) REVERT: H 52 LYS cc_start: 0.8733 (mmtp) cc_final: 0.8390 (mmtp) outliers start: 14 outliers final: 12 residues processed: 122 average time/residue: 0.1476 time to fit residues: 22.9040 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 : 0.446 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 7 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4811 r_free = 0.4811 target = 0.244635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.195193 restraints weight = 5037.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.200314 restraints weight = 2783.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.203634 restraints weight = 1909.597| |-----------------------------------------------------------------------------| r_work (final): 0.4492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.3139 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= 0.204 Angle : 0.700 9.445 5818 Z= 0.352 Chirality : 0.037 0.135 726 Planarity : 0.003 0.020 666 Dihedral : 4.458 25.313 688 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.47 % Favored : 95.33 % Rotamer: Outliers : 3.26 % Allowed : 27.17 % Favored : 69.57 % 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 (0.37), residues: 514 helix: 1.75 (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 0.018 0.001 TRP B 103 HIS 0.001 0.000 HIS B 160 PHE 0.029 0.001 PHE H 33 TYR 0.023 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: 1993.76 seconds wall clock time: 36 minutes 55.39 seconds (2215.39 seconds total)