Starting phenix.real_space_refine on Thu Nov 14 05:19:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yvu_39614/11_2024/8yvu_39614.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yvu_39614/11_2024/8yvu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yvu_39614/11_2024/8yvu_39614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yvu_39614/11_2024/8yvu_39614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yvu_39614/11_2024/8yvu_39614.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yvu_39614/11_2024/8yvu_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-5513/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: 3.15, per 1000 atoms: 0.75 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 391.0 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: 0.31 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: 1.03 Time building geometry restraints manager: 1.16 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.680 Find NCS groups from input model: 0.140 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.120 ------------------------------------------------------------------------------- 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 : 0.494 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: 0.1580 time to fit residues: 25.9828 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 : 0.488 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 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 : 0.436 Fit side-chains REVERT: D 49 GLN cc_start: 0.8611 (tm-30) cc_final: 0.7982 (tm-30) REVERT: E 214 ILE cc_start: 0.8827 (pt) cc_final: 0.8526 (pt) REVERT: E 227 GLN cc_start: 0.8501 (tm-30) cc_final: 0.7966 (tp-100) REVERT: E 228 GLN cc_start: 0.7160 (tm-30) cc_final: 0.6700 (tm-30) REVERT: E 229 GLN cc_start: 0.7182 (mm110) cc_final: 0.6963 (mm-40) REVERT: F 70 MET cc_start: 0.7214 (tpp) cc_final: 0.6974 (tpp) REVERT: F 75 PHE cc_start: 0.8552 (m-80) cc_final: 0.7888 (m-80) REVERT: F 158 TYR cc_start: 0.8307 (t80) cc_final: 0.7990 (t80) REVERT: F 185 MET cc_start: 0.7568 (tpt) cc_final: 0.7279 (tpt) REVERT: F 188 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8667 (pp) REVERT: H 41 LEU cc_start: 0.7386 (tp) cc_final: 0.7175 (tp) outliers start: 16 outliers final: 11 residues processed: 118 average time/residue: 0.1641 time to fit residues: 24.1139 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 : 0.489 ------------------------------------------------------------------------------- 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 24 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 4298 Z= 0.554 Angle : 0.933 10.650 5818 Z= 0.497 Chirality : 0.048 0.204 726 Planarity : 0.005 0.044 666 Dihedral : 5.837 29.309 688 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.42 % Favored : 93.19 % Rotamer: Outliers : 5.65 % Allowed : 18.26 % Favored : 76.09 % 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: 0.19 (0.37), residues: 514 helix: 0.86 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -3.07 (0.59), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 103 HIS 0.003 0.001 HIS F 87 PHE 0.031 0.003 PHE A 206 TYR 0.033 0.004 TYR C 26 ARG 0.004 0.001 ARG C 45 *********************** 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 136 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.441 Fit side-chains REVERT: A 205 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.6494 (tm-30) REVERT: A 211 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5544 (pp) REVERT: C 34 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8334 (pt) REVERT: D 55 ILE cc_start: 0.7987 (mm) cc_final: 0.7763 (mm) REVERT: E 214 ILE cc_start: 0.8776 (pt) cc_final: 0.8464 (pt) REVERT: E 231 THR cc_start: 0.8563 (m) cc_final: 0.8330 (m) REVERT: F 75 PHE cc_start: 0.8745 (m-80) cc_final: 0.7897 (m-80) REVERT: F 158 TYR cc_start: 0.8659 (t80) cc_final: 0.8258 (t80) REVERT: F 185 MET cc_start: 0.7602 (tpt) cc_final: 0.7165 (tpt) REVERT: F 188 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8769 (pp) REVERT: H 41 LEU cc_start: 0.7583 (tp) cc_final: 0.7340 (tp) REVERT: H 49 GLN cc_start: 0.8937 (tp-100) cc_final: 0.8686 (tp-100) REVERT: H 52 LYS cc_start: 0.9092 (mmtp) cc_final: 0.8761 (mmtp) outliers start: 26 outliers final: 15 residues processed: 128 average time/residue: 0.1607 time to fit residues: 25.7281 Evaluate side-chains 125 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 34 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 224 ILE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain H residue 50 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4298 Z= 0.195 Angle : 0.645 7.954 5818 Z= 0.341 Chirality : 0.037 0.146 726 Planarity : 0.003 0.027 666 Dihedral : 4.696 19.109 688 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.09 % Favored : 95.53 % Rotamer: Outliers : 4.35 % Allowed : 22.17 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.06 (0.37), residues: 514 helix: 1.53 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -2.75 (0.57), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 103 HIS 0.002 0.000 HIS B 160 PHE 0.017 0.001 PHE A 206 TYR 0.025 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 134 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: D 49 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7734 (tm-30) REVERT: E 214 ILE cc_start: 0.8844 (pt) cc_final: 0.8551 (pt) REVERT: E 227 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8210 (tp-100) REVERT: F 75 PHE cc_start: 0.8472 (m-80) cc_final: 0.8045 (m-80) REVERT: F 158 TYR cc_start: 0.8528 (t80) cc_final: 0.8121 (t80) REVERT: F 185 MET cc_start: 0.7662 (tpt) cc_final: 0.7307 (tpt) REVERT: F 188 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8539 (pp) REVERT: H 49 GLN cc_start: 0.8916 (tp-100) cc_final: 0.8624 (tp-100) outliers start: 20 outliers final: 12 residues processed: 126 average time/residue: 0.1559 time to fit residues: 24.9946 Evaluate side-chains 120 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain H residue 50 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 0.0000 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4298 Z= 0.213 Angle : 0.664 9.405 5818 Z= 0.345 Chirality : 0.038 0.166 726 Planarity : 0.003 0.025 666 Dihedral : 4.668 20.339 688 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.67 % Favored : 94.94 % Rotamer: Outliers : 5.00 % Allowed : 23.48 % Favored : 71.52 % 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: 1.15 (0.37), residues: 514 helix: 1.60 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -2.73 (0.56), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 103 HIS 0.002 0.000 HIS B 160 PHE 0.013 0.001 PHE D 33 TYR 0.026 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 140 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: B 58 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: D 49 GLN cc_start: 0.8441 (tm-30) cc_final: 0.7801 (tm-30) REVERT: E 214 ILE cc_start: 0.8831 (pt) cc_final: 0.8537 (pt) REVERT: F 75 PHE cc_start: 0.8416 (m-80) cc_final: 0.7996 (m-80) REVERT: F 158 TYR cc_start: 0.8540 (t80) cc_final: 0.8119 (t80) REVERT: F 185 MET cc_start: 0.7548 (tpt) cc_final: 0.7130 (tpt) REVERT: F 188 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8554 (pp) REVERT: H 49 GLN cc_start: 0.8910 (tp-100) cc_final: 0.8594 (tp-100) REVERT: H 52 LYS cc_start: 0.8908 (mmtp) cc_final: 0.8528 (mmtp) outliers start: 23 outliers final: 14 residues processed: 131 average time/residue: 0.1505 time to fit residues: 24.7587 Evaluate side-chains 129 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 D residue 31 ILE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 50 VAL 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 11 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 0.0770 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.2909 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= 0.199 Angle : 0.672 9.236 5818 Z= 0.344 Chirality : 0.038 0.146 726 Planarity : 0.003 0.023 666 Dihedral : 4.590 21.936 688 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.47 % Favored : 95.14 % Rotamer: Outliers : 5.65 % Allowed : 24.78 % 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: 1.71 (0.25), residues: 406 sheet: None (None), residues: 0 loop : -2.38 (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 0.015 0.001 PHE F 102 TYR 0.027 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 146 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: D 49 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7788 (tm-30) REVERT: E 214 ILE cc_start: 0.8814 (pt) cc_final: 0.8516 (pt) REVERT: E 227 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8234 (tp-100) REVERT: E 228 GLN cc_start: 0.7225 (tm-30) cc_final: 0.6956 (tm-30) REVERT: F 58 GLN cc_start: 0.8078 (mt0) cc_final: 0.7789 (mt0) REVERT: F 75 PHE cc_start: 0.8566 (m-80) cc_final: 0.8208 (m-80) REVERT: F 158 TYR cc_start: 0.8567 (t80) cc_final: 0.8139 (t80) REVERT: F 185 MET cc_start: 0.7563 (tpt) cc_final: 0.7158 (tpt) REVERT: F 188 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8578 (pp) REVERT: H 49 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8260 (tp-100) REVERT: H 52 LYS cc_start: 0.8950 (mmtp) cc_final: 0.8502 (mmtp) outliers start: 26 outliers final: 15 residues processed: 137 average time/residue: 0.1722 time to fit residues: 30.2760 Evaluate side-chains 133 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 50 VAL 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 H residue 50 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 overall best weight: 0.9542 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4298 Z= 0.219 Angle : 0.696 8.987 5818 Z= 0.351 Chirality : 0.038 0.135 726 Planarity : 0.003 0.024 666 Dihedral : 4.622 22.684 688 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.86 % Favored : 94.75 % Rotamer: Outliers : 5.43 % Allowed : 25.87 % Favored : 68.70 % 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: 1.29 (0.37), residues: 514 helix: 1.66 (0.25), residues: 408 sheet: None (None), residues: 0 loop : -2.39 (0.59), residues: 106 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 173 TYR 0.028 0.002 TYR F 100 ARG 0.006 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: 25 poor density : 117 time to evaluate : 0.437 Fit side-chains REVERT: D 49 GLN cc_start: 0.8455 (tm-30) cc_final: 0.7814 (tm-30) REVERT: E 214 ILE cc_start: 0.8809 (pt) cc_final: 0.8506 (pt) REVERT: E 227 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8242 (tp-100) REVERT: E 228 GLN cc_start: 0.7188 (tm-30) cc_final: 0.6915 (tm-30) REVERT: F 58 GLN cc_start: 0.8091 (mt0) cc_final: 0.7891 (mt0) REVERT: F 75 PHE cc_start: 0.8578 (m-80) cc_final: 0.8272 (m-80) REVERT: F 158 TYR cc_start: 0.8569 (t80) cc_final: 0.8158 (t80) REVERT: F 185 MET cc_start: 0.7586 (tpt) cc_final: 0.7161 (tpt) REVERT: F 188 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8570 (pp) REVERT: H 49 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8235 (tp-100) REVERT: H 50 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8407 (p) REVERT: H 52 LYS cc_start: 0.8964 (mmtp) cc_final: 0.8588 (mmtp) outliers start: 25 outliers final: 17 residues processed: 132 average time/residue: 0.1414 time to fit residues: 23.6636 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 : 0.430 ------------------------------------------------------------------------------- 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 46 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 50 VAL 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 H residue 50 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.3150 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= 0.221 Angle : 0.705 8.991 5818 Z= 0.355 Chirality : 0.038 0.145 726 Planarity : 0.003 0.024 666 Dihedral : 4.599 22.834 688 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.67 % Favored : 94.94 % Rotamer: Outliers : 5.43 % Allowed : 27.17 % Favored : 67.39 % 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: 1.14 (0.37), residues: 514 helix: 1.57 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.69 (0.58), 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 0.020 0.001 PHE F 102 TYR 0.026 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 139 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.437 Fit side-chains REVERT: D 49 GLN cc_start: 0.8465 (tm-30) cc_final: 0.7821 (tm-30) REVERT: E 214 ILE cc_start: 0.8716 (pt) cc_final: 0.8412 (pt) REVERT: E 227 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8262 (tp-100) REVERT: E 228 GLN cc_start: 0.7042 (tm-30) cc_final: 0.6529 (tm-30) REVERT: F 75 PHE cc_start: 0.8608 (m-80) cc_final: 0.7953 (m-80) REVERT: F 158 TYR cc_start: 0.8585 (t80) cc_final: 0.8143 (t80) REVERT: F 185 MET cc_start: 0.7596 (tpt) cc_final: 0.7159 (tpt) REVERT: F 188 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8572 (pp) REVERT: H 49 GLN cc_start: 0.8563 (tp-100) cc_final: 0.8260 (tp-100) REVERT: H 50 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8495 (p) REVERT: H 52 LYS cc_start: 0.8920 (mmtp) cc_final: 0.8488 (mmtp) outliers start: 25 outliers final: 17 residues processed: 128 average time/residue: 0.1453 time to fit residues: 23.7575 Evaluate side-chains 132 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 50 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.3241 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= 0.203 Angle : 0.710 9.277 5818 Z= 0.358 Chirality : 0.038 0.177 726 Planarity : 0.003 0.022 666 Dihedral : 4.540 24.367 688 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.67 % Favored : 95.14 % Rotamer: Outliers : 5.00 % Allowed : 27.83 % Favored : 67.17 % 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: 1.17 (0.37), residues: 514 helix: 1.60 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.73 (0.57), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 103 HIS 0.002 0.000 HIS B 160 PHE 0.012 0.001 PHE E 223 TYR 0.028 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 139 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.478 Fit side-chains REVERT: B 188 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7038 (mt) REVERT: D 49 GLN cc_start: 0.8452 (tm-30) cc_final: 0.7816 (tm-30) REVERT: E 214 ILE cc_start: 0.8798 (pt) cc_final: 0.8489 (pt) REVERT: E 227 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8252 (tp-100) REVERT: E 228 GLN cc_start: 0.6976 (tm-30) cc_final: 0.6509 (tm-30) REVERT: F 58 GLN cc_start: 0.8076 (mt0) cc_final: 0.7151 (pm20) REVERT: F 75 PHE cc_start: 0.8610 (m-80) cc_final: 0.8319 (m-80) REVERT: F 158 TYR cc_start: 0.8569 (t80) cc_final: 0.8124 (t80) REVERT: F 188 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8699 (pp) REVERT: H 49 GLN cc_start: 0.8559 (tp-100) cc_final: 0.8244 (tp-100) REVERT: H 50 VAL cc_start: 0.8747 (p) cc_final: 0.8477 (p) REVERT: H 52 LYS cc_start: 0.8929 (mmtp) cc_final: 0.8475 (mmtp) outliers start: 23 outliers final: 17 residues processed: 132 average time/residue: 0.1654 time to fit residues: 27.3481 Evaluate side-chains 130 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 188 LEU 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 D residue 50 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 224 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4298 Z= 0.197 Angle : 0.738 14.358 5818 Z= 0.365 Chirality : 0.038 0.148 726 Planarity : 0.003 0.022 666 Dihedral : 4.499 25.502 688 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.28 % Favored : 95.53 % Rotamer: Outliers : 4.57 % Allowed : 28.26 % Favored : 67.17 % 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 (0.38), residues: 514 helix: 1.68 (0.25), residues: 408 sheet: None (None), residues: 0 loop : -2.41 (0.59), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.001 0.000 HIS B 162 PHE 0.012 0.001 PHE F 60 TYR 0.026 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 135 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.378 Fit side-chains REVERT: B 188 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7037 (mt) REVERT: D 49 GLN cc_start: 0.8455 (tm-30) cc_final: 0.7824 (tm-30) REVERT: E 214 ILE cc_start: 0.8780 (pt) cc_final: 0.8480 (pt) REVERT: E 227 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8267 (tp-100) REVERT: E 228 GLN cc_start: 0.6983 (tm-30) cc_final: 0.6517 (tm-30) REVERT: F 58 GLN cc_start: 0.8071 (mt0) cc_final: 0.7147 (pm20) REVERT: F 75 PHE cc_start: 0.8609 (m-80) cc_final: 0.8154 (m-80) REVERT: F 158 TYR cc_start: 0.8555 (t80) cc_final: 0.8119 (t80) REVERT: F 188 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8723 (pp) REVERT: H 49 GLN cc_start: 0.8558 (tp-100) cc_final: 0.8243 (tp-100) REVERT: H 50 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8359 (p) REVERT: H 52 LYS cc_start: 0.8965 (mmtp) cc_final: 0.8528 (mmtp) outliers start: 21 outliers final: 18 residues processed: 128 average time/residue: 0.1427 time to fit residues: 23.0452 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 : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 219 ASP 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 188 LEU 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 D residue 50 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 224 ILE 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 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.0270 chunk 43 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.4808 r_free = 0.4808 target = 0.243879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.198251 restraints weight = 5004.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.200609 restraints weight = 3156.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.201997 restraints weight = 2572.653| |-----------------------------------------------------------------------------| r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4298 Z= 0.190 Angle : 0.708 9.136 5818 Z= 0.352 Chirality : 0.037 0.138 726 Planarity : 0.003 0.022 666 Dihedral : 4.530 29.444 688 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.28 % Favored : 95.53 % Rotamer: Outliers : 4.35 % Allowed : 28.04 % Favored : 67.61 % 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: 1.36 (0.38), residues: 514 helix: 1.72 (0.25), residues: 408 sheet: None (None), residues: 0 loop : -2.46 (0.59), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.002 0.000 HIS B 160 PHE 0.012 0.001 PHE F 60 TYR 0.024 0.002 TYR D 26 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: 1136.51 seconds wall clock time: 26 minutes 44.67 seconds (1604.67 seconds total)