Starting phenix.real_space_refine on Thu Jul 2 16:09:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubf_42085/07_2026/8ubf_42085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubf_42085/07_2026/8ubf_42085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ubf_42085/07_2026/8ubf_42085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubf_42085/07_2026/8ubf_42085.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubf_42085/07_2026/8ubf_42085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubf_42085/07_2026/8ubf_42085.cif" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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: 5 Type Number sf(0) Gaussians P 102 5.49 5 S 36 5.16 5 C 5560 2.51 5 N 1682 2.21 5 O 1911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9291 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2593 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 10, 'TRANS': 306} Chain breaks: 1 Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "F" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "H" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna3p': 9} Chain: "I" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1973 Classifications: {'RNA': 92} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 42, 'rna3p_pyr': 34} Link IDs: {'rna2p': 16, 'rna3p': 75} Chain breaks: 2 Time building chain proxies: 1.94, per 1000 atoms: 0.21 Number of scatterers: 9291 At special positions: 0 Unit cell: (85, 87, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 102 15.00 O 1911 8.00 N 1682 7.00 C 5560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 263.1 milliseconds 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1654 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 2 sheets defined 76.2% alpha, 1.8% beta 32 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.558A pdb=" N ASP A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.993A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 80 through 91 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.558A pdb=" N GLY A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.591A pdb=" N ALA A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 183 through 199 removed outlier: 3.733A pdb=" N GLN A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 241 Processing helix chain 'A' and resid 275 through 289 removed outlier: 4.021A pdb=" N ARG A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.892A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.901A pdb=" N TYR A 323 " --> pdb=" O MET A 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.748A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 38 through 62 removed outlier: 4.269A pdb=" N VAL B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 removed outlier: 3.880A pdb=" N LEU B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 122 Processing helix chain 'C' and resid 12 through 34 removed outlier: 3.880A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 51 through 60 removed outlier: 3.519A pdb=" N LEU C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 88 removed outlier: 3.584A pdb=" N LEU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 121 Processing helix chain 'D' and resid 14 through 32 removed outlier: 3.825A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 51 through 62 removed outlier: 3.560A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 Processing helix chain 'D' and resid 95 through 121 Processing helix chain 'E' and resid 13 through 34 removed outlier: 3.716A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 65 through 86 removed outlier: 3.637A pdb=" N ASP E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'F' and resid 14 through 32 removed outlier: 4.502A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Proline residue: F 29 - end of helix Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 51 through 61 removed outlier: 3.523A pdb=" N LEU F 55 " --> pdb=" O GLY F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 87 removed outlier: 3.613A pdb=" N GLY F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 93 removed outlier: 3.935A pdb=" N HIS F 92 " --> pdb=" O GLN F 89 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA F 93 " --> pdb=" O LYS F 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 89 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.293A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 213 removed outlier: 3.657A pdb=" N HIS A 133 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 252 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 265 471 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1251 1.31 - 1.44: 3278 1.44 - 1.57: 4914 1.57 - 1.70: 201 1.70 - 1.84: 61 Bond restraints: 9705 Sorted by residual: bond pdb=" N LYS D 90 " pdb=" CA LYS D 90 " ideal model delta sigma weight residual 1.463 1.391 0.073 6.90e-03 2.10e+04 1.11e+02 bond pdb=" CA LYS D 90 " pdb=" C LYS D 90 " ideal model delta sigma weight residual 1.521 1.596 -0.075 1.08e-02 8.57e+03 4.85e+01 bond pdb=" C LYS D 90 " pdb=" O LYS D 90 " ideal model delta sigma weight residual 1.244 1.181 0.062 9.10e-03 1.21e+04 4.71e+01 bond pdb=" N ILE C 88 " pdb=" CA ILE C 88 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" CB TRP A 15 " pdb=" CG TRP A 15 " ideal model delta sigma weight residual 1.498 1.418 0.080 3.10e-02 1.04e+03 6.62e+00 ... (remaining 9700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 13178 2.41 - 4.83: 371 4.83 - 7.24: 41 7.24 - 9.66: 12 9.66 - 12.07: 2 Bond angle restraints: 13604 Sorted by residual: angle pdb=" N PRO C 91 " pdb=" CA PRO C 91 " pdb=" CB PRO C 91 " ideal model delta sigma weight residual 103.25 95.59 7.66 1.05e+00 9.07e-01 5.32e+01 angle pdb=" O LYS D 90 " pdb=" C LYS D 90 " pdb=" N PRO D 91 " ideal model delta sigma weight residual 120.27 125.05 -4.78 6.90e-01 2.10e+00 4.81e+01 angle pdb=" CA LYS D 90 " pdb=" C LYS D 90 " pdb=" N PRO D 91 " ideal model delta sigma weight residual 120.58 116.04 4.54 7.40e-01 1.83e+00 3.76e+01 angle pdb=" C LYS D 90 " pdb=" N PRO D 91 " pdb=" CA PRO D 91 " ideal model delta sigma weight residual 119.84 112.38 7.46 1.25e+00 6.40e-01 3.56e+01 angle pdb=" N GLN F 32 " pdb=" CA GLN F 32 " pdb=" C GLN F 32 " ideal model delta sigma weight residual 113.18 107.68 5.50 1.21e+00 6.83e-01 2.06e+01 ... (remaining 13599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 5242 35.29 - 70.58: 648 70.58 - 105.87: 55 105.87 - 141.15: 1 141.15 - 176.44: 3 Dihedral angle restraints: 5949 sinusoidal: 3385 harmonic: 2564 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 56.23 175.77 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U I 3 " pdb=" C1' U I 3 " pdb=" N1 U I 3 " pdb=" C2 U I 3 " ideal model delta sinusoidal sigma weight residual -160.00 -87.90 -72.10 1 1.50e+01 4.44e-03 2.96e+01 dihedral pdb=" CA ALA A 163 " pdb=" C ALA A 163 " pdb=" N THR A 164 " pdb=" CA THR A 164 " ideal model delta harmonic sigma weight residual 180.00 153.55 26.45 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 5946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1477 0.087 - 0.174: 101 0.174 - 0.262: 6 0.262 - 0.349: 2 0.349 - 0.436: 3 Chirality restraints: 1589 Sorted by residual: chirality pdb=" P U H 118 " pdb=" OP1 U H 118 " pdb=" OP2 U H 118 " pdb=" O5' U H 118 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" P U I 7 " pdb=" OP1 U I 7 " pdb=" OP2 U I 7 " pdb=" O5' U I 7 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CB ILE A 181 " pdb=" CA ILE A 181 " pdb=" CG1 ILE A 181 " pdb=" CG2 ILE A 181 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 1586 not shown) Planarity restraints: 1338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 90 " -0.042 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO C 91 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G I 4 " -0.000 2.00e-02 2.50e+03 1.39e-02 5.79e+00 pdb=" N9 G I 4 " -0.038 2.00e-02 2.50e+03 pdb=" C8 G I 4 " 0.019 2.00e-02 2.50e+03 pdb=" N7 G I 4 " 0.007 2.00e-02 2.50e+03 pdb=" C5 G I 4 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G I 4 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G I 4 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G I 4 " 0.007 2.00e-02 2.50e+03 pdb=" C2 G I 4 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G I 4 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G I 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G I 4 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 231 " 0.024 2.00e-02 2.50e+03 1.78e-02 5.54e+00 pdb=" CG PHE A 231 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 231 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 231 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 231 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 231 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 231 " 0.004 2.00e-02 2.50e+03 ... (remaining 1335 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2729 2.82 - 3.34: 9149 3.34 - 3.86: 18895 3.86 - 4.38: 22753 4.38 - 4.90: 32113 Nonbonded interactions: 85639 Sorted by model distance: nonbonded pdb=" O ARG A 31 " pdb=" OH TYR B 11 " model vdw 2.306 3.040 nonbonded pdb=" OG1 THR A 106 " pdb=" OD2 ASP A 198 " model vdw 2.341 3.040 nonbonded pdb=" O LYS C 90 " pdb=" C PRO C 91 " model vdw 2.369 3.270 nonbonded pdb=" NE2 HIS B 97 " pdb=" OP1 A H 123 " model vdw 2.419 3.120 nonbonded pdb=" O ALA A 108 " pdb=" N ARG A 110 " model vdw 2.420 3.120 ... (remaining 85634 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 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } 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=0.00 max=1.00 mean=0.99 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 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: 0.020 Set scattering table: 0.030 Process input model: 10.230 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 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 : 0.007 0.080 9705 Z= 0.362 Angle : 0.979 12.072 13604 Z= 0.586 Chirality : 0.053 0.436 1589 Planarity : 0.008 0.062 1338 Dihedral : 24.771 176.442 4295 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 3.23 % Allowed : 9.22 % Favored : 87.56 % Rotamer: Outliers : 22.69 % Allowed : 12.64 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.23), residues: 868 helix: -1.94 (0.17), residues: 656 sheet: -3.17 (1.11), residues: 18 loop : -4.21 (0.35), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 30 TYR 0.026 0.005 TYR A 107 PHE 0.040 0.005 PHE A 231 TRP 0.035 0.005 TRP A 309 HIS 0.023 0.003 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.36 ( 9705) covalent geometry : angle 0.97918 / 0.59 (13604) hydrogen bonds : bond 0.19722 / 12.65 ( 552) hydrogen bonds : angle 8.51678 / 5.96 ( 1518) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 331 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8174 (ptm160) REVERT: A 14 THR cc_start: 0.7743 (p) cc_final: 0.7497 (p) REVERT: A 63 TYR cc_start: 0.6104 (m-80) cc_final: 0.5053 (m-80) REVERT: A 99 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7845 (tm-30) REVERT: A 102 LEU cc_start: 0.8435 (mt) cc_final: 0.8208 (mp) REVERT: A 110 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7092 (ptm160) REVERT: A 128 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8626 (ttt180) REVERT: A 145 SER cc_start: 0.8724 (m) cc_final: 0.8502 (p) REVERT: A 156 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8481 (m-30) REVERT: A 158 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6661 (mttt) REVERT: A 200 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7562 (mm) REVERT: A 210 TRP cc_start: 0.9149 (p-90) cc_final: 0.8216 (p-90) REVERT: A 226 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8579 (tp30) REVERT: A 265 ILE cc_start: 0.9212 (mt) cc_final: 0.8940 (tp) REVERT: A 319 MET cc_start: 0.7278 (mtp) cc_final: 0.6980 (ptp) REVERT: B 1 MET cc_start: 0.7587 (tmm) cc_final: 0.7379 (tmm) REVERT: B 2 GLU cc_start: 0.8183 (tp30) cc_final: 0.7458 (pp20) REVERT: B 16 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8749 (tt) REVERT: B 22 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8692 (ttp-170) REVERT: B 65 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.7411 (p) REVERT: B 80 PHE cc_start: 0.8845 (t80) cc_final: 0.8627 (t80) REVERT: B 105 LEU cc_start: 0.8540 (mt) cc_final: 0.8296 (mp) REVERT: B 113 LEU cc_start: 0.9138 (tp) cc_final: 0.8930 (tt) REVERT: B 115 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.9116 (p) REVERT: D 53 VAL cc_start: 0.9239 (t) cc_final: 0.8917 (t) REVERT: D 68 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9094 (mt) REVERT: D 69 TYR cc_start: 0.9126 (m-10) cc_final: 0.8638 (m-80) REVERT: D 77 MET cc_start: 0.8942 (tpt) cc_final: 0.8724 (tpp) REVERT: D 99 VAL cc_start: 0.7994 (t) cc_final: 0.7752 (t) REVERT: D 120 VAL cc_start: 0.8318 (t) cc_final: 0.7814 (m) REVERT: E 43 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: E 56 PHE cc_start: 0.8610 (m-10) cc_final: 0.8342 (m-10) REVERT: E 108 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9081 (tp30) REVERT: F 21 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8508 (tm-30) REVERT: F 22 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8906 (mtm-85) REVERT: F 61 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8214 (tptp) REVERT: F 69 TYR cc_start: 0.8983 (m-80) cc_final: 0.8580 (m-80) outliers start: 167 outliers final: 25 residues processed: 422 average time/residue: 0.1445 time to fit residues: 77.1070 Evaluate side-chains 257 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 61 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0570 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN A 92 ASN A 116 HIS A 209 HIS A 248 HIS A 297 GLN C 92 HIS C 121 ASN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 103 GLN E 32 GLN ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.144770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.109906 restraints weight = 20250.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.113016 restraints weight = 12401.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.114881 restraints weight = 9402.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.116144 restraints weight = 8057.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.116700 restraints weight = 7311.010| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9705 Z= 0.201 Angle : 0.787 14.301 13604 Z= 0.424 Chirality : 0.045 0.239 1589 Planarity : 0.007 0.152 1338 Dihedral : 22.942 174.458 2675 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.64 % Favored : 90.44 % Rotamer: Outliers : 8.56 % Allowed : 18.89 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.27), residues: 868 helix: -0.39 (0.19), residues: 655 sheet: -2.42 (1.04), residues: 20 loop : -3.56 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 111 TYR 0.028 0.003 TYR B 69 PHE 0.047 0.003 PHE C 80 TRP 0.014 0.002 TRP B 116 HIS 0.009 0.002 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 ( 9705) covalent geometry : angle 0.78711 / 0.42 (13604) hydrogen bonds : bond 0.06926 / 4.43 ( 552) hydrogen bonds : angle 5.03259 / 3.55 ( 1518) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 258 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.8295 (m-80) cc_final: 0.8009 (m-80) REVERT: A 145 SER cc_start: 0.8685 (m) cc_final: 0.8461 (p) REVERT: A 158 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6684 (mttt) REVERT: A 200 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7440 (mm) REVERT: A 258 ILE cc_start: 0.8463 (mp) cc_final: 0.8244 (mp) REVERT: A 315 LEU cc_start: 0.7170 (tt) cc_final: 0.6939 (tt) REVERT: B 16 ILE cc_start: 0.9649 (OUTLIER) cc_final: 0.9401 (tt) REVERT: B 80 PHE cc_start: 0.9030 (t80) cc_final: 0.8818 (t80) REVERT: B 122 ARG cc_start: 0.6898 (mtt180) cc_final: 0.6681 (ptt-90) REVERT: D 16 ILE cc_start: 0.8487 (tt) cc_final: 0.8226 (tt) REVERT: D 56 PHE cc_start: 0.7998 (m-80) cc_final: 0.7739 (m-80) REVERT: D 69 TYR cc_start: 0.8292 (m-10) cc_final: 0.8040 (m-80) REVERT: E 55 LEU cc_start: 0.9042 (mt) cc_final: 0.8830 (mp) REVERT: E 67 LYS cc_start: 0.8126 (tppt) cc_final: 0.7785 (mptt) REVERT: F 69 TYR cc_start: 0.7911 (m-80) cc_final: 0.7589 (m-80) outliers start: 63 outliers final: 28 residues processed: 294 average time/residue: 0.1143 time to fit residues: 44.9907 Evaluate side-chains 232 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 77 optimal weight: 0.0670 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN D 98 GLN E 32 GLN E 38 HIS ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.145038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.109909 restraints weight = 20381.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.113056 restraints weight = 12533.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.114946 restraints weight = 9596.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.116177 restraints weight = 8254.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.116838 restraints weight = 7545.080| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9705 Z= 0.171 Angle : 0.713 8.307 13604 Z= 0.382 Chirality : 0.044 0.223 1589 Planarity : 0.007 0.123 1338 Dihedral : 22.184 173.791 2607 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.95 % Favored : 91.24 % Rotamer: Outliers : 5.71 % Allowed : 19.97 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.28), residues: 868 helix: 0.10 (0.20), residues: 657 sheet: -0.97 (1.13), residues: 20 loop : -3.03 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 298 TYR 0.024 0.002 TYR E 20 PHE 0.024 0.003 PHE A 231 TRP 0.013 0.002 TRP A 303 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 ( 9705) covalent geometry : angle 0.71320 / 0.38 (13604) hydrogen bonds : bond 0.05823 / 3.68 ( 552) hydrogen bonds : angle 4.55618 / 3.19 ( 1518) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7108 (m-30) cc_final: 0.6816 (m-30) REVERT: A 145 SER cc_start: 0.8610 (m) cc_final: 0.8301 (p) REVERT: A 200 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7516 (mm) REVERT: B 16 ILE cc_start: 0.9608 (tt) cc_final: 0.9281 (tt) REVERT: C 100 GLU cc_start: 0.6752 (tt0) cc_final: 0.6484 (tt0) REVERT: C 108 GLU cc_start: 0.6603 (tp30) cc_final: 0.6326 (tp30) REVERT: D 21 GLU cc_start: 0.7761 (tp30) cc_final: 0.7473 (tp30) REVERT: D 65 VAL cc_start: 0.7886 (OUTLIER) cc_final: 0.7105 (t) REVERT: D 69 TYR cc_start: 0.8266 (m-10) cc_final: 0.8010 (m-80) REVERT: E 108 GLU cc_start: 0.7701 (tp30) cc_final: 0.6643 (tp30) REVERT: F 69 TYR cc_start: 0.7864 (m-80) cc_final: 0.7528 (m-80) outliers start: 42 outliers final: 20 residues processed: 259 average time/residue: 0.1088 time to fit residues: 38.1846 Evaluate side-chains 219 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 63 optimal weight: 0.6980 chunk 8 optimal weight: 0.0870 chunk 65 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS C 13 GLN D 98 GLN D 103 GLN E 38 HIS F 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.144953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.110907 restraints weight = 20723.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.113864 restraints weight = 12874.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.115798 restraints weight = 9799.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.116920 restraints weight = 8401.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.117330 restraints weight = 7671.755| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9705 Z= 0.170 Angle : 0.692 10.011 13604 Z= 0.368 Chirality : 0.042 0.205 1589 Planarity : 0.006 0.113 1338 Dihedral : 21.858 176.669 2588 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.49 % Favored : 91.71 % Rotamer: Outliers : 4.62 % Allowed : 21.06 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.29), residues: 868 helix: 0.18 (0.20), residues: 661 sheet: 0.05 (1.34), residues: 20 loop : -2.96 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 22 TYR 0.038 0.002 TYR E 20 PHE 0.045 0.003 PHE C 80 TRP 0.015 0.001 TRP A 303 HIS 0.005 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 9705) covalent geometry : angle 0.69164 / 0.37 (13604) hydrogen bonds : bond 0.05578 / 3.53 ( 552) hydrogen bonds : angle 4.48779 / 3.15 ( 1518) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7115 (m-30) cc_final: 0.6838 (m-30) REVERT: A 145 SER cc_start: 0.8554 (m) cc_final: 0.8272 (p) REVERT: A 200 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7662 (mm) REVERT: A 275 SER cc_start: 0.2974 (OUTLIER) cc_final: 0.2636 (t) REVERT: B 16 ILE cc_start: 0.9573 (tt) cc_final: 0.9287 (tt) REVERT: C 108 GLU cc_start: 0.6520 (tp30) cc_final: 0.6313 (tp30) REVERT: D 65 VAL cc_start: 0.7823 (OUTLIER) cc_final: 0.6751 (t) REVERT: D 69 TYR cc_start: 0.8227 (m-10) cc_final: 0.8007 (m-80) REVERT: F 69 TYR cc_start: 0.7912 (m-80) cc_final: 0.7509 (m-80) REVERT: F 108 GLU cc_start: 0.7152 (tp30) cc_final: 0.6915 (tp30) outliers start: 34 outliers final: 21 residues processed: 231 average time/residue: 0.1116 time to fit residues: 34.7458 Evaluate side-chains 207 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 13 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 91 optimal weight: 30.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.144704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.110692 restraints weight = 20734.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.113601 restraints weight = 12770.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.115383 restraints weight = 9652.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.116566 restraints weight = 8258.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.117162 restraints weight = 7556.305| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 9705 Z= 0.182 Angle : 0.680 9.785 13604 Z= 0.361 Chirality : 0.042 0.201 1589 Planarity : 0.007 0.111 1338 Dihedral : 21.663 178.737 2585 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.26 % Favored : 92.17 % Rotamer: Outliers : 4.48 % Allowed : 21.88 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.29), residues: 868 helix: 0.23 (0.20), residues: 660 sheet: 0.93 (1.41), residues: 18 loop : -2.84 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 111 TYR 0.027 0.002 TYR E 20 PHE 0.042 0.003 PHE C 80 TRP 0.009 0.001 TRP A 303 HIS 0.020 0.002 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 9705) covalent geometry : angle 0.68006 / 0.36 (13604) hydrogen bonds : bond 0.05419 / 3.44 ( 552) hydrogen bonds : angle 4.41180 / 3.11 ( 1518) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7123 (m-30) cc_final: 0.6859 (m-30) REVERT: A 145 SER cc_start: 0.8481 (m) cc_final: 0.7872 (t) REVERT: B 16 ILE cc_start: 0.9571 (tt) cc_final: 0.9307 (tt) REVERT: B 63 ASN cc_start: 0.7677 (p0) cc_final: 0.7194 (p0) REVERT: C 108 GLU cc_start: 0.6626 (tp30) cc_final: 0.6276 (tp30) outliers start: 33 outliers final: 24 residues processed: 225 average time/residue: 0.1101 time to fit residues: 33.4951 Evaluate side-chains 210 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 89 optimal weight: 10.9990 chunk 27 optimal weight: 0.2980 chunk 86 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN A 87 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 103 GLN E 64 GLN F 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.144932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.109944 restraints weight = 20384.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.112841 restraints weight = 12816.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.114668 restraints weight = 9813.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.115572 restraints weight = 8428.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.116423 restraints weight = 7749.460| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9705 Z= 0.161 Angle : 0.669 10.342 13604 Z= 0.356 Chirality : 0.040 0.199 1589 Planarity : 0.006 0.111 1338 Dihedral : 21.508 179.679 2582 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.26 % Favored : 92.17 % Rotamer: Outliers : 4.21 % Allowed : 22.55 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.29), residues: 868 helix: 0.30 (0.20), residues: 655 sheet: 0.70 (1.40), residues: 18 loop : -2.73 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 22 TYR 0.022 0.002 TYR E 28 PHE 0.048 0.003 PHE B 80 TRP 0.010 0.001 TRP A 303 HIS 0.011 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 9705) covalent geometry : angle 0.66931 / 0.36 (13604) hydrogen bonds : bond 0.05339 / 3.38 ( 552) hydrogen bonds : angle 4.37646 / 3.09 ( 1518) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7206 (m-30) cc_final: 0.6928 (m-30) REVERT: A 145 SER cc_start: 0.8588 (m) cc_final: 0.7868 (t) REVERT: B 16 ILE cc_start: 0.9581 (tt) cc_final: 0.9315 (tt) REVERT: C 108 GLU cc_start: 0.6599 (tp30) cc_final: 0.6233 (tp30) REVERT: D 44 MET cc_start: 0.8020 (mtm) cc_final: 0.7804 (mtm) REVERT: D 52 GLN cc_start: 0.7687 (tp40) cc_final: 0.7443 (tp-100) outliers start: 31 outliers final: 22 residues processed: 217 average time/residue: 0.0961 time to fit residues: 28.4519 Evaluate side-chains 203 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 91 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 0.0980 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 0.0870 chunk 3 optimal weight: 0.0370 chunk 30 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN D 92 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 GLN F 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.145444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.110803 restraints weight = 21060.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.113957 restraints weight = 12987.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.115895 restraints weight = 9883.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.117064 restraints weight = 8448.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.117467 restraints weight = 7714.823| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 9705 Z= 0.152 Angle : 0.683 10.524 13604 Z= 0.360 Chirality : 0.040 0.198 1589 Planarity : 0.007 0.111 1338 Dihedral : 21.378 179.788 2582 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.68 % Favored : 92.97 % Rotamer: Outliers : 4.35 % Allowed : 23.37 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.29), residues: 868 helix: 0.31 (0.20), residues: 658 sheet: 0.87 (1.44), residues: 18 loop : -2.59 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 83 TYR 0.036 0.002 TYR D 69 PHE 0.044 0.003 PHE B 80 TRP 0.023 0.001 TRP A 303 HIS 0.012 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 9705) covalent geometry : angle 0.68309 / 0.36 (13604) hydrogen bonds : bond 0.05276 / 3.30 ( 552) hydrogen bonds : angle 4.31913 / 3.05 ( 1518) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7198 (m-30) cc_final: 0.6936 (m-30) REVERT: A 145 SER cc_start: 0.8646 (m) cc_final: 0.8006 (t) REVERT: A 210 TRP cc_start: 0.8737 (p-90) cc_final: 0.8041 (p-90) REVERT: B 16 ILE cc_start: 0.9567 (tt) cc_final: 0.9319 (tt) REVERT: B 32 GLN cc_start: 0.7313 (tt0) cc_final: 0.7074 (tt0) REVERT: B 63 ASN cc_start: 0.7622 (p0) cc_final: 0.7355 (p0) REVERT: C 108 GLU cc_start: 0.6446 (tp30) cc_final: 0.6173 (tp30) REVERT: D 52 GLN cc_start: 0.7740 (tp40) cc_final: 0.7525 (tp-100) REVERT: D 111 ARG cc_start: 0.7264 (mtm-85) cc_final: 0.7054 (mtm-85) REVERT: E 43 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8067 (tm-30) REVERT: F 69 TYR cc_start: 0.7946 (m-80) cc_final: 0.7586 (m-80) outliers start: 32 outliers final: 20 residues processed: 223 average time/residue: 0.0966 time to fit residues: 29.2779 Evaluate side-chains 212 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 103 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.8980 chunk 87 optimal weight: 30.0000 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN D 92 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 GLN F 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.144985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.110775 restraints weight = 20752.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.113857 restraints weight = 12780.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.115743 restraints weight = 9677.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.116702 restraints weight = 8268.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.117546 restraints weight = 7608.929| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 9705 Z= 0.174 Angle : 0.707 10.541 13604 Z= 0.369 Chirality : 0.041 0.305 1589 Planarity : 0.006 0.110 1338 Dihedral : 21.296 179.880 2582 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.26 % Favored : 92.51 % Rotamer: Outliers : 3.26 % Allowed : 25.95 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.29), residues: 868 helix: 0.38 (0.20), residues: 653 sheet: 0.97 (1.44), residues: 18 loop : -2.64 (0.46), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 122 TYR 0.015 0.002 TYR F 28 PHE 0.040 0.003 PHE B 80 TRP 0.025 0.001 TRP A 303 HIS 0.014 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 9705) covalent geometry : angle 0.70673 / 0.37 (13604) hydrogen bonds : bond 0.05294 / 3.34 ( 552) hydrogen bonds : angle 4.43291 / 3.12 ( 1518) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7317 (m-30) cc_final: 0.7037 (m-30) REVERT: A 145 SER cc_start: 0.8623 (m) cc_final: 0.7958 (t) REVERT: A 210 TRP cc_start: 0.8772 (p-90) cc_final: 0.8036 (p-90) REVERT: B 16 ILE cc_start: 0.9579 (tt) cc_final: 0.9344 (tt) REVERT: B 32 GLN cc_start: 0.7426 (tt0) cc_final: 0.7215 (tt0) REVERT: B 63 ASN cc_start: 0.7715 (p0) cc_final: 0.7468 (p0) REVERT: B 94 MET cc_start: 0.7605 (mtm) cc_final: 0.7235 (mtm) REVERT: C 108 GLU cc_start: 0.6399 (tp30) cc_final: 0.6189 (tp30) REVERT: F 69 TYR cc_start: 0.7911 (m-80) cc_final: 0.7671 (m-80) outliers start: 24 outliers final: 22 residues processed: 212 average time/residue: 0.1040 time to fit residues: 29.7354 Evaluate side-chains 207 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 57 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 0.0980 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN A 92 ASN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.145209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.110859 restraints weight = 20747.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.113937 restraints weight = 12819.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.115908 restraints weight = 9708.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.117091 restraints weight = 8274.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.117603 restraints weight = 7528.906| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 9705 Z= 0.157 Angle : 0.709 11.002 13604 Z= 0.371 Chirality : 0.041 0.242 1589 Planarity : 0.007 0.112 1338 Dihedral : 21.249 179.540 2582 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.80 % Favored : 92.97 % Rotamer: Outliers : 3.67 % Allowed : 25.68 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.29), residues: 868 helix: 0.35 (0.20), residues: 654 sheet: 1.15 (1.41), residues: 18 loop : -2.55 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 111 TYR 0.052 0.002 TYR D 69 PHE 0.043 0.003 PHE C 80 TRP 0.028 0.001 TRP A 303 HIS 0.021 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 9705) covalent geometry : angle 0.70947 / 0.37 (13604) hydrogen bonds : bond 0.05262 / 3.30 ( 552) hydrogen bonds : angle 4.41039 / 3.11 ( 1518) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7301 (m-30) cc_final: 0.7037 (m-30) REVERT: A 210 TRP cc_start: 0.8745 (p-90) cc_final: 0.8037 (p-90) REVERT: B 16 ILE cc_start: 0.9581 (tt) cc_final: 0.9351 (tt) REVERT: B 32 GLN cc_start: 0.7369 (tt0) cc_final: 0.6788 (tp-100) REVERT: B 63 ASN cc_start: 0.7699 (p0) cc_final: 0.7457 (p0) REVERT: E 43 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8045 (tm-30) REVERT: F 43 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8056 (tt0) REVERT: F 69 TYR cc_start: 0.7916 (m-80) cc_final: 0.7670 (m-80) outliers start: 27 outliers final: 19 residues processed: 218 average time/residue: 0.1058 time to fit residues: 31.4783 Evaluate side-chains 208 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 103 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 50 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 25 optimal weight: 0.0970 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN D 92 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.145380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.111551 restraints weight = 20896.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.114651 restraints weight = 12797.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.116557 restraints weight = 9660.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.117666 restraints weight = 8239.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.118191 restraints weight = 7529.696| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 9705 Z= 0.164 Angle : 0.733 10.866 13604 Z= 0.382 Chirality : 0.041 0.196 1589 Planarity : 0.007 0.113 1338 Dihedral : 21.205 179.299 2582 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.14 % Favored : 92.63 % Rotamer: Outliers : 2.58 % Allowed : 27.04 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.29), residues: 868 helix: 0.34 (0.20), residues: 654 sheet: 1.34 (1.39), residues: 18 loop : -2.53 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 111 TYR 0.014 0.002 TYR F 26 PHE 0.043 0.002 PHE B 80 TRP 0.030 0.001 TRP A 303 HIS 0.013 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 9705) covalent geometry : angle 0.73300 / 0.38 (13604) hydrogen bonds : bond 0.05273 / 3.33 ( 552) hydrogen bonds : angle 4.45496 / 3.14 ( 1518) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7355 (m-30) cc_final: 0.7048 (m-30) REVERT: A 210 TRP cc_start: 0.8751 (p-90) cc_final: 0.8061 (p-90) REVERT: B 16 ILE cc_start: 0.9583 (tt) cc_final: 0.9347 (tt) REVERT: B 32 GLN cc_start: 0.7373 (tt0) cc_final: 0.6825 (tp-100) REVERT: B 63 ASN cc_start: 0.7762 (p0) cc_final: 0.7524 (p0) REVERT: D 52 GLN cc_start: 0.7663 (tp40) cc_final: 0.7422 (tp-100) REVERT: E 43 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8055 (tm-30) REVERT: F 43 GLU cc_start: 0.8248 (tm-30) cc_final: 0.8030 (tt0) REVERT: F 69 TYR cc_start: 0.7917 (m-80) cc_final: 0.7648 (m-80) outliers start: 19 outliers final: 16 residues processed: 213 average time/residue: 0.1084 time to fit residues: 31.3935 Evaluate side-chains 207 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 103 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 32 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS D 92 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.141677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.106445 restraints weight = 20670.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.109219 restraints weight = 13245.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.111054 restraints weight = 10318.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.112108 restraints weight = 8880.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.112267 restraints weight = 8183.447| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 9705 Z= 0.259 Angle : 0.790 10.797 13604 Z= 0.409 Chirality : 0.043 0.276 1589 Planarity : 0.007 0.114 1338 Dihedral : 21.186 179.846 2578 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.03 % Favored : 92.63 % Rotamer: Outliers : 2.72 % Allowed : 26.63 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.28), residues: 868 helix: 0.17 (0.20), residues: 656 sheet: 1.43 (1.42), residues: 18 loop : -2.58 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 111 TYR 0.041 0.003 TYR D 69 PHE 0.047 0.003 PHE B 80 TRP 0.029 0.002 TRP A 303 HIS 0.017 0.002 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.26 ( 9705) covalent geometry : angle 0.78979 / 0.41 (13604) hydrogen bonds : bond 0.05571 / 3.55 ( 552) hydrogen bonds : angle 4.66548 / 3.30 ( 1518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1824.08 seconds wall clock time: 32 minutes 27.54 seconds (1947.54 seconds total)