Starting phenix.real_space_refine on Wed Aug 5 09:08:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubf_42085/08_2026/8ubf_42085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubf_42085/08_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_42085/08_2026/8ubf_42085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubf_42085/08_2026/8ubf_42085.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubf_42085/08_2026/8ubf_42085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubf_42085/08_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-2.2rc3-6140/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: 2.04, per 1000 atoms: 0.22 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: 1.01 Conformation dependent library (CDL) restraints added in 283.6 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: 1.23 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: 1.65 Time building geometry restraints manager: 1.30 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: 13124 2.41 - 4.83: 425 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=" O4' G I 93 " pdb=" C1' G I 93 " pdb=" N9 G I 93 " ideal model delta sigma weight residual 108.50 111.79 -3.29 7.00e-01 2.04e+00 2.21e+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: 1391 0.087 - 0.174: 185 0.174 - 0.262: 8 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.800 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.060 ------------------------------------------------------------------------------- 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= 0.376 Angle : 1.023 12.072 13604 Z= 0.641 Chirality : 0.062 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 0.00688 / 0.38 ( 9705) covalent geometry : angle 1.02288 / 0.64 (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 : 0.299 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: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8187 (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 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: 0.6664 (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: 28 residues processed: 422 average time/residue: 0.1358 time to fit residues: 72.7613 Evaluate side-chains 260 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 36 ARG 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 36 ARG 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: 0.5980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.145383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.111086 restraints weight = 20035.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.114160 restraints weight = 12211.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.116150 restraints weight = 9239.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.117260 restraints weight = 7861.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.118079 restraints weight = 7156.075| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9705 Z= 0.208 Angle : 0.809 13.576 13604 Z= 0.432 Chirality : 0.047 0.270 1589 Planarity : 0.007 0.147 1338 Dihedral : 22.675 176.614 2683 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.92 % Allowed : 7.95 % Favored : 91.13 % Rotamer: Outliers : 8.42 % Allowed : 19.29 % 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: -1.78 (0.27), residues: 868 helix: -0.38 (0.19), residues: 655 sheet: -2.31 (1.05), residues: 20 loop : -3.56 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 36 TYR 0.032 0.003 TYR B 69 PHE 0.047 0.003 PHE C 80 TRP 0.016 0.002 TRP B 116 HIS 0.007 0.002 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 ( 9705) covalent geometry : angle 0.80917 / 0.43 (13604) hydrogen bonds : bond 0.06803 / 4.35 ( 552) hydrogen bonds : angle 4.96325 / 3.51 ( 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 323 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 261 time to evaluate : 0.314 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: A 83 ASP cc_start: 0.7428 (m-30) cc_final: 0.7103 (m-30) REVERT: A 107 TYR cc_start: 0.8211 (m-80) cc_final: 0.7816 (m-80) REVERT: A 145 SER cc_start: 0.8679 (m) cc_final: 0.8461 (p) REVERT: A 158 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6722 (mttt) REVERT: A 200 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7465 (mm) REVERT: A 315 LEU cc_start: 0.7192 (tt) cc_final: 0.6962 (tt) REVERT: B 16 ILE cc_start: 0.9650 (OUTLIER) cc_final: 0.9390 (tt) REVERT: B 21 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7411 (tm-30) REVERT: B 80 PHE cc_start: 0.8993 (t80) cc_final: 0.8781 (t80) REVERT: B 122 ARG cc_start: 0.6890 (mtt180) cc_final: 0.6647 (ptt-90) REVERT: C 17 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8631 (m) REVERT: D 16 ILE cc_start: 0.8496 (tt) cc_final: 0.8265 (tt) REVERT: D 44 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7716 (mtm) REVERT: D 56 PHE cc_start: 0.7978 (m-80) cc_final: 0.7767 (m-80) REVERT: D 69 TYR cc_start: 0.8266 (m-10) cc_final: 0.8003 (m-80) REVERT: D 108 GLU cc_start: 0.5757 (tm-30) cc_final: 0.5545 (tm-30) REVERT: E 67 LYS cc_start: 0.8133 (tppt) cc_final: 0.7861 (mptt) REVERT: F 49 LEU cc_start: 0.9086 (tp) cc_final: 0.8868 (tp) REVERT: F 69 TYR cc_start: 0.7866 (m-80) cc_final: 0.7589 (m-80) outliers start: 62 outliers final: 27 residues processed: 296 average time/residue: 0.1089 time to fit residues: 43.2869 Evaluate side-chains 238 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 158 LYS 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 B residue 25 SER Chi-restraints excluded: chain C residue 17 VAL 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 15 LEU 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: 0.6980 chunk 59 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS C 64 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.145208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.110031 restraints weight = 20297.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.113160 restraints weight = 12595.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.115164 restraints weight = 9622.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116365 restraints weight = 8226.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.116921 restraints weight = 7514.239| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9705 Z= 0.176 Angle : 0.711 8.450 13604 Z= 0.379 Chirality : 0.044 0.235 1589 Planarity : 0.006 0.121 1338 Dihedral : 22.061 174.543 2605 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.81 % Allowed : 8.06 % Favored : 91.13 % Rotamer: Outliers : 5.71 % Allowed : 19.70 % Favored : 74.59 % 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: -0.95 (0.28), residues: 868 helix: 0.12 (0.20), residues: 653 sheet: -0.36 (1.17), residues: 18 loop : -3.05 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 36 TYR 0.022 0.002 TYR E 20 PHE 0.046 0.003 PHE C 80 TRP 0.013 0.001 TRP A 303 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 ( 9705) covalent geometry : angle 0.71091 / 0.38 (13604) hydrogen bonds : bond 0.05961 / 3.76 ( 552) hydrogen bonds : angle 4.56219 / 3.20 ( 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 276 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.8179 (m-80) cc_final: 0.7960 (m-80) REVERT: A 145 SER cc_start: 0.8639 (m) cc_final: 0.8350 (p) REVERT: A 200 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7523 (mm) REVERT: B 16 ILE cc_start: 0.9606 (tt) cc_final: 0.9302 (tt) REVERT: C 100 GLU cc_start: 0.6784 (tt0) cc_final: 0.6481 (tt0) REVERT: C 108 GLU cc_start: 0.6656 (tp30) cc_final: 0.6390 (tp30) REVERT: D 21 GLU cc_start: 0.7667 (tp30) cc_final: 0.7353 (tp30) REVERT: D 65 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.6990 (t) REVERT: D 69 TYR cc_start: 0.8245 (m-10) cc_final: 0.7997 (m-80) REVERT: E 19 ARG cc_start: 0.7621 (tpp-160) cc_final: 0.7328 (tpp-160) REVERT: E 108 GLU cc_start: 0.7562 (tp30) cc_final: 0.7151 (tp30) REVERT: F 69 TYR cc_start: 0.7911 (m-80) cc_final: 0.7575 (m-80) outliers start: 42 outliers final: 21 residues processed: 260 average time/residue: 0.1000 time to fit residues: 35.2587 Evaluate side-chains 224 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 181 ILE 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 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 C residue 113 LEU 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 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 16 ILE 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: 0.5980 chunk 8 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN A 92 ASN C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 103 GLN ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4179 r_free = 0.4179 target = 0.144214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.109581 restraints weight = 20480.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.112629 restraints weight = 12595.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.114592 restraints weight = 9518.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.115842 restraints weight = 8055.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.116017 restraints weight = 7333.963| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9705 Z= 0.175 Angle : 0.692 8.805 13604 Z= 0.369 Chirality : 0.043 0.237 1589 Planarity : 0.006 0.111 1338 Dihedral : 21.744 176.766 2587 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.49 % Favored : 91.82 % Rotamer: Outliers : 5.16 % Allowed : 21.33 % Favored : 73.51 % 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: -0.79 (0.29), residues: 868 helix: 0.19 (0.20), residues: 659 sheet: 0.81 (1.39), residues: 18 loop : -2.99 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 22 TYR 0.038 0.002 TYR E 20 PHE 0.046 0.003 PHE C 80 TRP 0.014 0.001 TRP A 303 HIS 0.004 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 9705) covalent geometry : angle 0.69224 / 0.37 (13604) hydrogen bonds : bond 0.05698 / 3.60 ( 552) hydrogen bonds : angle 4.50264 / 3.17 ( 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 247 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.196 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: 0.7193 (m-30) cc_final: 0.6679 (m-30) REVERT: A 145 SER cc_start: 0.8598 (m) cc_final: 0.8253 (p) REVERT: B 16 ILE cc_start: 0.9594 (tt) cc_final: 0.9277 (tt) REVERT: B 63 ASN cc_start: 0.7761 (p0) cc_final: 0.7229 (p0) REVERT: D 44 MET cc_start: 0.8027 (mtm) cc_final: 0.7826 (mtm) REVERT: D 52 GLN cc_start: 0.7820 (tp40) cc_final: 0.7560 (tp40) REVERT: D 65 VAL cc_start: 0.7860 (OUTLIER) cc_final: 0.6962 (t) REVERT: D 69 TYR cc_start: 0.8302 (m-10) cc_final: 0.8041 (m-80) REVERT: F 69 TYR cc_start: 0.7947 (m-80) cc_final: 0.7511 (m-80) outliers start: 38 outliers final: 24 residues processed: 236 average time/residue: 0.0922 time to fit residues: 29.7245 Evaluate side-chains 210 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 94 VAL 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 65 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 53 VAL Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 82 LEU 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: 0.7980 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 91 optimal weight: 30.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 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 = 0.4157 r_free = 0.4157 target = 0.142535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.107822 restraints weight = 20577.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.110703 restraints weight = 12946.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.112531 restraints weight = 9951.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.113391 restraints weight = 8547.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.114247 restraints weight = 7884.671| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 9705 Z= 0.213 Angle : 0.716 10.647 13604 Z= 0.375 Chirality : 0.042 0.236 1589 Planarity : 0.006 0.110 1338 Dihedral : 21.574 179.084 2585 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.72 % Favored : 91.82 % Rotamer: Outliers : 4.48 % Allowed : 23.23 % 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: -0.77 (0.28), residues: 868 helix: 0.21 (0.20), residues: 659 sheet: 0.70 (1.35), residues: 18 loop : -3.00 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 111 TYR 0.027 0.003 TYR E 20 PHE 0.036 0.003 PHE B 80 TRP 0.009 0.001 TRP C 81 HIS 0.008 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 ( 9705) covalent geometry : angle 0.71564 / 0.38 (13604) hydrogen bonds : bond 0.05625 / 3.59 ( 552) hydrogen bonds : angle 4.50388 / 3.19 ( 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 229 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7333 (m-30) cc_final: 0.6860 (m-30) REVERT: A 145 SER cc_start: 0.8557 (m) cc_final: 0.8327 (p) REVERT: A 256 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7260 (mtp85) REVERT: B 16 ILE cc_start: 0.9584 (tt) cc_final: 0.9314 (tt) REVERT: C 108 GLU cc_start: 0.6687 (tp30) cc_final: 0.6428 (tp30) REVERT: D 52 GLN cc_start: 0.7963 (tp40) cc_final: 0.7697 (tp40) REVERT: D 65 VAL cc_start: 0.7841 (OUTLIER) cc_final: 0.6975 (t) REVERT: D 69 TYR cc_start: 0.8269 (m-10) cc_final: 0.8041 (m-80) REVERT: E 108 GLU cc_start: 0.7619 (tp30) cc_final: 0.6470 (tp30) outliers start: 33 outliers final: 22 residues processed: 221 average time/residue: 0.0908 time to fit residues: 27.6250 Evaluate side-chains 211 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 256 ARG 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 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 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 82 LEU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 100 GLU 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: 0.5980 chunk 4 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN D 92 HIS D 98 GLN D 103 GLN ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 GLN F 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.144104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.109395 restraints weight = 20388.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.112373 restraints weight = 12645.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.114283 restraints weight = 9610.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.114669 restraints weight = 8220.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.114669 restraints weight = 7765.836| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5112 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= 0.166 Angle : 0.696 10.310 13604 Z= 0.363 Chirality : 0.042 0.234 1589 Planarity : 0.006 0.110 1338 Dihedral : 21.447 179.901 2583 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.37 % Favored : 92.17 % Rotamer: Outliers : 5.16 % Allowed : 22.42 % Favored : 72.42 % 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: -0.63 (0.28), residues: 868 helix: 0.28 (0.20), residues: 653 sheet: 1.03 (1.36), residues: 18 loop : -2.79 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 111 TYR 0.021 0.002 TYR E 20 PHE 0.049 0.003 PHE B 80 TRP 0.010 0.001 TRP A 303 HIS 0.007 0.001 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 9705) covalent geometry : angle 0.69602 / 0.36 (13604) hydrogen bonds : bond 0.05477 / 3.44 ( 552) hydrogen bonds : angle 4.43990 / 3.16 ( 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 240 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.289 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: 0.7238 (m-30) cc_final: 0.6969 (m-30) REVERT: A 145 SER cc_start: 0.8536 (m) cc_final: 0.8242 (p) REVERT: A 256 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7242 (mtp85) REVERT: B 16 ILE cc_start: 0.9580 (tt) cc_final: 0.9343 (tt) REVERT: B 63 ASN cc_start: 0.7758 (p0) cc_final: 0.7377 (p0) REVERT: C 108 GLU cc_start: 0.6670 (tp30) cc_final: 0.6380 (tp30) REVERT: D 52 GLN cc_start: 0.7765 (tp40) cc_final: 0.7503 (tp40) REVERT: D 64 GLN cc_start: 0.6566 (tp-100) cc_final: 0.6340 (tp-100) REVERT: F 108 GLU cc_start: 0.6805 (tm-30) cc_final: 0.6054 (tm-30) outliers start: 38 outliers final: 24 residues processed: 228 average time/residue: 0.0900 time to fit residues: 27.7532 Evaluate side-chains 213 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 256 ARG 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 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 94 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 44 MET 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 F residue 82 LEU 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: 40.0000 chunk 25 optimal weight: 0.0020 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN C 64 GLN D 32 GLN D 92 HIS D 103 GLN E 38 HIS E 64 GLN F 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.143907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.109973 restraints weight = 20495.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.112938 restraints weight = 12702.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.114700 restraints weight = 9656.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.115563 restraints weight = 8297.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.116482 restraints weight = 7608.965| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5305 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= 0.166 Angle : 0.711 10.642 13604 Z= 0.366 Chirality : 0.042 0.269 1589 Planarity : 0.006 0.111 1338 Dihedral : 21.337 179.837 2582 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.26 % Favored : 92.40 % Rotamer: Outliers : 4.89 % Allowed : 24.18 % Favored : 70.92 % 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: -0.50 (0.29), residues: 868 helix: 0.35 (0.20), residues: 654 sheet: 1.33 (1.40), residues: 18 loop : -2.66 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 119 TYR 0.014 0.002 TYR F 28 PHE 0.043 0.003 PHE B 80 TRP 0.023 0.001 TRP A 303 HIS 0.003 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 9705) covalent geometry : angle 0.71099 / 0.37 (13604) hydrogen bonds : bond 0.05361 / 3.37 ( 552) hydrogen bonds : angle 4.43031 / 3.14 ( 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 233 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.178 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: 0.7260 (m-30) cc_final: 0.6951 (m-30) REVERT: A 145 SER cc_start: 0.8586 (m) cc_final: 0.8321 (p) REVERT: A 210 TRP cc_start: 0.8756 (p-90) cc_final: 0.8041 (p-90) REVERT: B 16 ILE cc_start: 0.9575 (tt) cc_final: 0.9348 (tt) REVERT: B 47 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7846 (mttp) REVERT: C 108 GLU cc_start: 0.6632 (tp30) cc_final: 0.6348 (tp30) REVERT: D 52 GLN cc_start: 0.7935 (tp40) cc_final: 0.7662 (tp40) REVERT: D 89 GLN cc_start: 0.7344 (mm-40) cc_final: 0.7137 (mm-40) REVERT: E 43 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8075 (tm-30) REVERT: F 108 GLU cc_start: 0.6792 (tm-30) cc_final: 0.6472 (tp30) outliers start: 36 outliers final: 27 residues processed: 218 average time/residue: 0.0922 time to fit residues: 27.0393 Evaluate side-chains 214 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 86 VAL 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 47 LYS 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 44 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 97 HIS 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 13 GLN Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 8.9990 chunk 87 optimal weight: 50.0000 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN C 64 GLN D 92 HIS ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 HIS E 64 GLN F 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.143050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.107722 restraints weight = 20406.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.110759 restraints weight = 12763.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.111923 restraints weight = 9786.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.113623 restraints weight = 8616.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.114171 restraints weight = 7791.268| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 9705 Z= 0.200 Angle : 0.722 11.091 13604 Z= 0.373 Chirality : 0.042 0.232 1589 Planarity : 0.007 0.111 1338 Dihedral : 21.267 179.548 2582 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.03 % Favored : 92.74 % Rotamer: Outliers : 4.62 % Allowed : 25.00 % Favored : 70.38 % 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: 0.34 (0.20), residues: 655 sheet: 2.05 (1.40), residues: 17 loop : -2.59 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 83 TYR 0.018 0.002 TYR F 28 PHE 0.039 0.003 PHE B 80 TRP 0.024 0.001 TRP A 303 HIS 0.011 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 9705) covalent geometry : angle 0.72165 / 0.37 (13604) hydrogen bonds : bond 0.05410 / 3.41 ( 552) hydrogen bonds : angle 4.49691 / 3.20 ( 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 224 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.389 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: A 83 ASP cc_start: 0.7402 (m-30) cc_final: 0.7065 (m-30) REVERT: A 145 SER cc_start: 0.8640 (m) cc_final: 0.8364 (p) REVERT: B 16 ILE cc_start: 0.9600 (tt) cc_final: 0.9378 (tt) REVERT: B 47 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7870 (mttp) REVERT: C 108 GLU cc_start: 0.6756 (tp30) cc_final: 0.6424 (tp30) REVERT: D 52 GLN cc_start: 0.8056 (tp40) cc_final: 0.7782 (tp40) REVERT: E 43 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8160 (tm-30) REVERT: F 108 GLU cc_start: 0.6642 (tm-30) cc_final: 0.6422 (tp30) outliers start: 34 outliers final: 26 residues processed: 212 average time/residue: 0.0893 time to fit residues: 25.7440 Evaluate side-chains 211 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 86 VAL 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 47 LYS 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 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 97 HIS 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 F residue 13 GLN Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 100 GLU 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: 0.9980 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN 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 = 0.4174 r_free = 0.4174 target = 0.143939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.110104 restraints weight = 20287.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.113060 restraints weight = 12607.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.114918 restraints weight = 9595.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.116063 restraints weight = 8202.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116357 restraints weight = 7480.928| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 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 0.083 9705 Z= 0.162 Angle : 0.728 11.141 13604 Z= 0.375 Chirality : 0.041 0.235 1589 Planarity : 0.006 0.113 1338 Dihedral : 21.215 179.989 2582 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.80 % Favored : 92.97 % Rotamer: Outliers : 4.21 % Allowed : 25.68 % Favored : 70.11 % 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: -0.39 (0.29), residues: 868 helix: 0.43 (0.20), residues: 650 sheet: 2.30 (1.47), residues: 17 loop : -2.61 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 111 TYR 0.013 0.002 TYR F 28 PHE 0.037 0.002 PHE B 80 TRP 0.027 0.001 TRP A 303 HIS 0.021 0.002 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 9705) covalent geometry : angle 0.72823 / 0.38 (13604) hydrogen bonds : bond 0.05328 / 3.33 ( 552) hydrogen bonds : angle 4.47329 / 3.17 ( 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 224 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.294 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: 0.7229 (m-30) cc_final: 0.6932 (m-30) REVERT: A 145 SER cc_start: 0.8566 (m) cc_final: 0.8333 (p) REVERT: A 210 TRP cc_start: 0.8729 (p-90) cc_final: 0.8019 (p-90) REVERT: A 319 MET cc_start: 0.6943 (ptt) cc_final: 0.6690 (ptp) REVERT: B 16 ILE cc_start: 0.9580 (tt) cc_final: 0.9362 (tt) REVERT: C 108 GLU cc_start: 0.6636 (tp30) cc_final: 0.6406 (tp30) REVERT: D 52 GLN cc_start: 0.7924 (tp40) cc_final: 0.7635 (tp40) REVERT: F 108 GLU cc_start: 0.6684 (tm-30) cc_final: 0.6415 (tp30) outliers start: 31 outliers final: 23 residues processed: 213 average time/residue: 0.0851 time to fit residues: 24.6616 Evaluate side-chains 205 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 86 VAL 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 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 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 GLU 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: 0.5980 chunk 88 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 75 optimal weight: 0.0870 chunk 57 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN ** A 87 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.144533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.110109 restraints weight = 20393.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.113171 restraints weight = 12601.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.115179 restraints weight = 9517.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116377 restraints weight = 8102.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.116925 restraints weight = 7379.554| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 9705 Z= 0.161 Angle : 0.737 11.574 13604 Z= 0.381 Chirality : 0.041 0.227 1589 Planarity : 0.007 0.114 1338 Dihedral : 21.244 179.462 2582 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.57 % Favored : 93.20 % Rotamer: Outliers : 3.26 % Allowed : 26.49 % Favored : 70.24 % 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: -0.41 (0.29), residues: 868 helix: 0.40 (0.20), residues: 648 sheet: 2.24 (1.38), residues: 17 loop : -2.54 (0.46), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 83 TYR 0.017 0.002 TYR E 26 PHE 0.035 0.002 PHE B 80 TRP 0.030 0.001 TRP A 303 HIS 0.012 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 9705) covalent geometry : angle 0.73674 / 0.38 (13604) hydrogen bonds : bond 0.05287 / 3.31 ( 552) hydrogen bonds : angle 4.48072 / 3.19 ( 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 216 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.196 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: 0.7318 (m-30) cc_final: 0.7037 (m-30) REVERT: A 145 SER cc_start: 0.8566 (m) cc_final: 0.8309 (p) REVERT: A 210 TRP cc_start: 0.8744 (p-90) cc_final: 0.8029 (p-90) REVERT: B 16 ILE cc_start: 0.9575 (tt) cc_final: 0.9358 (tt) REVERT: C 108 GLU cc_start: 0.6653 (tp30) cc_final: 0.6374 (tp30) REVERT: D 52 GLN cc_start: 0.7915 (tp40) cc_final: 0.7694 (tp40) REVERT: F 108 GLU cc_start: 0.6587 (tm-30) cc_final: 0.6267 (tp30) outliers start: 24 outliers final: 20 residues processed: 209 average time/residue: 0.0870 time to fit residues: 24.7879 Evaluate side-chains 206 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 86 VAL 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 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 44 MET Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 GLU 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: 0.6980 chunk 59 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 86 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN A 87 GLN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN E 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.144013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.109922 restraints weight = 20361.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.112906 restraints weight = 12643.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.114867 restraints weight = 9599.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.116049 restraints weight = 8152.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.116323 restraints weight = 7420.634| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5824 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= 0.172 Angle : 0.733 10.849 13604 Z= 0.380 Chirality : 0.042 0.225 1589 Planarity : 0.007 0.115 1338 Dihedral : 21.102 179.310 2582 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.14 % Favored : 92.63 % Rotamer: Outliers : 3.12 % Allowed : 27.04 % Favored : 69.84 % 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: -0.46 (0.29), residues: 868 helix: 0.37 (0.20), residues: 648 sheet: 2.28 (1.39), residues: 17 loop : -2.59 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 111 TYR 0.017 0.002 TYR F 26 PHE 0.036 0.003 PHE B 80 TRP 0.029 0.001 TRP A 303 HIS 0.014 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 9705) covalent geometry : angle 0.73265 / 0.38 (13604) hydrogen bonds : bond 0.05285 / 3.31 ( 552) hydrogen bonds : angle 4.50081 / 3.21 ( 1518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1600.97 seconds wall clock time: 28 minutes 20.13 seconds (1700.13 seconds total)