Starting phenix.real_space_refine on Sun Jun 8 03:41:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubf_42085/06_2025/8ubf_42085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubf_42085/06_2025/8ubf_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_42085/06_2025/8ubf_42085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubf_42085/06_2025/8ubf_42085.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubf_42085/06_2025/8ubf_42085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubf_42085/06_2025/8ubf_42085.cif" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.41, per 1000 atoms: 0.80 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: 2.77 Conformation dependent library (CDL) restraints added in 938.8 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: 4.45 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: 3.21 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1251 1.31 - 1.44: 3278 1.44 - 1.57: 4914 1.57 - 1.70: 201 1.70 - 1.84: 61 Bond restraints: 9705 Sorted by residual: bond pdb=" N LYS D 90 " pdb=" CA LYS D 90 " ideal model delta sigma weight residual 1.463 1.391 0.073 6.90e-03 2.10e+04 1.11e+02 bond pdb=" CA LYS D 90 " pdb=" C LYS D 90 " ideal model delta sigma weight residual 1.521 1.596 -0.075 1.08e-02 8.57e+03 4.85e+01 bond pdb=" C LYS D 90 " pdb=" O LYS D 90 " ideal model delta sigma weight residual 1.244 1.181 0.062 9.10e-03 1.21e+04 4.71e+01 bond pdb=" N ILE C 88 " pdb=" CA ILE C 88 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" CB TRP A 15 " pdb=" CG TRP A 15 " ideal model delta sigma weight residual 1.498 1.418 0.080 3.10e-02 1.04e+03 6.62e+00 ... (remaining 9700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 13178 2.41 - 4.83: 371 4.83 - 7.24: 41 7.24 - 9.66: 12 9.66 - 12.07: 2 Bond angle restraints: 13604 Sorted by residual: angle pdb=" N PRO C 91 " pdb=" CA PRO C 91 " pdb=" CB PRO C 91 " ideal model delta sigma weight residual 103.25 95.59 7.66 1.05e+00 9.07e-01 5.32e+01 angle pdb=" O LYS D 90 " pdb=" C LYS D 90 " pdb=" N PRO D 91 " ideal model delta sigma weight residual 120.27 125.05 -4.78 6.90e-01 2.10e+00 4.81e+01 angle pdb=" CA LYS D 90 " pdb=" C LYS D 90 " pdb=" N PRO D 91 " ideal model delta sigma weight residual 120.58 116.04 4.54 7.40e-01 1.83e+00 3.76e+01 angle pdb=" C LYS D 90 " pdb=" N PRO D 91 " pdb=" CA PRO D 91 " ideal model delta sigma weight residual 119.84 112.38 7.46 1.25e+00 6.40e-01 3.56e+01 angle pdb=" N GLN F 32 " pdb=" CA GLN F 32 " pdb=" C GLN F 32 " ideal model delta sigma weight residual 113.18 107.68 5.50 1.21e+00 6.83e-01 2.06e+01 ... (remaining 13599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 5242 35.29 - 70.58: 648 70.58 - 105.87: 55 105.87 - 141.15: 1 141.15 - 176.44: 3 Dihedral angle restraints: 5949 sinusoidal: 3385 harmonic: 2564 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 56.23 175.77 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U I 3 " pdb=" C1' U I 3 " pdb=" N1 U I 3 " pdb=" C2 U I 3 " ideal model delta sinusoidal sigma weight residual -160.00 -87.90 -72.10 1 1.50e+01 4.44e-03 2.96e+01 dihedral pdb=" CA ALA A 163 " pdb=" C ALA A 163 " pdb=" N THR A 164 " pdb=" CA THR A 164 " ideal model delta harmonic sigma weight residual 180.00 153.55 26.45 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 5946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1477 0.087 - 0.174: 101 0.174 - 0.262: 6 0.262 - 0.349: 2 0.349 - 0.436: 3 Chirality restraints: 1589 Sorted by residual: chirality pdb=" P U H 118 " pdb=" OP1 U H 118 " pdb=" OP2 U H 118 " pdb=" O5' U H 118 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" P U I 7 " pdb=" OP1 U I 7 " pdb=" OP2 U I 7 " pdb=" O5' U I 7 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CB ILE A 181 " pdb=" CA ILE A 181 " pdb=" CG1 ILE A 181 " pdb=" CG2 ILE A 181 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 1586 not shown) Planarity restraints: 1338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 90 " -0.042 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO C 91 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G I 4 " -0.000 2.00e-02 2.50e+03 1.39e-02 5.79e+00 pdb=" N9 G I 4 " -0.038 2.00e-02 2.50e+03 pdb=" C8 G I 4 " 0.019 2.00e-02 2.50e+03 pdb=" N7 G I 4 " 0.007 2.00e-02 2.50e+03 pdb=" C5 G I 4 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G I 4 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G I 4 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G I 4 " 0.007 2.00e-02 2.50e+03 pdb=" C2 G I 4 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G I 4 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G I 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G I 4 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 231 " 0.024 2.00e-02 2.50e+03 1.78e-02 5.54e+00 pdb=" CG PHE A 231 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 231 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 231 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 231 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 231 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 231 " 0.004 2.00e-02 2.50e+03 ... (remaining 1335 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2729 2.82 - 3.34: 9149 3.34 - 3.86: 18895 3.86 - 4.38: 22753 4.38 - 4.90: 32113 Nonbonded interactions: 85639 Sorted by model distance: nonbonded pdb=" O ARG A 31 " pdb=" OH TYR B 11 " model vdw 2.306 3.040 nonbonded pdb=" OG1 THR A 106 " pdb=" OD2 ASP A 198 " model vdw 2.341 3.040 nonbonded pdb=" O LYS C 90 " pdb=" C PRO C 91 " model vdw 2.369 3.270 nonbonded pdb=" NE2 HIS B 97 " pdb=" OP1 A H 123 " model vdw 2.419 3.120 nonbonded pdb=" O ALA A 108 " pdb=" N ARG A 110 " model vdw 2.420 3.120 ... (remaining 85634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 255.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 31.110 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 290.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 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= 0.348 Angle : 0.979 12.072 13604 Z= 0.549 Chirality : 0.053 0.436 1589 Planarity : 0.008 0.062 1338 Dihedral : 24.771 176.442 4295 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 3.23 % Allowed : 9.22 % Favored : 87.56 % Rotamer: Outliers : 22.69 % Allowed : 12.64 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.035 0.005 TRP A 309 HIS 0.023 0.003 HIS C 38 PHE 0.040 0.005 PHE A 231 TYR 0.026 0.005 TYR A 107 ARG 0.010 0.001 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.19722 ( 552) hydrogen bonds : angle 8.51678 ( 1518) covalent geometry : bond 0.00687 ( 9705) covalent geometry : angle 0.97915 (13604) *********************** 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 : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8174 (ptm160) REVERT: A 14 THR cc_start: 0.7743 (p) cc_final: 0.7498 (p) REVERT: A 63 TYR cc_start: 0.6104 (m-80) cc_final: 0.5053 (m-80) REVERT: A 99 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7845 (tm-30) REVERT: A 102 LEU cc_start: 0.8435 (mt) cc_final: 0.8208 (mp) REVERT: A 110 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7092 (ptm160) REVERT: A 128 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8626 (ttt180) REVERT: A 145 SER cc_start: 0.8724 (m) cc_final: 0.8502 (p) REVERT: A 156 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8481 (m-30) REVERT: A 158 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6661 (mttt) REVERT: A 200 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7562 (mm) REVERT: A 210 TRP cc_start: 0.9149 (p-90) cc_final: 0.8217 (p-90) REVERT: A 226 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8579 (tp30) REVERT: A 258 ILE cc_start: 0.8718 (mp) cc_final: 0.8469 (mp) REVERT: A 319 MET cc_start: 0.7278 (mtp) cc_final: 0.6976 (ptp) REVERT: B 1 MET cc_start: 0.7588 (tmm) cc_final: 0.7367 (tmm) REVERT: B 2 GLU cc_start: 0.8183 (tp30) cc_final: 0.7793 (tp30) REVERT: B 16 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8748 (tt) REVERT: B 22 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8693 (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: 0.8305 (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: 0.8916 (t) REVERT: D 68 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9067 (mt) REVERT: D 69 TYR cc_start: 0.9126 (m-10) cc_final: 0.8639 (m-80) REVERT: D 77 MET cc_start: 0.8942 (tpt) cc_final: 0.8725 (tpp) REVERT: D 99 VAL cc_start: 0.7994 (t) cc_final: 0.7751 (t) REVERT: D 120 VAL cc_start: 0.8318 (t) cc_final: 0.7815 (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: 0.8509 (tm-30) REVERT: F 22 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8906 (mtm-85) REVERT: F 61 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8214 (tptp) REVERT: F 69 TYR cc_start: 0.8983 (m-80) cc_final: 0.8580 (m-80) outliers start: 167 outliers final: 25 residues processed: 422 average time/residue: 0.3072 time to fit residues: 162.2691 Evaluate side-chains 255 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 61 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 92 ASN A 297 GLN C 92 HIS C 121 ASN D 32 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.144722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.109580 restraints weight = 20289.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.112627 restraints weight = 12483.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.114556 restraints weight = 9486.128| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3973 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= 0.187 Angle : 0.720 11.553 13604 Z= 0.375 Chirality : 0.042 0.254 1589 Planarity : 0.007 0.139 1338 Dihedral : 22.247 172.274 2675 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 1.04 % Allowed : 8.18 % Favored : 90.78 % Rotamer: Outliers : 6.79 % Allowed : 18.34 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.29), residues: 868 helix: 0.10 (0.20), residues: 654 sheet: -1.84 (1.07), residues: 20 loop : -3.20 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 116 HIS 0.004 0.001 HIS B 38 PHE 0.042 0.003 PHE C 80 TYR 0.027 0.002 TYR B 69 ARG 0.007 0.001 ARG E 36 Details of bonding type rmsd hydrogen bonds : bond 0.05430 ( 552) hydrogen bonds : angle 4.58255 ( 1518) covalent geometry : bond 0.00419 ( 9705) covalent geometry : angle 0.71993 (13604) *********************** 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 305 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.7949 (m-80) cc_final: 0.7659 (m-80) REVERT: A 145 SER cc_start: 0.8636 (m) cc_final: 0.8384 (p) REVERT: A 158 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6698 (mttt) REVERT: A 200 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7556 (mm) REVERT: B 16 ILE cc_start: 0.9614 (tt) cc_final: 0.9307 (tt) REVERT: C 100 GLU cc_start: 0.6817 (tt0) cc_final: 0.6534 (tt0) REVERT: C 108 GLU cc_start: 0.6611 (tp30) cc_final: 0.6251 (tp30) REVERT: D 21 GLU cc_start: 0.7759 (tp30) cc_final: 0.7419 (tp30) REVERT: D 65 VAL cc_start: 0.8064 (OUTLIER) cc_final: 0.7432 (t) REVERT: D 69 TYR cc_start: 0.8322 (m-10) cc_final: 0.8067 (m-80) REVERT: F 69 TYR cc_start: 0.7935 (m-80) cc_final: 0.7604 (m-80) REVERT: F 90 LYS cc_start: 0.7974 (tptt) cc_final: 0.7731 (tptt) outliers start: 50 outliers final: 17 residues processed: 290 average time/residue: 0.2888 time to fit residues: 110.4423 Evaluate side-chains 224 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 275 SER Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU 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 63 ASN Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 95 THR 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 9 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN D 98 GLN D 103 GLN ** 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 = 0.4180 r_free = 0.4180 target = 0.144490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.109358 restraints weight = 20577.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.112402 restraints weight = 12712.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.114309 restraints weight = 9728.946| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9705 Z= 0.162 Angle : 0.667 7.756 13604 Z= 0.342 Chirality : 0.040 0.197 1589 Planarity : 0.006 0.120 1338 Dihedral : 21.530 179.194 2597 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.72 % Favored : 91.59 % Rotamer: Outliers : 4.48 % Allowed : 22.96 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.29), residues: 868 helix: 0.62 (0.20), residues: 648 sheet: -0.08 (1.25), residues: 18 loop : -2.66 (0.47), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 303 HIS 0.006 0.001 HIS A 328 PHE 0.019 0.002 PHE B 80 TYR 0.012 0.002 TYR F 26 ARG 0.008 0.001 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 552) hydrogen bonds : angle 4.25113 ( 1518) covalent geometry : bond 0.00362 ( 9705) covalent geometry : angle 0.66714 (13604) *********************** 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 260 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 1.571 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: 0.7234 (m-30) cc_final: 0.6914 (m-30) REVERT: A 210 TRP cc_start: 0.8710 (p-90) cc_final: 0.7962 (p-90) REVERT: B 16 ILE cc_start: 0.9616 (tt) cc_final: 0.9339 (tt) REVERT: B 119 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6687 (ttp-110) REVERT: C 108 GLU cc_start: 0.6588 (tp30) cc_final: 0.6170 (tp30) REVERT: C 117 ILE cc_start: 0.8906 (mt) cc_final: 0.8539 (mt) REVERT: D 44 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7741 (mtm) REVERT: D 52 GLN cc_start: 0.7684 (tp40) cc_final: 0.7435 (tp-100) REVERT: E 108 GLU cc_start: 0.7624 (tp30) cc_final: 0.7360 (tp30) REVERT: F 13 GLN cc_start: 0.6503 (OUTLIER) cc_final: 0.6262 (mp10) outliers start: 33 outliers final: 17 residues processed: 251 average time/residue: 0.3957 time to fit residues: 131.9461 Evaluate side-chains 211 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 44 MET 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 53 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 95 THR 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 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN D 98 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 = 0.4176 r_free = 0.4176 target = 0.144055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.109384 restraints weight = 20749.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.112241 restraints weight = 12984.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.114110 restraints weight = 9932.180| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9705 Z= 0.169 Angle : 0.671 9.449 13604 Z= 0.342 Chirality : 0.039 0.196 1589 Planarity : 0.006 0.113 1338 Dihedral : 21.242 179.948 2582 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.72 % Favored : 91.71 % Rotamer: Outliers : 3.80 % Allowed : 23.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.29), residues: 868 helix: 0.64 (0.20), residues: 654 sheet: 0.36 (1.38), residues: 20 loop : -2.52 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 81 HIS 0.003 0.001 HIS A 313 PHE 0.040 0.003 PHE B 80 TYR 0.014 0.002 TYR F 28 ARG 0.007 0.001 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.04762 ( 552) hydrogen bonds : angle 4.17688 ( 1518) covalent geometry : bond 0.00381 ( 9705) covalent geometry : angle 0.67094 (13604) *********************** 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 236 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7285 (m-30) cc_final: 0.6995 (m-30) REVERT: A 210 TRP cc_start: 0.8732 (p-90) cc_final: 0.7972 (p-90) REVERT: B 2 GLU cc_start: 0.7705 (pm20) cc_final: 0.7496 (pp20) REVERT: B 16 ILE cc_start: 0.9587 (tt) cc_final: 0.9381 (tt) REVERT: B 63 ASN cc_start: 0.7683 (p0) cc_final: 0.7176 (p0) REVERT: C 108 GLU cc_start: 0.6566 (tp30) cc_final: 0.6330 (tp30) REVERT: D 44 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7694 (mtm) REVERT: F 69 TYR cc_start: 0.7997 (m-80) cc_final: 0.7538 (m-80) REVERT: F 108 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6321 (tm-30) outliers start: 28 outliers final: 13 residues processed: 223 average time/residue: 0.2528 time to fit residues: 74.5521 Evaluate side-chains 207 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain F residue 95 THR 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 1 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 19 optimal weight: 0.0040 chunk 65 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 57 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS C 64 GLN D 52 GLN D 98 GLN D 103 GLN 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 = 0.4168 r_free = 0.4168 target = 0.143369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.109038 restraints weight = 20876.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.112017 restraints weight = 12854.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.113826 restraints weight = 9796.347| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9705 Z= 0.171 Angle : 0.664 8.300 13604 Z= 0.342 Chirality : 0.039 0.193 1589 Planarity : 0.006 0.111 1338 Dihedral : 21.081 178.556 2578 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.91 % Favored : 92.63 % Rotamer: Outliers : 3.94 % Allowed : 25.41 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.29), residues: 868 helix: 0.63 (0.20), residues: 655 sheet: 0.57 (1.40), residues: 20 loop : -2.47 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 303 HIS 0.005 0.001 HIS F 92 PHE 0.050 0.003 PHE C 80 TYR 0.020 0.002 TYR E 20 ARG 0.011 0.001 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 552) hydrogen bonds : angle 4.19359 ( 1518) covalent geometry : bond 0.00388 ( 9705) covalent geometry : angle 0.66412 (13604) *********************** 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 243 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7366 (m-30) cc_final: 0.7084 (m-30) REVERT: A 135 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7728 (tp) REVERT: A 210 TRP cc_start: 0.8741 (p-90) cc_final: 0.8198 (p-90) REVERT: A 216 ASP cc_start: 0.6728 (m-30) cc_final: 0.6421 (m-30) REVERT: B 79 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.7150 (mtt-85) REVERT: D 44 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7701 (mtm) REVERT: E 13 GLN cc_start: 0.7320 (tt0) cc_final: 0.6939 (tt0) REVERT: E 14 MET cc_start: 0.6657 (mmt) cc_final: 0.6267 (tpt) REVERT: F 43 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8152 (tt0) REVERT: F 69 TYR cc_start: 0.7909 (m-80) cc_final: 0.7466 (m-80) REVERT: F 108 GLU cc_start: 0.6704 (tm-30) cc_final: 0.6224 (tm-30) outliers start: 29 outliers final: 17 residues processed: 233 average time/residue: 0.2613 time to fit residues: 80.0146 Evaluate side-chains 216 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 16 ILE 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 95 THR Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 97 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.0070 chunk 2 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 90 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 85 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 87 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 98 GLN E 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.144422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.109923 restraints weight = 20794.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.112952 restraints weight = 12845.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.114528 restraints weight = 9802.121| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 9705 Z= 0.145 Angle : 0.672 10.290 13604 Z= 0.345 Chirality : 0.038 0.186 1589 Planarity : 0.006 0.111 1338 Dihedral : 20.915 177.386 2578 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.49 % Favored : 92.05 % Rotamer: Outliers : 3.40 % Allowed : 26.90 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.29), residues: 868 helix: 0.62 (0.20), residues: 659 sheet: 0.68 (1.33), residues: 20 loop : -2.49 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 303 HIS 0.006 0.001 HIS A 5 PHE 0.029 0.002 PHE C 80 TYR 0.013 0.002 TYR E 26 ARG 0.010 0.001 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 552) hydrogen bonds : angle 4.22773 ( 1518) covalent geometry : bond 0.00320 ( 9705) covalent geometry : angle 0.67247 (13604) *********************** 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 233 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7221 (m-30) cc_final: 0.6952 (m-30) REVERT: A 135 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7752 (tp) REVERT: A 210 TRP cc_start: 0.8677 (p-90) cc_final: 0.8149 (p-90) REVERT: A 216 ASP cc_start: 0.6699 (m-30) cc_final: 0.6454 (m-30) REVERT: B 63 ASN cc_start: 0.7765 (p0) cc_final: 0.7405 (p0) REVERT: B 108 GLU cc_start: 0.7741 (pt0) cc_final: 0.7535 (pt0) REVERT: D 44 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7721 (mtm) REVERT: E 14 MET cc_start: 0.6633 (mmt) cc_final: 0.6212 (tpt) REVERT: E 108 GLU cc_start: 0.7758 (tp30) cc_final: 0.6798 (tp30) REVERT: F 69 TYR cc_start: 0.7947 (m-80) cc_final: 0.7684 (m-80) REVERT: F 108 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6253 (tm-30) outliers start: 25 outliers final: 16 residues processed: 226 average time/residue: 0.2445 time to fit residues: 73.7560 Evaluate side-chains 206 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 244 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 25 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain E residue 30 ILE 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 72 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN C 98 GLN D 52 GLN D 92 HIS D 98 GLN D 103 GLN 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 = 0.4176 r_free = 0.4176 target = 0.143691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.109963 restraints weight = 20781.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.112877 restraints weight = 12956.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.114681 restraints weight = 9860.567| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.6322 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= 0.156 Angle : 0.675 10.216 13604 Z= 0.345 Chirality : 0.039 0.183 1589 Planarity : 0.006 0.111 1338 Dihedral : 20.817 177.254 2578 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.68 % Favored : 92.86 % Rotamer: Outliers : 3.40 % Allowed : 27.17 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.29), residues: 868 helix: 0.63 (0.20), residues: 659 sheet: 1.59 (1.27), residues: 18 loop : -2.35 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 303 HIS 0.006 0.001 HIS A 5 PHE 0.031 0.002 PHE C 80 TYR 0.040 0.002 TYR D 69 ARG 0.009 0.001 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.04769 ( 552) hydrogen bonds : angle 4.25800 ( 1518) covalent geometry : bond 0.00353 ( 9705) covalent geometry : angle 0.67484 (13604) *********************** 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 226 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7308 (m-30) cc_final: 0.7036 (m-30) REVERT: A 135 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7768 (tp) REVERT: A 210 TRP cc_start: 0.8681 (p-90) cc_final: 0.8151 (p-90) REVERT: A 216 ASP cc_start: 0.6787 (m-30) cc_final: 0.6533 (m-30) REVERT: A 275 SER cc_start: 0.3971 (OUTLIER) cc_final: 0.3739 (t) REVERT: D 44 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7616 (mtm) REVERT: E 14 MET cc_start: 0.6712 (mmt) cc_final: 0.6207 (tpt) REVERT: E 108 GLU cc_start: 0.7461 (tp30) cc_final: 0.6490 (tp30) REVERT: F 69 TYR cc_start: 0.7789 (m-80) cc_final: 0.7472 (m-80) REVERT: F 108 GLU cc_start: 0.6834 (tm-30) cc_final: 0.6170 (tm-30) outliers start: 25 outliers final: 17 residues processed: 218 average time/residue: 0.2526 time to fit residues: 74.5059 Evaluate side-chains 213 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 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 25 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 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 103 GLN Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain F residue 97 HIS 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 93 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 chunk 85 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 27 HIS A 87 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN C 64 GLN D 32 GLN D 52 GLN D 92 HIS D 98 GLN E 38 HIS E 64 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.144342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.109921 restraints weight = 20894.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.112913 restraints weight = 12978.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.114835 restraints weight = 9893.788| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.6525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 9705 Z= 0.150 Angle : 0.688 11.223 13604 Z= 0.352 Chirality : 0.039 0.217 1589 Planarity : 0.006 0.112 1338 Dihedral : 20.730 176.652 2578 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.26 % Favored : 92.40 % Rotamer: Outliers : 3.12 % Allowed : 27.58 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.29), residues: 868 helix: 0.60 (0.20), residues: 660 sheet: 1.92 (1.25), residues: 18 loop : -2.27 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 303 HIS 0.006 0.001 HIS A 5 PHE 0.032 0.002 PHE C 80 TYR 0.014 0.002 TYR F 69 ARG 0.013 0.001 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 552) hydrogen bonds : angle 4.27387 ( 1518) covalent geometry : bond 0.00339 ( 9705) covalent geometry : angle 0.68766 (13604) *********************** 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 232 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7331 (m-30) cc_final: 0.7063 (m-30) REVERT: A 135 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7699 (tp) REVERT: A 210 TRP cc_start: 0.8681 (p-90) cc_final: 0.8138 (p-90) REVERT: A 216 ASP cc_start: 0.6757 (m-30) cc_final: 0.6440 (m-30) REVERT: A 275 SER cc_start: 0.4048 (OUTLIER) cc_final: 0.3762 (t) REVERT: D 43 GLU cc_start: 0.7267 (mt-10) cc_final: 0.7048 (tt0) REVERT: D 44 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7613 (mtm) REVERT: D 95 THR cc_start: 0.7197 (OUTLIER) cc_final: 0.6911 (m) REVERT: E 14 MET cc_start: 0.6600 (mmt) cc_final: 0.6119 (tpt) REVERT: E 43 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7915 (tm-30) REVERT: F 43 GLU cc_start: 0.8254 (tm-30) cc_final: 0.8039 (tt0) REVERT: F 65 VAL cc_start: 0.8442 (t) cc_final: 0.8214 (p) REVERT: F 69 TYR cc_start: 0.7834 (m-80) cc_final: 0.7623 (m-80) REVERT: F 108 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6103 (tm-30) outliers start: 23 outliers final: 16 residues processed: 225 average time/residue: 0.2528 time to fit residues: 75.9807 Evaluate side-chains 215 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 132 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 244 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 B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 18 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 79 optimal weight: 0.1980 chunk 51 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 57 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN C 64 GLN D 32 GLN D 92 HIS E 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.144960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.111007 restraints weight = 20841.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.114051 restraints weight = 12968.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.115928 restraints weight = 9881.458| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.6661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 9705 Z= 0.148 Angle : 0.695 11.051 13604 Z= 0.353 Chirality : 0.039 0.216 1589 Planarity : 0.006 0.113 1338 Dihedral : 20.664 176.105 2578 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.91 % Favored : 92.74 % Rotamer: Outliers : 2.72 % Allowed : 28.67 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.29), residues: 868 helix: 0.58 (0.20), residues: 663 sheet: 2.37 (1.30), residues: 18 loop : -2.18 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 303 HIS 0.010 0.001 HIS A 27 PHE 0.035 0.002 PHE C 80 TYR 0.022 0.002 TYR E 20 ARG 0.009 0.001 ARG E 22 Details of bonding type rmsd hydrogen bonds : bond 0.04708 ( 552) hydrogen bonds : angle 4.35664 ( 1518) covalent geometry : bond 0.00334 ( 9705) covalent geometry : angle 0.69505 (13604) *********************** 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 217 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7321 (m-30) cc_final: 0.7069 (m-30) REVERT: A 135 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7668 (tp) REVERT: A 210 TRP cc_start: 0.8671 (p-90) cc_final: 0.8125 (p-90) REVERT: A 216 ASP cc_start: 0.6716 (m-30) cc_final: 0.6373 (m-30) REVERT: A 275 SER cc_start: 0.4126 (OUTLIER) cc_final: 0.3847 (t) REVERT: C 108 GLU cc_start: 0.6377 (tp30) cc_final: 0.6104 (tp30) REVERT: D 43 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7035 (tt0) REVERT: D 44 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7573 (mtm) REVERT: E 14 MET cc_start: 0.6577 (mmt) cc_final: 0.6128 (tpt) REVERT: F 69 TYR cc_start: 0.7835 (m-80) cc_final: 0.7618 (m-80) REVERT: F 108 GLU cc_start: 0.6838 (tm-30) cc_final: 0.6145 (tm-30) outliers start: 20 outliers final: 15 residues processed: 210 average time/residue: 0.2322 time to fit residues: 65.4674 Evaluate side-chains 210 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 244 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 25 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 59 optimal weight: 2.9990 chunk 51 optimal weight: 0.0970 chunk 70 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN C 64 GLN D 32 GLN D 52 GLN D 92 HIS E 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.144368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.110279 restraints weight = 20634.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.113203 restraints weight = 12808.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.115037 restraints weight = 9750.202| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.6856 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= 0.163 Angle : 0.716 11.031 13604 Z= 0.366 Chirality : 0.040 0.235 1589 Planarity : 0.006 0.109 1338 Dihedral : 20.633 179.333 2578 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.83 % Favored : 91.94 % Rotamer: Outliers : 2.31 % Allowed : 27.85 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.29), residues: 868 helix: 0.57 (0.20), residues: 664 sheet: 2.73 (1.34), residues: 18 loop : -2.19 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 303 HIS 0.005 0.001 HIS A 313 PHE 0.036 0.003 PHE C 80 TYR 0.026 0.002 TYR E 20 ARG 0.015 0.001 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 552) hydrogen bonds : angle 4.39990 ( 1518) covalent geometry : bond 0.00374 ( 9705) covalent geometry : angle 0.71597 (13604) ********************** 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 213 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7355 (m-30) cc_final: 0.7065 (m-30) REVERT: A 135 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7714 (tp) REVERT: A 145 SER cc_start: 0.8579 (m) cc_final: 0.8361 (p) REVERT: A 210 TRP cc_start: 0.8684 (p-90) cc_final: 0.8142 (p-90) REVERT: A 216 ASP cc_start: 0.6764 (m-30) cc_final: 0.6406 (m-30) REVERT: C 108 GLU cc_start: 0.6382 (tp30) cc_final: 0.6146 (tp30) REVERT: D 13 GLN cc_start: 0.5654 (mt0) cc_final: 0.5418 (mt0) REVERT: D 44 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7605 (mtm) REVERT: E 14 MET cc_start: 0.6546 (mmt) cc_final: 0.6169 (tpt) REVERT: F 69 TYR cc_start: 0.7920 (m-80) cc_final: 0.7676 (m-80) REVERT: F 108 GLU cc_start: 0.6821 (tm-30) cc_final: 0.6153 (tm-30) outliers start: 17 outliers final: 14 residues processed: 206 average time/residue: 0.2324 time to fit residues: 64.5817 Evaluate side-chains 207 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 25 optimal weight: 0.0000 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 61 optimal weight: 0.0470 overall best weight: 0.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN D 92 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.146476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.112664 restraints weight = 20722.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.115762 restraints weight = 12744.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.117600 restraints weight = 9654.160| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.7065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 9705 Z= 0.145 Angle : 0.701 10.961 13604 Z= 0.359 Chirality : 0.039 0.183 1589 Planarity : 0.006 0.110 1338 Dihedral : 20.523 177.072 2578 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.91 % Favored : 92.86 % Rotamer: Outliers : 2.58 % Allowed : 28.26 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.29), residues: 868 helix: 0.65 (0.20), residues: 663 sheet: 2.91 (1.35), residues: 18 loop : -2.18 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 303 HIS 0.008 0.001 HIS A 313 PHE 0.037 0.002 PHE C 80 TYR 0.025 0.001 TYR E 20 ARG 0.008 0.001 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 552) hydrogen bonds : angle 4.36604 ( 1518) covalent geometry : bond 0.00328 ( 9705) covalent geometry : angle 0.70144 (13604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4119.40 seconds wall clock time: 74 minutes 42.70 seconds (4482.70 seconds total)