Starting phenix.real_space_refine on Thu Jul 2 20:41:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubd_42083/07_2026/8ubd_42083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubd_42083/07_2026/8ubd_42083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ubd_42083/07_2026/8ubd_42083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubd_42083/07_2026/8ubd_42083.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ubd_42083/07_2026/8ubd_42083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubd_42083/07_2026/8ubd_42083.map" } resolution = 3.05 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= 0.031 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 149 5.49 5 S 36 5.16 5 C 6058 2.51 5 N 1869 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10368 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2665 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 11, 'TRANS': 313} 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: "G" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 289 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna3p': 12} Chain: "H" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 270 Classifications: {'RNA': 13} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna3p': 12} Chain: "I" Number of atoms: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2628 Classifications: {'RNA': 123} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 12, 'rna3p_pur': 52, 'rna3p_pyr': 47} Link IDs: {'rna2p': 24, 'rna3p': 98} Chain breaks: 2 Time building chain proxies: 1.95, per 1000 atoms: 0.19 Number of scatterers: 10368 At special positions: 0 Unit cell: (82, 98, 129, 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 149 15.00 O 2256 8.00 N 1869 7.00 C 6058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 265.4 milliseconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1670 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 2 sheets defined 76.1% alpha, 2.0% beta 45 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 32 through 39 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 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 removed outlier: 3.591A pdb=" N ILE A 146 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.606A 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: 3.993A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 removed outlier: 3.566A pdb=" N LYS A 206 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLN A 207 " --> pdb=" O GLU A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 203 through 207' Processing helix chain 'A' and resid 223 through 241 Processing helix chain 'A' and resid 273 through 289 Processing helix chain 'A' and resid 294 through 310 removed outlier: 3.903A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TRP A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 310 " --> pdb=" O HIS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.668A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.516A 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: 4.182A pdb=" N VAL B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 88 removed outlier: 3.501A 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: 3.714A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.609A 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 38 through 50 Processing helix chain 'C' and resid 51 through 60 Processing helix chain 'C' and resid 64 through 87 Processing helix chain 'C' and resid 95 through 121 Processing helix chain 'D' and resid 14 through 34 removed outlier: 3.769A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.596A 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 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 51 through 62 removed outlier: 3.523A 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 32 removed outlier: 3.716A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.608A 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 38 through 50 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 65 through 86 removed outlier: 3.671A 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: 4.488A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.778A 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 38 through 50 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 64 through 87 removed outlier: 3.574A pdb=" N GLY F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 Proline residue: F 91 - end of helix No H-bonds generated for 'chain 'F' and resid 88 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.385A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 213 removed outlier: 3.698A pdb=" N HIS A 133 " --> pdb=" O GLY A 221 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1320 1.31 - 1.44: 3777 1.44 - 1.56: 5444 1.56 - 1.69: 300 1.69 - 1.82: 60 Bond restraints: 10901 Sorted by residual: bond pdb=" CA ASN C 63 " pdb=" CB ASN C 63 " ideal model delta sigma weight residual 1.530 1.637 -0.107 1.69e-02 3.50e+03 4.01e+01 bond pdb=" CA GLU B 100 " pdb=" CB GLU B 100 " ideal model delta sigma weight residual 1.528 1.621 -0.092 1.56e-02 4.11e+03 3.49e+01 bond pdb=" CG MET C 77 " pdb=" SD MET C 77 " ideal model delta sigma weight residual 1.803 1.685 0.118 2.50e-02 1.60e+03 2.22e+01 bond pdb=" O3' G I 53 " pdb=" P U I 54 " ideal model delta sigma weight residual 1.607 1.676 -0.069 1.50e-02 4.44e+03 2.14e+01 bond pdb=" CA ARG B 111 " pdb=" CB ARG B 111 " ideal model delta sigma weight residual 1.529 1.460 0.069 1.55e-02 4.16e+03 2.01e+01 ... (remaining 10896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 15215 5.06 - 10.13: 229 10.13 - 15.19: 6 15.19 - 20.25: 2 20.25 - 25.32: 1 Bond angle restraints: 15453 Sorted by residual: angle pdb=" C3' U I 3 " pdb=" O3' U I 3 " pdb=" P G I 4 " ideal model delta sigma weight residual 120.20 103.76 16.44 1.50e+00 4.44e-01 1.20e+02 angle pdb=" OP2 A I 88 " pdb=" P A I 88 " pdb=" O5' A I 88 " ideal model delta sigma weight residual 108.00 82.68 25.32 3.00e+00 1.11e-01 7.12e+01 angle pdb=" C3' G I 122 " pdb=" O3' G I 122 " pdb=" P A I 123 " ideal model delta sigma weight residual 120.20 108.00 12.20 1.50e+00 4.44e-01 6.61e+01 angle pdb=" C3' G I 105 " pdb=" O3' G I 105 " pdb=" P U I 106 " ideal model delta sigma weight residual 120.20 108.49 11.71 1.50e+00 4.44e-01 6.10e+01 angle pdb=" C4' A I 13 " pdb=" C3' A I 13 " pdb=" O3' A I 13 " ideal model delta sigma weight residual 113.00 102.41 10.59 1.50e+00 4.44e-01 4.98e+01 ... (remaining 15448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 5908 35.76 - 71.51: 776 71.51 - 107.27: 74 107.27 - 143.03: 3 143.03 - 178.79: 3 Dihedral angle restraints: 6764 sinusoidal: 4175 harmonic: 2589 Sorted by residual: dihedral pdb=" O4' C I 82 " pdb=" C1' C I 82 " pdb=" N1 C I 82 " pdb=" C2 C I 82 " ideal model delta sinusoidal sigma weight residual 232.00 53.21 178.79 1 1.70e+01 3.46e-03 6.64e+01 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 60.87 171.13 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" C5' C I 91 " pdb=" C4' C I 91 " pdb=" C3' C I 91 " pdb=" O3' C I 91 " ideal model delta sinusoidal sigma weight residual 147.00 99.97 47.03 1 8.00e+00 1.56e-02 4.78e+01 ... (remaining 6761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 1603 0.161 - 0.321: 195 0.321 - 0.482: 28 0.482 - 0.642: 7 0.642 - 0.803: 3 Chirality restraints: 1836 Sorted by residual: chirality pdb=" P C I 113 " pdb=" OP1 C I 113 " pdb=" OP2 C I 113 " pdb=" O5' C I 113 " both_signs ideal model delta sigma weight residual True 2.41 -1.61 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" P G H 117 " pdb=" OP1 G H 117 " pdb=" OP2 G H 117 " pdb=" O5' G H 117 " both_signs ideal model delta sigma weight residual True 2.41 3.07 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" P A I 88 " pdb=" OP1 A I 88 " pdb=" OP2 A I 88 " pdb=" O5' A I 88 " both_signs ideal model delta sigma weight residual True 2.41 -3.07 -0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 1833 not shown) Planarity restraints: 1396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " -0.099 2.00e-02 2.50e+03 5.08e-02 5.17e+01 pdb=" CG TYR C 28 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U I 7 " -0.063 2.00e-02 2.50e+03 3.28e-02 2.43e+01 pdb=" N1 U I 7 " 0.043 2.00e-02 2.50e+03 pdb=" C2 U I 7 " 0.027 2.00e-02 2.50e+03 pdb=" O2 U I 7 " 0.022 2.00e-02 2.50e+03 pdb=" N3 U I 7 " -0.037 2.00e-02 2.50e+03 pdb=" C4 U I 7 " -0.023 2.00e-02 2.50e+03 pdb=" O4 U I 7 " -0.002 2.00e-02 2.50e+03 pdb=" C5 U I 7 " 0.009 2.00e-02 2.50e+03 pdb=" C6 U I 7 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 11 " -0.017 2.00e-02 2.50e+03 2.92e-02 1.70e+01 pdb=" CG TYR B 11 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR B 11 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 11 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 11 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR B 11 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 11 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR B 11 " 0.032 2.00e-02 2.50e+03 ... (remaining 1393 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 662 2.69 - 3.24: 10846 3.24 - 3.79: 22486 3.79 - 4.35: 28956 4.35 - 4.90: 40487 Nonbonded interactions: 103437 Sorted by model distance: nonbonded pdb=" OP2 A I 88 " pdb=" C5' A I 88 " model vdw 2.132 2.752 nonbonded pdb=" O SER E 33 " pdb=" O2' C I 23 " model vdw 2.196 3.040 nonbonded pdb=" C4' G I 92 " pdb=" OP1 G I 93 " model vdw 2.205 3.470 nonbonded pdb=" NE2 HIS A 202 " pdb=" O3' G I 129 " model vdw 2.213 3.120 nonbonded pdb=" NE2 GLN E 98 " pdb=" O3' C I 17 " model vdw 2.219 3.120 ... (remaining 103432 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 individual isotropic 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: 2.160 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 10.800 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 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 : 0.012 0.118 10901 Z= 0.748 Angle : 1.616 25.318 15453 Z= 1.036 Chirality : 0.116 0.803 1836 Planarity : 0.011 0.108 1396 Dihedral : 25.589 178.787 5094 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 43.56 Ramachandran Plot: Outliers : 3.77 % Allowed : 10.16 % Favored : 86.07 % Rotamer: Outliers : 20.43 % Allowed : 14.25 % Favored : 65.32 % Cbeta Deviations : 0.24 % 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: -3.87 (0.23), residues: 876 helix: -1.87 (0.16), residues: 667 sheet: -4.97 (0.82), residues: 24 loop : -4.18 (0.35), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.003 ARG C 79 TYR 0.099 0.011 TYR C 28 PHE 0.048 0.008 PHE A 231 TRP 0.044 0.009 TRP C 116 HIS 0.029 0.005 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.01226 / 0.75 (10901) covalent geometry : angle 1.61583 / 1.04 (15453) hydrogen bonds : bond 0.19844 / 12.94 ( 596) hydrogen bonds : angle 9.09892 / 6.42 ( 1608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 234 time to evaluate : 0.295 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 1 MET cc_start: 0.5506 (OUTLIER) cc_final: 0.4603 (ptm) REVERT: A 31 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7200 (ptm-80) REVERT: A 75 LEU cc_start: 0.4063 (OUTLIER) cc_final: 0.3853 (tt) REVERT: A 107 TYR cc_start: 0.8645 (m-80) cc_final: 0.8260 (m-80) REVERT: A 123 GLN cc_start: 0.6296 (tt0) cc_final: 0.5639 (tt0) REVERT: A 127 ARG cc_start: 0.5664 (OUTLIER) cc_final: 0.3815 (mtt180) REVERT: A 165 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6939 (mtp180) REVERT: A 172 LEU cc_start: 0.7708 (tp) cc_final: 0.7353 (tt) REVERT: A 227 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.7015 (mp) REVERT: A 228 ARG cc_start: 0.8201 (ttp-110) cc_final: 0.7826 (ttm110) REVERT: A 236 ASP cc_start: 0.7994 (m-30) cc_final: 0.7631 (t70) REVERT: A 245 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6947 (tmtt) REVERT: A 269 HIS cc_start: 0.6950 (p-80) cc_final: 0.6591 (p90) REVERT: A 296 LEU cc_start: 0.3980 (OUTLIER) cc_final: 0.3630 (mt) REVERT: B 66 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8151 (m) REVERT: B 89 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6555 (mt0) REVERT: C 13 GLN cc_start: 0.5585 (tm-30) cc_final: 0.5187 (pm20) REVERT: C 14 MET cc_start: 0.6206 (OUTLIER) cc_final: 0.5802 (mmm) REVERT: C 18 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7268 (pt0) REVERT: C 21 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6584 (tt0) REVERT: C 38 HIS cc_start: 0.7755 (m-70) cc_final: 0.7478 (m-70) REVERT: C 47 LYS cc_start: 0.7184 (mttm) cc_final: 0.6858 (ttpp) REVERT: C 54 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7086 (tp30) REVERT: C 72 ASP cc_start: 0.7333 (t70) cc_final: 0.6916 (t0) REVERT: D 19 ARG cc_start: 0.6980 (mmt-90) cc_final: 0.6309 (mmt-90) REVERT: D 26 TYR cc_start: 0.6561 (t80) cc_final: 0.5839 (t80) REVERT: D 43 GLU cc_start: 0.6428 (mt-10) cc_final: 0.6212 (tt0) REVERT: D 52 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.5335 (tm-30) REVERT: D 62 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.7198 (p) REVERT: D 89 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7319 (tp40) REVERT: D 95 THR cc_start: 0.6746 (OUTLIER) cc_final: 0.6342 (p) REVERT: D 103 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7409 (mm-40) REVERT: D 108 GLU cc_start: 0.6985 (tt0) cc_final: 0.6674 (tp30) REVERT: D 111 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.7402 (mtt180) REVERT: E 52 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7705 (tp40) REVERT: E 54 GLU cc_start: 0.7222 (tt0) cc_final: 0.6884 (tm-30) REVERT: E 77 MET cc_start: 0.7490 (tpt) cc_final: 0.7167 (tpt) REVERT: E 119 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6543 (ppt170) REVERT: F 18 GLU cc_start: 0.7525 (mp0) cc_final: 0.7215 (pp20) REVERT: F 19 ARG cc_start: 0.6241 (tpp80) cc_final: 0.5895 (mmm160) REVERT: F 25 SER cc_start: 0.8163 (t) cc_final: 0.7830 (p) REVERT: F 26 TYR cc_start: 0.6575 (t80) cc_final: 0.6118 (t80) REVERT: F 43 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: F 47 LYS cc_start: 0.6543 (mttm) cc_final: 0.6174 (ttpt) REVERT: F 54 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6307 (tp30) REVERT: F 77 MET cc_start: 0.7335 (tpt) cc_final: 0.6777 (tpt) REVERT: F 85 LEU cc_start: 0.7450 (mt) cc_final: 0.7126 (mp) REVERT: F 90 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6906 (mmtp) REVERT: F 98 GLN cc_start: 0.7752 (mt0) cc_final: 0.7461 (mt0) outliers start: 152 outliers final: 33 residues processed: 337 average time/residue: 0.1360 time to fit residues: 58.6454 Evaluate side-chains 243 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 119 ARG Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 111 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN C 13 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS C 121 ASN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.236951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.179938 restraints weight = 12431.507| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 1.74 r_work: 0.3854 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 10901 Z= 0.292 Angle : 0.866 12.295 15453 Z= 0.468 Chirality : 0.048 0.283 1836 Planarity : 0.007 0.073 1396 Dihedral : 24.834 178.480 3491 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 29.34 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.88 % Favored : 91.32 % Rotamer: Outliers : 9.01 % Allowed : 17.07 % Favored : 73.92 % 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: -2.15 (0.26), residues: 876 helix: -0.66 (0.18), residues: 663 sheet: -4.06 (0.83), residues: 22 loop : -3.44 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 122 TYR 0.027 0.004 TYR C 28 PHE 0.025 0.003 PHE B 80 TRP 0.018 0.003 TRP D 116 HIS 0.021 0.003 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.29 (10901) covalent geometry : angle 0.86617 / 0.47 (15453) hydrogen bonds : bond 0.07715 / 4.84 ( 596) hydrogen bonds : angle 5.47279 / 3.84 ( 1608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 204 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7207 (mmt) cc_final: 0.5911 (ptm) REVERT: A 75 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.5261 (mm) REVERT: A 135 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7058 (tp) REVERT: A 152 TYR cc_start: 0.8235 (m-80) cc_final: 0.7612 (m-80) REVERT: A 165 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8045 (mtt180) REVERT: A 264 ARG cc_start: 0.7741 (ttt180) cc_final: 0.7481 (mmm-85) REVERT: A 276 SER cc_start: 0.0759 (OUTLIER) cc_final: 0.0519 (m) REVERT: B 89 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6782 (mt0) REVERT: D 26 TYR cc_start: 0.7542 (t80) cc_final: 0.6978 (t80) REVERT: D 43 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7222 (tt0) REVERT: D 52 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: D 68 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6195 (mm) REVERT: D 103 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7779 (mm-40) REVERT: F 18 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6585 (mp0) REVERT: F 43 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: F 44 MET cc_start: 0.8464 (mtp) cc_final: 0.8105 (mtp) outliers start: 67 outliers final: 22 residues processed: 251 average time/residue: 0.1091 time to fit residues: 36.9011 Evaluate side-chains 210 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 111 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 83 optimal weight: 0.5980 chunk 96 optimal weight: 50.0000 chunk 52 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 94 optimal weight: 40.0000 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 HIS A 306 HIS B 64 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.234850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.174958 restraints weight = 12417.764| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 1.82 r_work: 0.3793 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10901 Z= 0.232 Angle : 0.737 9.180 15453 Z= 0.397 Chirality : 0.043 0.284 1836 Planarity : 0.005 0.043 1396 Dihedral : 24.386 179.575 3400 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.99 % Favored : 91.32 % Rotamer: Outliers : 5.78 % Allowed : 19.89 % Favored : 74.33 % 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: -1.67 (0.27), residues: 876 helix: -0.37 (0.19), residues: 663 sheet: -3.03 (0.95), residues: 22 loop : -3.14 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 208 TYR 0.024 0.003 TYR C 28 PHE 0.023 0.003 PHE A 231 TRP 0.016 0.002 TRP D 116 HIS 0.011 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (10901) covalent geometry : angle 0.73661 / 0.40 (15453) hydrogen bonds : bond 0.06602 / 4.22 ( 596) hydrogen bonds : angle 5.08349 / 3.57 ( 1608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 0.323 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 1 MET cc_start: 0.7086 (mmt) cc_final: 0.5936 (ptm) REVERT: A 135 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6846 (tp) REVERT: A 165 ARG cc_start: 0.8323 (mtp85) cc_final: 0.8061 (mtt180) REVERT: A 264 ARG cc_start: 0.7912 (ttt180) cc_final: 0.7533 (mmm-85) REVERT: B 89 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6853 (mt0) REVERT: C 14 MET cc_start: 0.7070 (mmp) cc_final: 0.6858 (mmm) REVERT: C 95 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8643 (p) REVERT: C 98 GLN cc_start: 0.8231 (mt0) cc_final: 0.8005 (mt0) REVERT: D 43 GLU cc_start: 0.7276 (mt-10) cc_final: 0.7062 (tt0) REVERT: D 52 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.6974 (tm-30) REVERT: D 64 GLN cc_start: 0.6583 (pm20) cc_final: 0.6368 (pm20) REVERT: D 68 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6371 (mm) REVERT: D 103 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7777 (mm-40) REVERT: E 54 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7407 (tp30) REVERT: F 25 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.7777 (t) REVERT: F 43 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: F 44 MET cc_start: 0.8481 (mtp) cc_final: 0.8107 (mtp) outliers start: 43 outliers final: 21 residues processed: 226 average time/residue: 0.1080 time to fit residues: 33.4340 Evaluate side-chains 206 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 103 GLN 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 F residue 16 ILE Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS B 64 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.233882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.174780 restraints weight = 12416.010| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.71 r_work: 0.3799 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 10901 Z= 0.242 Angle : 0.715 8.529 15453 Z= 0.383 Chirality : 0.042 0.201 1836 Planarity : 0.005 0.041 1396 Dihedral : 24.204 179.437 3392 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.42 % Favored : 92.01 % Rotamer: Outliers : 5.38 % Allowed : 19.22 % Favored : 75.40 % 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: -1.42 (0.27), residues: 876 helix: -0.18 (0.19), residues: 665 sheet: -2.69 (0.97), residues: 24 loop : -3.19 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 19 TYR 0.026 0.003 TYR C 28 PHE 0.026 0.002 PHE A 231 TRP 0.010 0.002 TRP D 116 HIS 0.011 0.002 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 (10901) covalent geometry : angle 0.71520 / 0.38 (15453) hydrogen bonds : bond 0.06285 / 4.07 ( 596) hydrogen bonds : angle 4.98278 / 3.49 ( 1608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.249 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 1 MET cc_start: 0.7059 (mmt) cc_final: 0.5956 (ptm) REVERT: A 165 ARG cc_start: 0.8321 (mtp85) cc_final: 0.8017 (mtt180) REVERT: A 264 ARG cc_start: 0.7759 (ttt180) cc_final: 0.7504 (mmm-85) REVERT: B 33 SER cc_start: 0.7322 (p) cc_final: 0.7079 (m) REVERT: C 14 MET cc_start: 0.6997 (mmp) cc_final: 0.6738 (mmm) REVERT: C 95 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8651 (p) REVERT: D 52 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.6989 (tm-30) REVERT: D 68 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6601 (mm) REVERT: D 103 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7750 (mm-40) REVERT: E 16 ILE cc_start: 0.8184 (mt) cc_final: 0.7907 (tt) REVERT: F 43 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7360 (mt-10) outliers start: 40 outliers final: 25 residues processed: 221 average time/residue: 0.1163 time to fit residues: 34.9799 Evaluate side-chains 205 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 13 GLN 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 F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 69 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS A 269 HIS ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN C 64 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.235507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.177791 restraints weight = 12445.056| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 1.77 r_work: 0.3826 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10901 Z= 0.197 Angle : 0.683 11.834 15453 Z= 0.362 Chirality : 0.041 0.251 1836 Planarity : 0.005 0.043 1396 Dihedral : 24.012 178.793 3389 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.56 % Favored : 90.98 % Rotamer: Outliers : 4.17 % Allowed : 21.64 % Favored : 74.19 % 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: -1.12 (0.28), residues: 876 helix: -0.01 (0.19), residues: 665 sheet: -2.08 (0.97), residues: 24 loop : -2.96 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 42 TYR 0.026 0.003 TYR F 20 PHE 0.028 0.002 PHE A 231 TRP 0.019 0.002 TRP A 33 HIS 0.016 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (10901) covalent geometry : angle 0.68300 / 0.36 (15453) hydrogen bonds : bond 0.05901 / 3.84 ( 596) hydrogen bonds : angle 4.89616 / 3.45 ( 1608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7020 (mmt) cc_final: 0.5899 (ptm) REVERT: A 33 TRP cc_start: 0.7265 (t-100) cc_final: 0.6142 (m-90) REVERT: A 128 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7979 (ttm110) REVERT: A 165 ARG cc_start: 0.8293 (mtp85) cc_final: 0.8035 (mtt180) REVERT: A 184 LEU cc_start: 0.8013 (tp) cc_final: 0.7720 (tp) REVERT: A 250 GLN cc_start: 0.6982 (pt0) cc_final: 0.6423 (pm20) REVERT: A 264 ARG cc_start: 0.7618 (ttt180) cc_final: 0.7134 (mmm160) REVERT: B 33 SER cc_start: 0.6979 (p) cc_final: 0.6776 (m) REVERT: B 82 LEU cc_start: 0.8402 (mt) cc_final: 0.7990 (mp) REVERT: D 52 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: D 103 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7845 (mm-40) REVERT: E 16 ILE cc_start: 0.8134 (mt) cc_final: 0.7885 (tt) REVERT: E 54 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7402 (mt-10) REVERT: F 43 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7409 (mt-10) outliers start: 31 outliers final: 19 residues processed: 203 average time/residue: 0.1162 time to fit residues: 31.8279 Evaluate side-chains 195 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 73 optimal weight: 0.0980 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 94 optimal weight: 40.0000 chunk 55 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 59 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.237485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.180567 restraints weight = 12666.352| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.55 r_work: 0.3889 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10901 Z= 0.184 Angle : 0.674 10.877 15453 Z= 0.356 Chirality : 0.039 0.208 1836 Planarity : 0.005 0.044 1396 Dihedral : 23.869 178.274 3385 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.76 % Favored : 91.78 % Rotamer: Outliers : 3.49 % Allowed : 22.04 % Favored : 74.46 % 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: -0.92 (0.28), residues: 876 helix: 0.13 (0.19), residues: 668 sheet: -1.44 (1.13), residues: 24 loop : -2.98 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 22 TYR 0.024 0.002 TYR F 69 PHE 0.026 0.002 PHE A 260 TRP 0.017 0.002 TRP D 116 HIS 0.009 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (10901) covalent geometry : angle 0.67361 / 0.36 (15453) hydrogen bonds : bond 0.05721 / 3.74 ( 596) hydrogen bonds : angle 4.81677 / 3.38 ( 1608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6966 (mmt) cc_final: 0.5941 (ptm) REVERT: A 33 TRP cc_start: 0.7170 (t-100) cc_final: 0.6113 (m-90) REVERT: A 128 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8040 (ttp-170) REVERT: A 165 ARG cc_start: 0.8274 (mtp85) cc_final: 0.8056 (mtt180) REVERT: A 250 GLN cc_start: 0.6709 (pt0) cc_final: 0.6156 (pm20) REVERT: A 264 ARG cc_start: 0.7496 (ttt180) cc_final: 0.7052 (mmm160) REVERT: A 266 TRP cc_start: 0.7441 (m-90) cc_final: 0.6209 (m-90) REVERT: D 52 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: D 103 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7801 (mm-40) REVERT: E 16 ILE cc_start: 0.7973 (mt) cc_final: 0.7746 (tt) REVERT: E 54 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7403 (mt-10) REVERT: F 108 GLU cc_start: 0.7396 (tp30) cc_final: 0.6852 (tp30) REVERT: F 116 TRP cc_start: 0.6888 (t60) cc_final: 0.6526 (t60) outliers start: 26 outliers final: 21 residues processed: 202 average time/residue: 0.0988 time to fit residues: 27.3024 Evaluate side-chains 197 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 34 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 209 HIS ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 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 = 0.4720 r_free = 0.4720 target = 0.237144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.179559 restraints weight = 12499.245| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 1.67 r_work: 0.3872 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 10901 Z= 0.198 Angle : 0.673 9.916 15453 Z= 0.355 Chirality : 0.039 0.205 1836 Planarity : 0.005 0.046 1396 Dihedral : 23.761 178.074 3385 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.76 % Favored : 91.89 % Rotamer: Outliers : 3.36 % Allowed : 22.85 % Favored : 73.79 % 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: -0.87 (0.28), residues: 876 helix: 0.14 (0.19), residues: 664 sheet: -1.35 (1.15), residues: 24 loop : -2.81 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 111 TYR 0.043 0.003 TYR A 58 PHE 0.025 0.002 PHE A 231 TRP 0.011 0.002 TRP D 116 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (10901) covalent geometry : angle 0.67336 / 0.36 (15453) hydrogen bonds : bond 0.05686 / 3.71 ( 596) hydrogen bonds : angle 4.84146 / 3.39 ( 1608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6956 (mmt) cc_final: 0.5988 (ptm) REVERT: A 33 TRP cc_start: 0.7170 (t-100) cc_final: 0.6022 (m-90) REVERT: A 128 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7887 (ttm110) REVERT: A 165 ARG cc_start: 0.8309 (mtp85) cc_final: 0.8084 (mtt180) REVERT: A 250 GLN cc_start: 0.6758 (pt0) cc_final: 0.6169 (pm20) REVERT: A 261 LEU cc_start: 0.8202 (mp) cc_final: 0.7974 (mp) REVERT: A 266 TRP cc_start: 0.7368 (m-90) cc_final: 0.6184 (m-90) REVERT: D 52 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: D 103 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7801 (mm-40) REVERT: E 16 ILE cc_start: 0.8004 (mt) cc_final: 0.7769 (tt) REVERT: E 54 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7406 (mt-10) REVERT: F 32 GLN cc_start: 0.7576 (tm-30) cc_final: 0.7335 (pp30) REVERT: F 37 LYS cc_start: 0.7748 (ttmt) cc_final: 0.7349 (tttp) REVERT: F 43 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7351 (mt-10) REVERT: F 116 TRP cc_start: 0.6983 (t60) cc_final: 0.6635 (t60) outliers start: 25 outliers final: 20 residues processed: 190 average time/residue: 0.1186 time to fit residues: 30.5461 Evaluate side-chains 194 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 111 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 45 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 0.0000 chunk 34 optimal weight: 0.0980 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.239406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.183610 restraints weight = 12598.841| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 1.63 r_work: 0.3916 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10901 Z= 0.161 Angle : 0.655 9.770 15453 Z= 0.345 Chirality : 0.039 0.205 1836 Planarity : 0.005 0.046 1396 Dihedral : 23.608 177.875 3385 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.76 % Favored : 92.01 % Rotamer: Outliers : 3.23 % Allowed : 24.06 % Favored : 72.72 % 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: -0.67 (0.28), residues: 876 helix: 0.27 (0.20), residues: 662 sheet: -1.48 (1.11), residues: 24 loop : -2.64 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 42 TYR 0.026 0.002 TYR A 213 PHE 0.081 0.003 PHE A 260 TRP 0.021 0.002 TRP D 116 HIS 0.007 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (10901) covalent geometry : angle 0.65482 / 0.34 (15453) hydrogen bonds : bond 0.05458 / 3.56 ( 596) hydrogen bonds : angle 4.72306 / 3.31 ( 1608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7030 (mmt) cc_final: 0.6028 (ptm) REVERT: A 33 TRP cc_start: 0.7070 (t-100) cc_final: 0.6005 (m-90) REVERT: A 165 ARG cc_start: 0.8278 (mtp85) cc_final: 0.7654 (mtt180) REVERT: A 184 LEU cc_start: 0.7949 (tp) cc_final: 0.7552 (tp) REVERT: A 250 GLN cc_start: 0.6459 (pt0) cc_final: 0.6077 (pm20) REVERT: A 266 TRP cc_start: 0.7266 (m-90) cc_final: 0.6172 (m-90) REVERT: B 108 GLU cc_start: 0.7632 (tt0) cc_final: 0.7313 (pt0) REVERT: D 19 ARG cc_start: 0.6798 (mmm-85) cc_final: 0.6546 (mmm-85) REVERT: D 52 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: E 54 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7442 (mt-10) REVERT: F 32 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7270 (pp30) REVERT: F 37 LYS cc_start: 0.7639 (ttmt) cc_final: 0.7252 (tttp) REVERT: F 43 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: F 116 TRP cc_start: 0.6927 (t60) cc_final: 0.6622 (t60) outliers start: 24 outliers final: 18 residues processed: 199 average time/residue: 0.1038 time to fit residues: 28.6188 Evaluate side-chains 189 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 0.5980 chunk 67 optimal weight: 0.0980 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 94 optimal weight: 40.0000 chunk 79 optimal weight: 0.7980 chunk 36 optimal weight: 0.0970 chunk 76 optimal weight: 0.0870 chunk 37 optimal weight: 0.3980 chunk 62 optimal weight: 0.0870 chunk 68 optimal weight: 0.5980 overall best weight: 0.1534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.242260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.188271 restraints weight = 12660.011| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 1.68 r_work: 0.3924 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10901 Z= 0.148 Angle : 0.647 8.919 15453 Z= 0.343 Chirality : 0.038 0.205 1836 Planarity : 0.005 0.050 1396 Dihedral : 23.461 177.846 3382 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.85 % Favored : 92.69 % Rotamer: Outliers : 3.09 % Allowed : 24.73 % Favored : 72.18 % 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: -0.49 (0.28), residues: 876 helix: 0.38 (0.20), residues: 660 sheet: -1.46 (1.09), residues: 24 loop : -2.44 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 22 TYR 0.050 0.002 TYR A 58 PHE 0.026 0.002 PHE A 260 TRP 0.021 0.002 TRP D 116 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (10901) covalent geometry : angle 0.64682 / 0.34 (15453) hydrogen bonds : bond 0.05445 / 3.55 ( 596) hydrogen bonds : angle 4.69888 / 3.29 ( 1608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6962 (mmt) cc_final: 0.5984 (ptm) REVERT: A 33 TRP cc_start: 0.7042 (t-100) cc_final: 0.5992 (m-90) REVERT: A 75 LEU cc_start: 0.5672 (OUTLIER) cc_final: 0.5358 (tm) REVERT: A 128 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7671 (ttm110) REVERT: A 165 ARG cc_start: 0.8274 (mtp85) cc_final: 0.7997 (mtt180) REVERT: A 184 LEU cc_start: 0.7896 (tp) cc_final: 0.7489 (tp) REVERT: A 250 GLN cc_start: 0.6390 (pt0) cc_final: 0.6043 (pm20) REVERT: A 266 TRP cc_start: 0.7250 (m-90) cc_final: 0.6182 (m-90) REVERT: A 290 HIS cc_start: 0.0938 (OUTLIER) cc_final: 0.0220 (t-90) REVERT: B 108 GLU cc_start: 0.7654 (tt0) cc_final: 0.7366 (pt0) REVERT: D 52 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.6943 (tm-30) REVERT: E 54 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7416 (mt-10) REVERT: F 32 GLN cc_start: 0.7331 (tm-30) cc_final: 0.7112 (pp30) REVERT: F 43 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: F 116 TRP cc_start: 0.6868 (t60) cc_final: 0.6571 (t60) outliers start: 23 outliers final: 14 residues processed: 191 average time/residue: 0.1206 time to fit residues: 30.9279 Evaluate side-chains 187 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 43 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.239458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.182835 restraints weight = 12551.784| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 1.71 r_work: 0.3886 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10901 Z= 0.174 Angle : 0.652 9.019 15453 Z= 0.344 Chirality : 0.038 0.190 1836 Planarity : 0.005 0.045 1396 Dihedral : 23.372 177.786 3382 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.62 % Favored : 92.92 % Rotamer: Outliers : 2.69 % Allowed : 24.73 % Favored : 72.58 % 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: -0.49 (0.28), residues: 876 helix: 0.37 (0.20), residues: 660 sheet: -1.52 (1.08), residues: 24 loop : -2.36 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 22 TYR 0.033 0.003 TYR A 58 PHE 0.024 0.002 PHE B 80 TRP 0.018 0.002 TRP D 116 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (10901) covalent geometry : angle 0.65232 / 0.34 (15453) hydrogen bonds : bond 0.05475 / 3.55 ( 596) hydrogen bonds : angle 4.68038 / 3.28 ( 1608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6991 (mmt) cc_final: 0.6059 (ptm) REVERT: A 33 TRP cc_start: 0.7106 (t-100) cc_final: 0.6031 (m-90) REVERT: A 75 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.5570 (tm) REVERT: A 128 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7723 (ttp-170) REVERT: A 165 ARG cc_start: 0.8297 (mtp85) cc_final: 0.8004 (mtt180) REVERT: A 184 LEU cc_start: 0.7970 (tp) cc_final: 0.7558 (tp) REVERT: A 250 GLN cc_start: 0.6551 (pt0) cc_final: 0.6157 (pm20) REVERT: A 266 TRP cc_start: 0.7232 (m-90) cc_final: 0.6250 (m-90) REVERT: A 290 HIS cc_start: 0.1067 (OUTLIER) cc_final: 0.0319 (t-90) REVERT: B 43 GLU cc_start: 0.7585 (tt0) cc_final: 0.7364 (tt0) REVERT: B 108 GLU cc_start: 0.7656 (tt0) cc_final: 0.7383 (pt0) REVERT: D 52 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: E 54 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7448 (mt-10) REVERT: F 32 GLN cc_start: 0.7417 (tm-30) cc_final: 0.7199 (pp30) REVERT: F 37 LYS cc_start: 0.7416 (ttmm) cc_final: 0.7148 (tttp) REVERT: F 43 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: F 116 TRP cc_start: 0.6978 (t60) cc_final: 0.6689 (t60) outliers start: 20 outliers final: 15 residues processed: 186 average time/residue: 0.1215 time to fit residues: 30.5650 Evaluate side-chains 188 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 43 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 96 optimal weight: 50.0000 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.0270 chunk 99 optimal weight: 8.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.239363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.183235 restraints weight = 12701.533| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 1.78 r_work: 0.3882 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10901 Z= 0.179 Angle : 0.656 11.887 15453 Z= 0.345 Chirality : 0.038 0.187 1836 Planarity : 0.005 0.046 1396 Dihedral : 23.327 177.633 3382 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.62 % Favored : 92.92 % Rotamer: Outliers : 2.55 % Allowed : 25.27 % Favored : 72.18 % 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: -0.45 (0.28), residues: 876 helix: 0.44 (0.20), residues: 655 sheet: -1.57 (1.07), residues: 24 loop : -2.44 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 22 TYR 0.048 0.003 TYR A 58 PHE 0.025 0.002 PHE B 80 TRP 0.017 0.002 TRP D 116 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (10901) covalent geometry : angle 0.65612 / 0.34 (15453) hydrogen bonds : bond 0.05437 / 3.51 ( 596) hydrogen bonds : angle 4.71431 / 3.29 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2535.58 seconds wall clock time: 44 minutes 28.84 seconds (2668.84 seconds total)