Starting phenix.real_space_refine on Wed Aug 5 14:17:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubd_42083/08_2026/8ubd_42083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubd_42083/08_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_42083/08_2026/8ubd_42083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubd_42083/08_2026/8ubd_42083.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ubd_42083/08_2026/8ubd_42083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubd_42083/08_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.28, per 1000 atoms: 0.22 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: 0.75 Conformation dependent library (CDL) restraints added in 215.5 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: 1.32 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: 1.91 Time building geometry restraints manager: 0.99 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=" O3' G I 53 " pdb=" P U I 54 " ideal model delta sigma weight residual 1.607 1.676 -0.069 1.20e-02 6.94e+03 3.35e+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=" P G G 379 " pdb=" O5' G G 379 " ideal model delta sigma weight residual 1.593 1.638 -0.045 1.00e-02 1.00e+04 2.04e+01 ... (remaining 10896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 15225 5.06 - 10.13: 220 10.13 - 15.19: 5 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 119.70 103.76 15.94 1.20e+00 6.94e-01 1.76e+02 angle pdb=" C3' G I 122 " pdb=" O3' G I 122 " pdb=" P A I 123 " ideal model delta sigma weight residual 119.70 108.00 11.70 1.20e+00 6.94e-01 9.50e+01 angle pdb=" C3' G I 105 " pdb=" O3' G I 105 " pdb=" P U I 106 " ideal model delta sigma weight residual 119.70 108.49 11.21 1.20e+00 6.94e-01 8.73e+01 angle pdb=" O5' A I 88 " pdb=" C5' A I 88 " pdb=" C4' A I 88 " ideal model delta sigma weight residual 109.40 102.56 6.84 8.00e-01 1.56e+00 7.31e+01 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 ... (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: 1614 0.161 - 0.321: 186 0.321 - 0.482: 26 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.710 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.110 ------------------------------------------------------------------------------- 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= 0.776 Angle : 1.592 25.318 15453 Z= 1.053 Chirality : 0.114 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 0.01228 / 0.78 (10901) covalent geometry : angle 1.59239 / 1.05 (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 : 0.227 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: 0.3619 (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: 0.6885 (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: 0.7831 (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: 0.6983 (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: 0.1302 time to fit residues: 56.5414 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 : 0.215 ------------------------------------------------------------------------------- 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: 30.0000 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: 9.9990 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 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.236714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.179392 restraints weight = 12413.495| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 1.59 r_work: 0.3861 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 10901 Z= 0.279 Angle : 0.893 10.660 15453 Z= 0.468 Chirality : 0.051 0.240 1836 Planarity : 0.007 0.078 1396 Dihedral : 24.695 179.068 3491 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 29.13 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.88 % Favored : 91.32 % Rotamer: Outliers : 9.27 % Allowed : 17.34 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.20 (0.26), residues: 876 helix: -0.70 (0.18), residues: 665 sheet: -4.03 (0.83), residues: 22 loop : -3.48 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 36 TYR 0.027 0.003 TYR C 28 PHE 0.022 0.003 PHE B 80 TRP 0.019 0.003 TRP D 116 HIS 0.018 0.003 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.28 (10901) covalent geometry : angle 0.89282 / 0.47 (15453) hydrogen bonds : bond 0.08082 / 5.13 ( 596) hydrogen bonds : angle 5.51945 / 3.88 ( 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 272 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 203 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7223 (mmt) cc_final: 0.5939 (ptm) REVERT: A 135 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7104 (tp) REVERT: A 152 TYR cc_start: 0.8300 (m-80) cc_final: 0.7630 (m-80) REVERT: A 165 ARG cc_start: 0.8361 (mtp85) cc_final: 0.8055 (mtt180) REVERT: A 264 ARG cc_start: 0.7746 (ttt180) cc_final: 0.7509 (mmm-85) REVERT: B 89 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.6639 (mt0) REVERT: C 90 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.7033 (mtmt) REVERT: D 26 TYR cc_start: 0.7497 (t80) cc_final: 0.6949 (t80) REVERT: D 52 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: D 68 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6147 (mm) REVERT: D 103 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7762 (mm-40) REVERT: F 18 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6600 (mp0) REVERT: F 37 LYS cc_start: 0.8072 (tttt) cc_final: 0.7859 (ttpt) REVERT: F 43 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: F 77 MET cc_start: 0.7813 (tpt) cc_final: 0.7363 (tpt) outliers start: 69 outliers final: 22 residues processed: 251 average time/residue: 0.1207 time to fit residues: 40.7863 Evaluate side-chains 210 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 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 290 HIS Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 13 GLN 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 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 111 ARG Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 50.0000 chunk 52 optimal weight: 0.4980 chunk 10 optimal weight: 0.4980 chunk 44 optimal weight: 0.1980 chunk 101 optimal weight: 20.0000 chunk 37 optimal weight: 0.4980 chunk 69 optimal weight: 0.1980 chunk 94 optimal weight: 50.0000 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN A 116 HIS ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 HIS B 64 GLN ** D 13 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 = 0.4745 r_free = 0.4745 target = 0.239295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.184804 restraints weight = 12359.765| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 1.61 r_work: 0.3866 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10901 Z= 0.208 Angle : 0.736 9.163 15453 Z= 0.394 Chirality : 0.043 0.253 1836 Planarity : 0.006 0.064 1396 Dihedral : 24.211 179.937 3404 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 25.52 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.68 % Favored : 90.64 % Rotamer: Outliers : 5.11 % Allowed : 21.24 % Favored : 73.66 % 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: -1.59 (0.27), residues: 876 helix: -0.32 (0.19), residues: 663 sheet: -2.99 (0.97), residues: 22 loop : -3.10 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 22 TYR 0.025 0.003 TYR C 28 PHE 0.023 0.003 PHE F 80 TRP 0.017 0.002 TRP D 116 HIS 0.010 0.002 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (10901) covalent geometry : angle 0.73613 / 0.39 (15453) hydrogen bonds : bond 0.06608 / 4.23 ( 596) hydrogen bonds : angle 5.04815 / 3.55 ( 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 234 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.302 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: 0.7110 (mmt) cc_final: 0.5950 (ptm) REVERT: A 135 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6880 (tp) REVERT: A 165 ARG cc_start: 0.8302 (mtp85) cc_final: 0.8096 (mtt180) REVERT: A 184 LEU cc_start: 0.8108 (tp) cc_final: 0.7817 (tp) REVERT: A 264 ARG cc_start: 0.7840 (ttt180) cc_final: 0.7516 (mmm-85) REVERT: C 14 MET cc_start: 0.6954 (mmp) cc_final: 0.6730 (mmm) REVERT: C 72 ASP cc_start: 0.7513 (t0) cc_final: 0.7301 (t0) REVERT: C 95 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8656 (p) REVERT: D 52 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: D 68 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6261 (mm) REVERT: D 103 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7712 (mm-40) REVERT: E 54 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6155 (mt-10) REVERT: F 43 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: F 44 MET cc_start: 0.8379 (mtp) cc_final: 0.8059 (mtp) outliers start: 38 outliers final: 17 residues processed: 222 average time/residue: 0.1067 time to fit residues: 32.7945 Evaluate side-chains 202 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 C residue 95 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 101 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN A 269 HIS A 290 HIS B 64 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.232508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.174651 restraints weight = 12432.062| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 1.72 r_work: 0.3767 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 10901 Z= 0.310 Angle : 0.773 8.455 15453 Z= 0.405 Chirality : 0.044 0.301 1836 Planarity : 0.006 0.043 1396 Dihedral : 24.002 179.515 3389 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 25.68 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.33 % Favored : 91.10 % Rotamer: Outliers : 4.97 % Allowed : 20.43 % Favored : 74.60 % 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: -1.60 (0.27), residues: 876 helix: -0.31 (0.19), residues: 668 sheet: -2.80 (0.96), residues: 24 loop : -3.29 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 22 TYR 0.035 0.004 TYR F 20 PHE 0.026 0.003 PHE A 231 TRP 0.011 0.002 TRP C 81 HIS 0.011 0.002 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00723 / 0.31 (10901) covalent geometry : angle 0.77257 / 0.41 (15453) hydrogen bonds : bond 0.06687 / 4.32 ( 596) hydrogen bonds : angle 5.14940 / 3.61 ( 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 227 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7123 (mmt) cc_final: 0.5958 (ptm) REVERT: A 135 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6991 (tp) REVERT: A 165 ARG cc_start: 0.8397 (mtp85) cc_final: 0.8095 (mtt180) REVERT: A 264 ARG cc_start: 0.7788 (ttt180) cc_final: 0.7528 (mmm-85) REVERT: C 14 MET cc_start: 0.7060 (mmp) cc_final: 0.6835 (mmm) REVERT: C 72 ASP cc_start: 0.7588 (t0) cc_final: 0.7382 (t0) REVERT: C 95 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8648 (p) REVERT: D 52 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: D 68 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6478 (mm) REVERT: D 103 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7795 (mm-40) REVERT: F 43 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7394 (mp0) outliers start: 37 outliers final: 23 residues processed: 215 average time/residue: 0.1058 time to fit residues: 31.1097 Evaluate side-chains 202 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 230 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 62 SER 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 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 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: 1.9990 chunk 50 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 89 optimal weight: 30.0000 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.235115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.176131 restraints weight = 12327.860| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 1.65 r_work: 0.3834 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10901 Z= 0.220 Angle : 0.702 8.244 15453 Z= 0.371 Chirality : 0.041 0.245 1836 Planarity : 0.005 0.043 1396 Dihedral : 23.877 179.099 3389 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 23.43 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.65 % Favored : 91.89 % Rotamer: Outliers : 4.44 % Allowed : 22.18 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.33 (0.27), residues: 876 helix: -0.17 (0.19), residues: 669 sheet: -2.09 (0.97), residues: 24 loop : -3.07 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 36 TYR 0.026 0.003 TYR F 20 PHE 0.027 0.003 PHE A 231 TRP 0.015 0.002 TRP D 116 HIS 0.018 0.002 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (10901) covalent geometry : angle 0.70241 / 0.37 (15453) hydrogen bonds : bond 0.06178 / 4.01 ( 596) hydrogen bonds : angle 4.93454 / 3.46 ( 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 221 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 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: 0.7120 (mmt) cc_final: 0.5978 (ptm) REVERT: A 33 TRP cc_start: 0.6787 (t-100) cc_final: 0.6476 (m-90) REVERT: A 128 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8084 (ttp-170) REVERT: A 165 ARG cc_start: 0.8328 (mtp85) cc_final: 0.8057 (mtt180) REVERT: A 250 GLN cc_start: 0.6780 (pt0) cc_final: 0.6226 (pm20) REVERT: A 264 ARG cc_start: 0.7641 (ttt180) cc_final: 0.7388 (mmm-85) REVERT: B 33 SER cc_start: 0.7037 (p) cc_final: 0.6813 (m) REVERT: B 82 LEU cc_start: 0.8381 (mt) cc_final: 0.7993 (mp) REVERT: C 72 ASP cc_start: 0.7394 (t0) cc_final: 0.7111 (t0) REVERT: C 95 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8582 (p) REVERT: D 52 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: D 68 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6543 (mm) REVERT: D 103 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7738 (mm-40) REVERT: F 43 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: F 116 TRP cc_start: 0.7084 (t60) cc_final: 0.6592 (t60) outliers start: 33 outliers final: 21 residues processed: 211 average time/residue: 0.1094 time to fit residues: 31.5039 Evaluate side-chains 204 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 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 B residue 8 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 64 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 73 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 94 optimal weight: 50.0000 chunk 55 optimal weight: 0.3980 chunk 75 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 HIS ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN C 64 GLN ** C 98 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 = 0.4713 r_free = 0.4713 target = 0.236382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.178896 restraints weight = 12576.537| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 1.57 r_work: 0.3894 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10901 Z= 0.195 Angle : 0.690 8.563 15453 Z= 0.365 Chirality : 0.040 0.256 1836 Planarity : 0.005 0.066 1396 Dihedral : 23.742 178.869 3386 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 23.32 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.11 % Favored : 91.44 % Rotamer: Outliers : 3.90 % Allowed : 23.25 % Favored : 72.85 % 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: -1.18 (0.27), residues: 876 helix: -0.08 (0.19), residues: 664 sheet: -1.50 (1.08), residues: 24 loop : -2.92 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 22 TYR 0.026 0.003 TYR C 28 PHE 0.028 0.003 PHE A 231 TRP 0.017 0.002 TRP D 116 HIS 0.013 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (10901) covalent geometry : angle 0.68996 / 0.36 (15453) hydrogen bonds : bond 0.05942 / 3.88 ( 596) hydrogen bonds : angle 4.89412 / 3.43 ( 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: 29 poor density : 182 time to evaluate : 0.181 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: 0.7121 (mmt) cc_final: 0.5993 (ptm) REVERT: A 33 TRP cc_start: 0.6725 (t-100) cc_final: 0.6478 (m-90) REVERT: A 128 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7987 (ttp-170) REVERT: A 165 ARG cc_start: 0.8284 (mtp85) cc_final: 0.8052 (mtt180) REVERT: A 184 LEU cc_start: 0.7975 (tp) cc_final: 0.7568 (tp) REVERT: A 250 GLN cc_start: 0.6702 (pt0) cc_final: 0.6217 (pm20) REVERT: B 1 MET cc_start: 0.6246 (ppp) cc_final: 0.6034 (tmm) REVERT: B 33 SER cc_start: 0.6897 (p) cc_final: 0.6689 (m) REVERT: C 72 ASP cc_start: 0.7302 (t0) cc_final: 0.7073 (t0) REVERT: D 52 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: D 103 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7809 (mm-40) REVERT: F 43 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7320 (mt-10) REVERT: F 44 MET cc_start: 0.8437 (mtp) cc_final: 0.8187 (mtp) REVERT: F 116 TRP cc_start: 0.7052 (t60) cc_final: 0.6608 (t60) outliers start: 29 outliers final: 22 residues processed: 199 average time/residue: 0.0992 time to fit residues: 26.8723 Evaluate side-chains 196 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 57 ASN 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 B residue 8 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 115 SER 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 113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 0.1980 chunk 98 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 89 optimal weight: 30.0000 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 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 = 0.4724 r_free = 0.4724 target = 0.237347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.180788 restraints weight = 12445.815| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 1.65 r_work: 0.3884 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10901 Z= 0.187 Angle : 0.687 9.933 15453 Z= 0.359 Chirality : 0.040 0.226 1836 Planarity : 0.005 0.047 1396 Dihedral : 23.602 178.669 3383 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.65 % Favored : 92.01 % Rotamer: Outliers : 4.17 % Allowed : 24.19 % Favored : 71.64 % 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: -1.04 (0.28), residues: 876 helix: 0.02 (0.19), residues: 664 sheet: -1.31 (1.13), residues: 24 loop : -2.88 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 111 TYR 0.027 0.003 TYR F 69 PHE 0.027 0.002 PHE A 231 TRP 0.016 0.002 TRP D 116 HIS 0.010 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (10901) covalent geometry : angle 0.68689 / 0.36 (15453) hydrogen bonds : bond 0.05811 / 3.79 ( 596) hydrogen bonds : angle 4.88131 / 3.40 ( 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 208 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6979 (mmt) cc_final: 0.6055 (ptm) REVERT: A 33 TRP cc_start: 0.6719 (t-100) cc_final: 0.6437 (m-90) REVERT: A 83 ASP cc_start: 0.7880 (m-30) cc_final: 0.7618 (m-30) REVERT: A 165 ARG cc_start: 0.8291 (mtp85) cc_final: 0.8059 (mtt180) REVERT: A 184 LEU cc_start: 0.7935 (tp) cc_final: 0.7521 (tp) REVERT: A 250 GLN cc_start: 0.6760 (pt0) cc_final: 0.6094 (pm20) REVERT: A 266 TRP cc_start: 0.7452 (m-90) cc_final: 0.6077 (m-90) REVERT: B 33 SER cc_start: 0.6850 (OUTLIER) cc_final: 0.6643 (m) REVERT: C 72 ASP cc_start: 0.7328 (t0) cc_final: 0.7071 (t0) REVERT: D 52 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: F 32 GLN cc_start: 0.7708 (pp30) cc_final: 0.7502 (pp30) REVERT: F 116 TRP cc_start: 0.7067 (t60) cc_final: 0.6681 (t60) outliers start: 31 outliers final: 24 residues processed: 195 average time/residue: 0.1104 time to fit residues: 29.2620 Evaluate side-chains 198 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 57 ASN 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 230 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 65 VAL 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 Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 30.0000 chunk 45 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 72 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 0.0040 chunk 34 optimal weight: 0.0980 overall best weight: 0.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.239796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.185181 restraints weight = 12532.109| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 1.66 r_work: 0.3904 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10901 Z= 0.161 Angle : 0.676 8.435 15453 Z= 0.354 Chirality : 0.039 0.226 1836 Planarity : 0.005 0.047 1396 Dihedral : 23.416 178.507 3380 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.42 % Favored : 92.24 % Rotamer: Outliers : 3.36 % Allowed : 24.87 % Favored : 71.77 % 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: -0.77 (0.28), residues: 876 helix: 0.20 (0.19), residues: 661 sheet: -1.44 (1.08), residues: 24 loop : -2.66 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG C 36 TYR 0.023 0.002 TYR F 69 PHE 0.025 0.002 PHE A 231 TRP 0.020 0.002 TRP D 116 HIS 0.012 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (10901) covalent geometry : angle 0.67572 / 0.35 (15453) hydrogen bonds : bond 0.05635 / 3.69 ( 596) hydrogen bonds : angle 4.76572 / 3.33 ( 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: 25 poor density : 183 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7023 (mmt) cc_final: 0.5996 (ptm) REVERT: A 33 TRP cc_start: 0.6680 (t-100) cc_final: 0.6418 (m-90) REVERT: A 165 ARG cc_start: 0.8277 (mtp85) cc_final: 0.7712 (mtt180) REVERT: A 184 LEU cc_start: 0.7918 (tp) cc_final: 0.7512 (tp) REVERT: A 250 GLN cc_start: 0.6446 (pt0) cc_final: 0.5982 (pm20) REVERT: A 266 TRP cc_start: 0.7242 (m-90) cc_final: 0.6187 (m-90) REVERT: B 108 GLU cc_start: 0.7632 (tt0) cc_final: 0.7311 (pt0) REVERT: D 52 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: F 43 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: F 77 MET cc_start: 0.7611 (tpt) cc_final: 0.7408 (tpt) REVERT: F 116 TRP cc_start: 0.6978 (t60) cc_final: 0.6641 (t60) outliers start: 25 outliers final: 17 residues processed: 198 average time/residue: 0.1165 time to fit residues: 31.6655 Evaluate side-chains 190 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 239 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain E residue 50 LEU 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: 0.9980 chunk 67 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 94 optimal weight: 50.0000 chunk 79 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 76 optimal weight: 0.8980 chunk 37 optimal weight: 0.0980 chunk 62 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 89 GLN ** 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 = 0.4731 r_free = 0.4731 target = 0.238458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.181848 restraints weight = 12575.557| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 1.64 r_work: 0.3898 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10901 Z= 0.179 Angle : 0.687 10.580 15453 Z= 0.359 Chirality : 0.039 0.229 1836 Planarity : 0.005 0.053 1396 Dihedral : 23.344 178.464 3380 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.19 % Favored : 92.47 % Rotamer: Outliers : 2.96 % Allowed : 26.48 % Favored : 70.56 % 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: -0.76 (0.28), residues: 876 helix: 0.19 (0.19), residues: 660 sheet: -1.53 (1.06), residues: 24 loop : -2.56 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 22 TYR 0.037 0.003 TYR A 232 PHE 0.025 0.002 PHE B 80 TRP 0.015 0.002 TRP D 116 HIS 0.010 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (10901) covalent geometry : angle 0.68714 / 0.36 (15453) hydrogen bonds : bond 0.05645 / 3.67 ( 596) hydrogen bonds : angle 4.77488 / 3.33 ( 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 191 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6992 (mmt) cc_final: 0.6093 (ptm) REVERT: A 33 TRP cc_start: 0.6701 (t-100) cc_final: 0.6424 (m-90) REVERT: A 75 LEU cc_start: 0.5664 (OUTLIER) cc_final: 0.5372 (tm) REVERT: A 83 ASP cc_start: 0.7857 (m-30) cc_final: 0.7531 (m-30) REVERT: A 165 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7689 (mtt180) REVERT: A 184 LEU cc_start: 0.7869 (tp) cc_final: 0.7449 (tp) REVERT: A 250 GLN cc_start: 0.6413 (pt0) cc_final: 0.5952 (pm20) REVERT: A 266 TRP cc_start: 0.7268 (m-90) cc_final: 0.6116 (m-90) REVERT: B 43 GLU cc_start: 0.7533 (tt0) cc_final: 0.7306 (tt0) REVERT: B 108 GLU cc_start: 0.7650 (tt0) cc_final: 0.7329 (pt0) REVERT: D 52 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: E 16 ILE cc_start: 0.8029 (mt) cc_final: 0.7810 (tt) REVERT: F 43 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: F 116 TRP cc_start: 0.6963 (t60) cc_final: 0.6643 (t60) outliers start: 22 outliers final: 18 residues processed: 183 average time/residue: 0.1109 time to fit residues: 27.4705 Evaluate side-chains 185 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 57 ASN 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 239 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain E residue 50 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 0.0870 chunk 21 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 53 optimal weight: 0.1980 chunk 78 optimal weight: 0.0970 chunk 89 optimal weight: 30.0000 chunk 68 optimal weight: 0.8980 chunk 52 optimal weight: 0.0170 overall best weight: 0.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4801 r_free = 0.4801 target = 0.245998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.192083 restraints weight = 12482.861| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 1.66 r_work: 0.3960 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10901 Z= 0.146 Angle : 0.664 10.578 15453 Z= 0.349 Chirality : 0.038 0.232 1836 Planarity : 0.005 0.094 1396 Dihedral : 23.212 178.340 3380 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.31 % Favored : 92.47 % Rotamer: Outliers : 2.82 % Allowed : 27.15 % Favored : 70.03 % 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: -0.62 (0.28), residues: 876 helix: 0.31 (0.20), residues: 661 sheet: -1.42 (1.06), residues: 24 loop : -2.63 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG C 36 TYR 0.023 0.002 TYR A 58 PHE 0.023 0.002 PHE A 231 TRP 0.024 0.002 TRP D 116 HIS 0.011 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (10901) covalent geometry : angle 0.66415 / 0.35 (15453) hydrogen bonds : bond 0.05470 / 3.53 ( 596) hydrogen bonds : angle 4.69559 / 3.27 ( 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 202 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 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: A 1 MET cc_start: 0.6905 (mmt) cc_final: 0.5955 (ptm) REVERT: A 33 TRP cc_start: 0.6630 (t-100) cc_final: 0.6359 (m-90) REVERT: A 75 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5549 (tm) REVERT: A 165 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7761 (mtt180) REVERT: A 184 LEU cc_start: 0.7913 (tp) cc_final: 0.7493 (tp) REVERT: A 232 TYR cc_start: 0.7738 (m-80) cc_final: 0.7526 (m-80) REVERT: A 250 GLN cc_start: 0.6359 (pt0) cc_final: 0.5975 (pm20) REVERT: A 256 ARG cc_start: 0.7623 (mmm-85) cc_final: 0.7195 (tpp80) REVERT: A 266 TRP cc_start: 0.7017 (m-90) cc_final: 0.6097 (m-90) REVERT: B 108 GLU cc_start: 0.7515 (tt0) cc_final: 0.7224 (pt0) REVERT: D 52 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.6966 (tm-30) REVERT: E 16 ILE cc_start: 0.7840 (mt) cc_final: 0.7612 (tt) REVERT: E 54 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6478 (mt-10) REVERT: F 43 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: F 116 TRP cc_start: 0.6830 (t60) cc_final: 0.6575 (t60) outliers start: 21 outliers final: 18 residues processed: 193 average time/residue: 0.1264 time to fit residues: 32.6733 Evaluate side-chains 190 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 239 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 64 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 96 optimal weight: 50.0000 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** 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 = 0.4740 r_free = 0.4740 target = 0.239590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.184498 restraints weight = 12602.620| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 1.67 r_work: 0.3881 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10901 Z= 0.194 Angle : 0.688 13.653 15453 Z= 0.357 Chirality : 0.039 0.233 1836 Planarity : 0.006 0.090 1396 Dihedral : 23.180 178.278 3380 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.96 % Favored : 92.81 % Rotamer: Outliers : 3.23 % Allowed : 27.15 % Favored : 69.62 % 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: -0.59 (0.28), residues: 876 helix: 0.32 (0.20), residues: 662 sheet: -1.36 (1.06), residues: 24 loop : -2.56 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 22 TYR 0.028 0.003 TYR A 58 PHE 0.028 0.002 PHE B 80 TRP 0.022 0.002 TRP D 116 HIS 0.011 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (10901) covalent geometry : angle 0.68785 / 0.36 (15453) hydrogen bonds : bond 0.05616 / 3.62 ( 596) hydrogen bonds : angle 4.76047 / 3.31 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2492.97 seconds wall clock time: 43 minutes 41.16 seconds (2621.16 seconds total)