Starting phenix.real_space_refine on Sat Aug 23 06:16:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubd_42083/08_2025/8ubd_42083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubd_42083/08_2025/8ubd_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_2025/8ubd_42083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubd_42083/08_2025/8ubd_42083.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ubd_42083/08_2025/8ubd_42083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubd_42083/08_2025/8ubd_42083.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 149 5.49 5 S 36 5.16 5 C 6058 2.51 5 N 1869 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 2.63, per 1000 atoms: 0.25 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: 0.81 Conformation dependent library (CDL) restraints added in 212.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.44 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: 1.80 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1320 1.31 - 1.44: 3777 1.44 - 1.56: 5444 1.56 - 1.69: 300 1.69 - 1.82: 60 Bond restraints: 10901 Sorted by residual: bond pdb=" CA ASN C 63 " pdb=" CB ASN C 63 " ideal model delta sigma weight residual 1.530 1.637 -0.107 1.69e-02 3.50e+03 4.01e+01 bond pdb=" CA GLU B 100 " pdb=" CB GLU B 100 " ideal model delta sigma weight residual 1.528 1.621 -0.092 1.56e-02 4.11e+03 3.49e+01 bond pdb=" CG MET C 77 " pdb=" SD MET C 77 " ideal model delta sigma weight residual 1.803 1.685 0.118 2.50e-02 1.60e+03 2.22e+01 bond pdb=" O3' G I 53 " pdb=" P U I 54 " ideal model delta sigma weight residual 1.607 1.676 -0.069 1.50e-02 4.44e+03 2.14e+01 bond pdb=" CA ARG B 111 " pdb=" CB ARG B 111 " ideal model delta sigma weight residual 1.529 1.460 0.069 1.55e-02 4.16e+03 2.01e+01 ... (remaining 10896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 15215 5.06 - 10.13: 229 10.13 - 15.19: 6 15.19 - 20.25: 2 20.25 - 25.32: 1 Bond angle restraints: 15453 Sorted by residual: angle pdb=" C3' U I 3 " pdb=" O3' U I 3 " pdb=" P G I 4 " ideal model delta sigma weight residual 120.20 103.76 16.44 1.50e+00 4.44e-01 1.20e+02 angle pdb=" OP2 A I 88 " pdb=" P A I 88 " pdb=" O5' A I 88 " ideal model delta sigma weight residual 108.00 82.68 25.32 3.00e+00 1.11e-01 7.12e+01 angle pdb=" C3' G I 122 " pdb=" O3' G I 122 " pdb=" P A I 123 " ideal model delta sigma weight residual 120.20 108.00 12.20 1.50e+00 4.44e-01 6.61e+01 angle pdb=" C3' G I 105 " pdb=" O3' G I 105 " pdb=" P U I 106 " ideal model delta sigma weight residual 120.20 108.49 11.71 1.50e+00 4.44e-01 6.10e+01 angle pdb=" C4' A I 13 " pdb=" C3' A I 13 " pdb=" O3' A I 13 " ideal model delta sigma weight residual 113.00 102.41 10.59 1.50e+00 4.44e-01 4.98e+01 ... (remaining 15448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 5908 35.76 - 71.51: 776 71.51 - 107.27: 74 107.27 - 143.03: 3 143.03 - 178.79: 3 Dihedral angle restraints: 6764 sinusoidal: 4175 harmonic: 2589 Sorted by residual: dihedral pdb=" O4' C I 82 " pdb=" C1' C I 82 " pdb=" N1 C I 82 " pdb=" C2 C I 82 " ideal model delta sinusoidal sigma weight residual 232.00 53.21 178.79 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 60.87 171.13 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" C5' C I 91 " pdb=" C4' C I 91 " pdb=" C3' C I 91 " pdb=" O3' C I 91 " ideal model delta sinusoidal sigma weight residual 147.00 99.97 47.03 1 8.00e+00 1.56e-02 4.78e+01 ... (remaining 6761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 1603 0.161 - 0.321: 195 0.321 - 0.482: 28 0.482 - 0.642: 7 0.642 - 0.803: 3 Chirality restraints: 1836 Sorted by residual: chirality pdb=" P C I 113 " pdb=" OP1 C I 113 " pdb=" OP2 C I 113 " pdb=" O5' C I 113 " both_signs ideal model delta sigma weight residual True 2.41 -1.61 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" P G H 117 " pdb=" OP1 G H 117 " pdb=" OP2 G H 117 " pdb=" O5' G H 117 " both_signs ideal model delta sigma weight residual True 2.41 3.07 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" P A I 88 " pdb=" OP1 A I 88 " pdb=" OP2 A I 88 " pdb=" O5' A I 88 " both_signs ideal model delta sigma weight residual True 2.41 -3.07 -0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 1833 not shown) Planarity restraints: 1396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " -0.099 2.00e-02 2.50e+03 5.08e-02 5.17e+01 pdb=" CG TYR C 28 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U I 7 " -0.063 2.00e-02 2.50e+03 3.28e-02 2.43e+01 pdb=" N1 U I 7 " 0.043 2.00e-02 2.50e+03 pdb=" C2 U I 7 " 0.027 2.00e-02 2.50e+03 pdb=" O2 U I 7 " 0.022 2.00e-02 2.50e+03 pdb=" N3 U I 7 " -0.037 2.00e-02 2.50e+03 pdb=" C4 U I 7 " -0.023 2.00e-02 2.50e+03 pdb=" O4 U I 7 " -0.002 2.00e-02 2.50e+03 pdb=" C5 U I 7 " 0.009 2.00e-02 2.50e+03 pdb=" C6 U I 7 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 11 " -0.017 2.00e-02 2.50e+03 2.92e-02 1.70e+01 pdb=" CG TYR B 11 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR B 11 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 11 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 11 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR B 11 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 11 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR B 11 " 0.032 2.00e-02 2.50e+03 ... (remaining 1393 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 662 2.69 - 3.24: 10846 3.24 - 3.79: 22486 3.79 - 4.35: 28956 4.35 - 4.90: 40487 Nonbonded interactions: 103437 Sorted by model distance: nonbonded pdb=" OP2 A I 88 " pdb=" C5' A I 88 " model vdw 2.132 2.752 nonbonded pdb=" O SER E 33 " pdb=" O2' C I 23 " model vdw 2.196 3.040 nonbonded pdb=" C4' G I 92 " pdb=" OP1 G I 93 " model vdw 2.205 3.470 nonbonded pdb=" NE2 HIS A 202 " pdb=" O3' G I 129 " model vdw 2.213 3.120 nonbonded pdb=" NE2 GLN E 98 " pdb=" O3' C I 17 " model vdw 2.219 3.120 ... (remaining 103432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.310 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 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= 0.720 Angle : 1.616 25.318 15453 Z= 0.978 Chirality : 0.116 0.803 1836 Planarity : 0.011 0.108 1396 Dihedral : 25.589 178.787 5094 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 43.56 Ramachandran Plot: Outliers : 3.77 % Allowed : 10.16 % Favored : 86.07 % Rotamer: Outliers : 20.43 % Allowed : 14.25 % Favored : 65.32 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.01226 (10901) covalent geometry : angle 1.61587 (15453) hydrogen bonds : bond 0.19844 ( 596) hydrogen bonds : angle 9.09892 ( 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 : 0.220 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: 0.6592 (p90) REVERT: A 296 LEU cc_start: 0.3980 (OUTLIER) cc_final: 0.3630 (mt) REVERT: B 66 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8151 (m) REVERT: B 89 GLN cc_start: 0.6881 (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: 0.7371 (OUTLIER) cc_final: 0.7086 (tp30) REVERT: C 72 ASP cc_start: 0.7333 (t70) cc_final: 0.6916 (t0) REVERT: D 19 ARG cc_start: 0.6980 (mmt-90) cc_final: 0.6309 (mmt-90) REVERT: D 26 TYR cc_start: 0.6561 (t80) cc_final: 0.5839 (t80) REVERT: D 43 GLU cc_start: 0.6428 (mt-10) cc_final: 0.6212 (tt0) REVERT: D 52 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.5335 (tm-30) REVERT: D 62 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.7198 (p) REVERT: D 89 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7319 (tp40) REVERT: D 95 THR cc_start: 0.6746 (OUTLIER) cc_final: 0.6342 (p) REVERT: D 103 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7409 (mm-40) REVERT: D 108 GLU cc_start: 0.6985 (tt0) cc_final: 0.6674 (tp30) REVERT: D 111 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.7402 (mtt180) REVERT: E 52 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7705 (tp40) REVERT: E 54 GLU cc_start: 0.7222 (tt0) cc_final: 0.6884 (tm-30) REVERT: E 77 MET cc_start: 0.7490 (tpt) cc_final: 0.7167 (tpt) REVERT: E 119 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6543 (ppt170) REVERT: F 18 GLU cc_start: 0.7525 (mp0) cc_final: 0.7215 (pp20) REVERT: F 19 ARG cc_start: 0.6241 (tpp80) cc_final: 0.5895 (mmm160) REVERT: F 25 SER cc_start: 0.8163 (t) cc_final: 0.7831 (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: 0.6776 (tpt) REVERT: F 85 LEU cc_start: 0.7450 (mt) cc_final: 0.7126 (mp) REVERT: F 90 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6906 (mmtp) REVERT: F 98 GLN cc_start: 0.7752 (mt0) cc_final: 0.7461 (mt0) outliers start: 152 outliers final: 33 residues processed: 337 average time/residue: 0.1376 time to fit residues: 58.9229 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 : 0.310 ------------------------------------------------------------------------------- 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: 10.0000 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: 3.9990 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... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 116 HIS A 286 ASN A 290 HIS A 306 HIS B 64 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN D 32 GLN E 52 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.234273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.177488 restraints weight = 12334.666| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 1.66 r_work: 0.3819 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10901 Z= 0.238 Angle : 0.783 9.143 15453 Z= 0.400 Chirality : 0.042 0.200 1836 Planarity : 0.006 0.057 1396 Dihedral : 24.285 179.742 3491 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.31 % Favored : 91.89 % Rotamer: Outliers : 7.39 % Allowed : 18.55 % Favored : 74.06 % 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 aren not related in a simple way. whole: -1.53 (0.28), residues: 876 helix: -0.22 (0.19), residues: 665 sheet: -4.13 (0.78), residues: 26 loop : -3.15 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 22 TYR 0.024 0.003 TYR C 28 PHE 0.019 0.003 PHE F 80 TRP 0.021 0.002 TRP D 116 HIS 0.011 0.002 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00545 (10901) covalent geometry : angle 0.78256 (15453) hydrogen bonds : bond 0.06041 ( 596) hydrogen bonds : angle 5.02320 ( 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 269 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 0.332 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: 0.7471 (mmt) cc_final: 0.6037 (ptm) REVERT: A 105 TYR cc_start: 0.8068 (m-10) cc_final: 0.7697 (m-80) REVERT: A 135 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6994 (tp) REVERT: A 193 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7637 (t80) REVERT: D 43 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7278 (tt0) REVERT: D 52 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: D 63 ASN cc_start: 0.6215 (OUTLIER) cc_final: 0.5967 (t0) REVERT: D 103 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7865 (mm-40) REVERT: F 44 MET cc_start: 0.8356 (mtp) cc_final: 0.8127 (mtm) outliers start: 55 outliers final: 21 residues processed: 255 average time/residue: 0.1157 time to fit residues: 39.5722 Evaluate side-chains 205 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 193 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 63 ASN 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 94 MET Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE 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: 0.5980 chunk 96 optimal weight: 30.0000 chunk 52 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 69 optimal weight: 0.3980 chunk 94 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS B 64 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.237668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.180793 restraints weight = 12622.780| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 1.64 r_work: 0.3858 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10901 Z= 0.197 Angle : 0.691 8.282 15453 Z= 0.352 Chirality : 0.039 0.199 1836 Planarity : 0.005 0.048 1396 Dihedral : 23.742 177.074 3390 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.53 % Favored : 92.01 % Rotamer: Outliers : 4.97 % Allowed : 20.30 % Favored : 74.73 % 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 aren not related in a simple way. whole: -1.10 (0.27), residues: 876 helix: 0.08 (0.19), residues: 658 sheet: -2.84 (0.94), residues: 24 loop : -3.03 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 228 TYR 0.020 0.002 TYR C 28 PHE 0.019 0.002 PHE D 80 TRP 0.016 0.002 TRP D 116 HIS 0.010 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00454 (10901) covalent geometry : angle 0.69105 (15453) hydrogen bonds : bond 0.05402 ( 596) hydrogen bonds : angle 4.70636 ( 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 233 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 0.321 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: 0.7362 (mmt) cc_final: 0.6111 (ptm) REVERT: A 105 TYR cc_start: 0.7962 (m-10) cc_final: 0.7574 (m-80) REVERT: A 135 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6917 (tp) REVERT: A 250 GLN cc_start: 0.6612 (pt0) cc_final: 0.6237 (pm20) REVERT: A 266 TRP cc_start: 0.7312 (m-90) cc_final: 0.5886 (m-90) REVERT: A 269 HIS cc_start: 0.6076 (p-80) cc_final: 0.5550 (p-80) REVERT: D 52 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.6985 (tm-30) outliers start: 37 outliers final: 22 residues processed: 222 average time/residue: 0.1098 time to fit residues: 32.8017 Evaluate side-chains 204 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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 C residue 115 SER Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 37 optimal weight: 0.0980 chunk 100 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS B 64 GLN F 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.237944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.180506 restraints weight = 12751.298| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.68 r_work: 0.3863 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10901 Z= 0.186 Angle : 0.662 8.013 15453 Z= 0.339 Chirality : 0.038 0.201 1836 Planarity : 0.005 0.048 1396 Dihedral : 23.394 176.673 3383 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.31 % Favored : 92.24 % Rotamer: Outliers : 4.57 % Allowed : 21.10 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.28), residues: 876 helix: 0.34 (0.19), residues: 653 sheet: -1.69 (1.13), residues: 24 loop : -2.97 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 19 TYR 0.030 0.003 TYR A 58 PHE 0.022 0.002 PHE B 80 TRP 0.015 0.002 TRP D 116 HIS 0.014 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00427 (10901) covalent geometry : angle 0.66215 (15453) hydrogen bonds : bond 0.05234 ( 596) hydrogen bonds : angle 4.64835 ( 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 216 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7327 (mmt) cc_final: 0.6063 (ptm) REVERT: A 128 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7562 (ttp-170) REVERT: A 135 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6757 (tp) REVERT: A 136 LYS cc_start: 0.6325 (OUTLIER) cc_final: 0.5855 (tptm) REVERT: A 184 LEU cc_start: 0.7971 (tp) cc_final: 0.7655 (tp) REVERT: A 214 MET cc_start: 0.8123 (tpp) cc_final: 0.7921 (tpp) REVERT: A 250 GLN cc_start: 0.6542 (pt0) cc_final: 0.6115 (pm20) REVERT: A 290 HIS cc_start: 0.0642 (OUTLIER) cc_final: 0.0048 (t-90) REVERT: B 108 GLU cc_start: 0.7703 (tt0) cc_final: 0.7410 (pt0) REVERT: D 52 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: E 54 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7275 (tp30) REVERT: F 19 ARG cc_start: 0.6980 (ttm-80) cc_final: 0.6742 (mmm-85) outliers start: 34 outliers final: 22 residues processed: 205 average time/residue: 0.1118 time to fit residues: 30.7678 Evaluate side-chains 195 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 135 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 115 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 D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN F 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.233097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.174535 restraints weight = 12420.284| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.62 r_work: 0.3808 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 10901 Z= 0.263 Angle : 0.715 7.935 15453 Z= 0.362 Chirality : 0.039 0.194 1836 Planarity : 0.005 0.051 1396 Dihedral : 23.381 176.583 3383 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.31 % Favored : 92.35 % Rotamer: Outliers : 4.30 % Allowed : 22.18 % Favored : 73.52 % 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 aren not related in a simple way. whole: -0.86 (0.27), residues: 876 helix: 0.18 (0.19), residues: 663 sheet: -1.38 (1.13), residues: 24 loop : -2.90 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 36 TYR 0.040 0.003 TYR A 58 PHE 0.031 0.003 PHE B 80 TRP 0.017 0.002 TRP D 116 HIS 0.014 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00619 (10901) covalent geometry : angle 0.71472 (15453) hydrogen bonds : bond 0.05738 ( 596) hydrogen bonds : angle 4.85250 ( 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 205 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7332 (mmt) cc_final: 0.6018 (ptm) REVERT: A 105 TYR cc_start: 0.8208 (m-80) cc_final: 0.7893 (m-80) REVERT: A 128 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7481 (ttp-170) REVERT: A 135 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6891 (tp) REVERT: A 136 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6145 (tptm) REVERT: A 184 LEU cc_start: 0.8153 (tp) cc_final: 0.7931 (tp) REVERT: A 193 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.7572 (t80) REVERT: A 290 HIS cc_start: 0.1057 (OUTLIER) cc_final: 0.0288 (t-90) REVERT: D 52 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: E 113 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7899 (tt) outliers start: 32 outliers final: 20 residues processed: 191 average time/residue: 0.1336 time to fit residues: 33.9117 Evaluate side-chains 193 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG 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 135 LEU Chi-restraints excluded: chain A residue 136 LYS 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 193 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain C residue 115 SER 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 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 73 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 94 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 0.0470 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 0.0870 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN F 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.238879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.182617 restraints weight = 12823.288| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 1.75 r_work: 0.3894 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10901 Z= 0.165 Angle : 0.645 9.572 15453 Z= 0.328 Chirality : 0.036 0.202 1836 Planarity : 0.005 0.050 1396 Dihedral : 23.197 175.981 3381 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.85 % Favored : 92.81 % Rotamer: Outliers : 4.17 % Allowed : 22.31 % Favored : 73.52 % 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 aren not related in a simple way. whole: -0.52 (0.28), residues: 876 helix: 0.40 (0.20), residues: 661 sheet: -1.39 (1.06), residues: 24 loop : -2.68 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 111 TYR 0.025 0.003 TYR A 58 PHE 0.025 0.002 PHE A 260 TRP 0.014 0.002 TRP D 116 HIS 0.011 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00379 (10901) covalent geometry : angle 0.64534 (15453) hydrogen bonds : bond 0.05211 ( 596) hydrogen bonds : angle 4.57680 ( 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 204 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7303 (mmt) cc_final: 0.6066 (ptm) REVERT: A 40 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7051 (pt0) REVERT: A 83 ASP cc_start: 0.7979 (m-30) cc_final: 0.7707 (m-30) REVERT: A 105 TYR cc_start: 0.8252 (m-80) cc_final: 0.7984 (m-80) REVERT: A 128 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7341 (ttm110) REVERT: A 136 LYS cc_start: 0.6520 (OUTLIER) cc_final: 0.6103 (tptm) REVERT: A 193 TYR cc_start: 0.7801 (OUTLIER) cc_final: 0.7492 (t80) REVERT: A 250 GLN cc_start: 0.6641 (pt0) cc_final: 0.6127 (pm20) REVERT: A 290 HIS cc_start: 0.0998 (OUTLIER) cc_final: 0.0025 (t-90) REVERT: D 52 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7424 (tm-30) REVERT: F 37 LYS cc_start: 0.7735 (ttmt) cc_final: 0.7380 (tttp) outliers start: 31 outliers final: 20 residues processed: 195 average time/residue: 0.1196 time to fit residues: 31.4664 Evaluate side-chains 185 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 177 VAL 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 193 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 115 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 E residue 75 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 30 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 0.0870 chunk 100 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 89 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN E 13 GLN F 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.240106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.182696 restraints weight = 12803.038| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 1.73 r_work: 0.3909 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10901 Z= 0.161 Angle : 0.642 8.383 15453 Z= 0.325 Chirality : 0.036 0.196 1836 Planarity : 0.005 0.049 1396 Dihedral : 23.085 175.923 3379 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.85 % Favored : 92.92 % Rotamer: Outliers : 3.36 % Allowed : 23.52 % Favored : 73.12 % 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 aren not related in a simple way. whole: -0.51 (0.28), residues: 876 helix: 0.42 (0.20), residues: 662 sheet: -1.68 (0.98), residues: 24 loop : -2.69 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 19 TYR 0.025 0.002 TYR F 69 PHE 0.026 0.002 PHE B 80 TRP 0.011 0.001 TRP D 116 HIS 0.012 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00366 (10901) covalent geometry : angle 0.64205 (15453) hydrogen bonds : bond 0.05257 ( 596) hydrogen bonds : angle 4.54494 ( 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 183 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7290 (mmt) cc_final: 0.5930 (ptm) REVERT: A 40 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6970 (pt0) REVERT: A 83 ASP cc_start: 0.8006 (m-30) cc_final: 0.7690 (m-30) REVERT: A 105 TYR cc_start: 0.8249 (m-80) cc_final: 0.7897 (m-80) REVERT: A 136 LYS cc_start: 0.6400 (OUTLIER) cc_final: 0.5713 (tptm) REVERT: A 193 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7459 (t80) REVERT: A 250 GLN cc_start: 0.6653 (pt0) cc_final: 0.6109 (pm20) REVERT: A 290 HIS cc_start: 0.0877 (OUTLIER) cc_final: 0.0118 (t-90) REVERT: D 18 GLU cc_start: 0.7814 (tm-30) cc_final: 0.6973 (tt0) REVERT: E 54 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7529 (mt-10) REVERT: E 67 LYS cc_start: 0.8687 (mmtp) cc_final: 0.8094 (mtmt) REVERT: F 37 LYS cc_start: 0.7717 (ttmt) cc_final: 0.7360 (tttp) outliers start: 25 outliers final: 20 residues processed: 173 average time/residue: 0.1191 time to fit residues: 28.1569 Evaluate side-chains 177 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 136 LYS Chi-restraints excluded: chain A residue 177 VAL 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 193 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 108 GLU 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 16 ILE Chi-restraints excluded: chain F residue 30 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 0.0570 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 0.0870 chunk 34 optimal weight: 0.5980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** F 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.240856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.184269 restraints weight = 12757.061| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 1.69 r_work: 0.3928 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.6481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10901 Z= 0.152 Angle : 0.638 8.588 15453 Z= 0.324 Chirality : 0.036 0.194 1836 Planarity : 0.005 0.050 1396 Dihedral : 22.999 175.967 3379 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.74 % Favored : 93.04 % Rotamer: Outliers : 3.49 % Allowed : 23.79 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.28), residues: 876 helix: 0.51 (0.20), residues: 661 sheet: -1.60 (1.01), residues: 24 loop : -2.51 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 22 TYR 0.023 0.002 TYR C 28 PHE 0.021 0.002 PHE B 80 TRP 0.009 0.001 TRP D 116 HIS 0.011 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00345 (10901) covalent geometry : angle 0.63780 (15453) hydrogen bonds : bond 0.05233 ( 596) hydrogen bonds : angle 4.50743 ( 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 181 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7271 (mmt) cc_final: 0.5892 (ptm) REVERT: A 40 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6996 (pt0) REVERT: A 83 ASP cc_start: 0.8018 (m-30) cc_final: 0.7710 (m-30) REVERT: A 105 TYR cc_start: 0.8194 (m-80) cc_final: 0.7870 (m-80) REVERT: A 136 LYS cc_start: 0.6305 (OUTLIER) cc_final: 0.5964 (tptm) REVERT: A 193 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7460 (t80) REVERT: A 250 GLN cc_start: 0.6644 (pt0) cc_final: 0.6178 (pm20) REVERT: A 290 HIS cc_start: 0.0923 (OUTLIER) cc_final: 0.0136 (t-90) REVERT: B 43 GLU cc_start: 0.7761 (tt0) cc_final: 0.7544 (tt0) REVERT: E 67 LYS cc_start: 0.8700 (mmtp) cc_final: 0.8109 (mtmt) REVERT: F 37 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7325 (tttp) outliers start: 26 outliers final: 19 residues processed: 172 average time/residue: 0.1271 time to fit residues: 29.5556 Evaluate side-chains 175 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 136 LYS Chi-restraints excluded: chain A residue 177 VAL 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 193 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 108 GLU 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 16 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 0.0980 chunk 56 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 94 optimal weight: 20.0000 chunk 79 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 62 optimal weight: 0.0870 chunk 68 optimal weight: 0.5980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 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 = 0.4750 r_free = 0.4750 target = 0.240665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.185153 restraints weight = 12773.485| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 1.78 r_work: 0.3910 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10901 Z= 0.161 Angle : 0.647 8.607 15453 Z= 0.325 Chirality : 0.036 0.191 1836 Planarity : 0.005 0.093 1396 Dihedral : 22.939 175.968 3379 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.74 % Favored : 93.04 % Rotamer: Outliers : 3.49 % Allowed : 24.33 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.28), residues: 876 helix: 0.55 (0.20), residues: 660 sheet: -1.00 (0.88), residues: 30 loop : -2.52 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 22 TYR 0.022 0.002 TYR C 28 PHE 0.021 0.002 PHE B 80 TRP 0.015 0.001 TRP D 116 HIS 0.012 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00369 (10901) covalent geometry : angle 0.64741 (15453) hydrogen bonds : bond 0.05288 ( 596) hydrogen bonds : angle 4.54900 ( 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 184 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7278 (mmt) cc_final: 0.5790 (ptm) REVERT: A 40 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6952 (pt0) REVERT: A 83 ASP cc_start: 0.8059 (m-30) cc_final: 0.7742 (m-30) REVERT: A 105 TYR cc_start: 0.8243 (m-80) cc_final: 0.7988 (m-80) REVERT: A 128 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7298 (ttm110) REVERT: A 136 LYS cc_start: 0.6385 (OUTLIER) cc_final: 0.6052 (tptm) REVERT: A 193 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7628 (t80) REVERT: A 250 GLN cc_start: 0.6692 (pt0) cc_final: 0.6233 (pm20) REVERT: A 290 HIS cc_start: 0.0950 (OUTLIER) cc_final: 0.0212 (t-90) REVERT: B 43 GLU cc_start: 0.7795 (tt0) cc_final: 0.7589 (tt0) REVERT: C 14 MET cc_start: 0.6038 (tpt) cc_final: 0.5702 (mmm) REVERT: D 19 ARG cc_start: 0.6616 (mmm-85) cc_final: 0.6407 (mmm-85) REVERT: E 67 LYS cc_start: 0.8685 (mmtp) cc_final: 0.8148 (mtmt) outliers start: 26 outliers final: 22 residues processed: 175 average time/residue: 0.1347 time to fit residues: 31.2856 Evaluate side-chains 180 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 177 VAL 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 193 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain C residue 89 GLN 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 16 ILE Chi-restraints excluded: chain F residue 30 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 78 optimal weight: 0.3980 chunk 89 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** F 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.238422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.181956 restraints weight = 12646.373| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 1.77 r_work: 0.3864 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.6615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10901 Z= 0.193 Angle : 0.676 8.822 15453 Z= 0.338 Chirality : 0.037 0.187 1836 Planarity : 0.005 0.051 1396 Dihedral : 22.903 175.576 3379 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.74 % Favored : 93.04 % Rotamer: Outliers : 3.49 % Allowed : 24.33 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.28), residues: 876 helix: 0.40 (0.20), residues: 665 sheet: -1.13 (0.88), residues: 30 loop : -2.59 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 111 TYR 0.025 0.003 TYR A 58 PHE 0.024 0.002 PHE B 80 TRP 0.017 0.002 TRP D 116 HIS 0.012 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00449 (10901) covalent geometry : angle 0.67584 (15453) hydrogen bonds : bond 0.05512 ( 596) hydrogen bonds : angle 4.63475 ( 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 181 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7268 (mmt) cc_final: 0.5960 (ptm) REVERT: A 31 ARG cc_start: 0.8173 (ptm-80) cc_final: 0.7949 (ptm-80) REVERT: A 67 LEU cc_start: 0.2192 (OUTLIER) cc_final: 0.1773 (pt) REVERT: A 128 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7314 (ttm110) REVERT: A 136 LYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6452 (tptm) REVERT: A 193 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7562 (t80) REVERT: A 220 LEU cc_start: 0.7577 (mt) cc_final: 0.7244 (mp) REVERT: A 234 LEU cc_start: 0.7716 (tp) cc_final: 0.7486 (mt) REVERT: A 250 GLN cc_start: 0.6844 (pt0) cc_final: 0.6323 (pm20) REVERT: A 290 HIS cc_start: 0.1007 (OUTLIER) cc_final: 0.0032 (t-90) REVERT: B 11 TYR cc_start: 0.6823 (t80) cc_final: 0.6416 (t80) REVERT: D 19 ARG cc_start: 0.6820 (mmm-85) cc_final: 0.6600 (mmm-85) REVERT: D 52 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7632 (tm130) REVERT: E 67 LYS cc_start: 0.8630 (mmtp) cc_final: 0.8166 (mtmt) outliers start: 26 outliers final: 19 residues processed: 173 average time/residue: 0.1254 time to fit residues: 28.8229 Evaluate side-chains 176 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 177 VAL 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 193 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 89 GLN 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 16 ILE Chi-restraints excluded: chain F residue 30 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.0270 chunk 50 optimal weight: 0.5980 chunk 96 optimal weight: 30.0000 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 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 = 0.4712 r_free = 0.4712 target = 0.235852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.176983 restraints weight = 12725.584| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.72 r_work: 0.3853 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 10901 Z= 0.248 Angle : 0.727 9.940 15453 Z= 0.363 Chirality : 0.039 0.184 1836 Planarity : 0.005 0.053 1396 Dihedral : 22.893 174.763 3379 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.96 % Favored : 92.69 % Rotamer: Outliers : 3.49 % Allowed : 24.73 % 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 aren not related in a simple way. whole: -0.78 (0.28), residues: 876 helix: 0.20 (0.19), residues: 664 sheet: -1.82 (0.98), residues: 24 loop : -2.69 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 36 TYR 0.036 0.003 TYR A 58 PHE 0.033 0.003 PHE B 80 TRP 0.014 0.002 TRP D 116 HIS 0.014 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00588 (10901) covalent geometry : angle 0.72722 (15453) hydrogen bonds : bond 0.05872 ( 596) hydrogen bonds : angle 4.88794 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2665.25 seconds wall clock time: 46 minutes 37.72 seconds (2797.72 seconds total)