Starting phenix.real_space_refine on Wed Aug 5 14:24:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ub7_42077/08_2026/8ub7_42077.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ub7_42077/08_2026/8ub7_42077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ub7_42077/08_2026/8ub7_42077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ub7_42077/08_2026/8ub7_42077.map" model { file = "/net/cci-nas-00/data/ceres_data/8ub7_42077/08_2026/8ub7_42077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ub7_42077/08_2026/8ub7_42077.cif" } resolution = 3.2 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= 0.029 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: 6 Type Number sf(0) Gaussians P 151 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 6073 2.51 5 N 1871 2.21 5 O 2267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10399 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2690 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} 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: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2605 Classifications: {'RNA': 122} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 11, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 23, 'rna3p': 98} Chain breaks: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.85, per 1000 atoms: 0.18 Number of scatterers: 10399 At special positions: 0 Unit cell: (81, 105, 134, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 151 15.00 Mg 1 11.99 O 2267 8.00 N 1871 7.00 C 6073 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: 0.87 Conformation dependent library (CDL) restraints added in 237.6 milliseconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1676 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 3 sheets defined 75.7% alpha, 2.6% beta 48 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.556A pdb=" N ASP A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.503A pdb=" N ALA A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.617A 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: 4.200A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 241 Processing helix chain 'A' and resid 273 through 289 Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.931A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.726A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.531A 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 50 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 64 through 88 removed outlier: 3.537A 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 32 removed outlier: 3.754A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 51 through 60 removed outlier: 3.507A pdb=" N LEU C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 88 removed outlier: 3.508A pdb=" N LEU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 121 Processing helix chain 'D' and resid 14 through 32 removed outlier: 3.775A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.613A 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: 3.529A 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: 3.749A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 66 through 86 removed outlier: 3.730A 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 34 removed outlier: 4.579A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Proline residue: F 29 - end of helix removed outlier: 3.557A pdb=" N ILE F 34 " --> pdb=" O ILE F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 64 through 87 removed outlier: 3.597A 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: 4.484A 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: 4.321A pdb=" N HIS A 248 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 265 474 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1406 1.32 - 1.45: 4069 1.45 - 1.58: 5098 1.58 - 1.71: 297 1.71 - 1.84: 61 Bond restraints: 10931 Sorted by residual: bond pdb=" C3' DCP A 401 " pdb=" C4' DCP A 401 " ideal model delta sigma weight residual 1.534 1.302 0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C1' DCP A 401 " pdb=" C2' DCP A 401 " ideal model delta sigma weight residual 1.534 1.356 0.178 2.00e-02 2.50e+03 7.97e+01 bond pdb=" C4' DCP A 401 " pdb=" O4' DCP A 401 " ideal model delta sigma weight residual 1.420 1.540 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" CA ARG A 4 " pdb=" C ARG A 4 " ideal model delta sigma weight residual 1.529 1.474 0.055 9.30e-03 1.16e+04 3.50e+01 bond pdb=" C1' DCP A 401 " pdb=" N1 DCP A 401 " ideal model delta sigma weight residual 1.460 1.572 -0.112 2.00e-02 2.50e+03 3.13e+01 ... (remaining 10926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 14086 2.55 - 5.09: 1262 5.09 - 7.64: 129 7.64 - 10.18: 17 10.18 - 12.73: 2 Bond angle restraints: 15496 Sorted by residual: angle pdb=" C ARG A 4 " pdb=" CA ARG A 4 " pdb=" CB ARG A 4 " ideal model delta sigma weight residual 116.54 107.41 9.13 1.15e+00 7.56e-01 6.30e+01 angle pdb=" N ARG A 6 " pdb=" CA ARG A 6 " pdb=" C ARG A 6 " ideal model delta sigma weight residual 111.55 120.36 -8.81 1.37e+00 5.33e-01 4.13e+01 angle pdb=" N ARG A 31 " pdb=" CA ARG A 31 " pdb=" C ARG A 31 " ideal model delta sigma weight residual 110.61 103.22 7.39 1.25e+00 6.40e-01 3.50e+01 angle pdb=" CA GLN F 103 " pdb=" CB GLN F 103 " pdb=" CG GLN F 103 " ideal model delta sigma weight residual 114.10 102.41 11.69 2.00e+00 2.50e-01 3.42e+01 angle pdb=" N GLN F 32 " pdb=" CA GLN F 32 " pdb=" C GLN F 32 " ideal model delta sigma weight residual 111.71 105.25 6.46 1.15e+00 7.56e-01 3.15e+01 ... (remaining 15491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 5944 35.16 - 70.32: 777 70.32 - 105.48: 74 105.48 - 140.64: 1 140.64 - 175.80: 4 Dihedral angle restraints: 6800 sinusoidal: 4201 harmonic: 2599 Sorted by residual: dihedral pdb=" C5' A I 56 " pdb=" C4' A I 56 " pdb=" C3' A I 56 " pdb=" O3' A I 56 " ideal model delta sinusoidal sigma weight residual 147.00 87.25 59.75 1 8.00e+00 1.56e-02 7.44e+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 -128.00 46.18 -174.18 1 1.70e+01 3.46e-03 6.63e+01 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 61.10 170.90 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 6797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1504 0.120 - 0.240: 293 0.240 - 0.360: 30 0.360 - 0.480: 6 0.480 - 0.600: 4 Chirality restraints: 1837 Sorted by residual: 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 -3.01 -0.60 2.00e-01 2.50e+01 9.00e+00 chirality pdb=" P U I 47 " pdb=" OP1 U I 47 " pdb=" OP2 U I 47 " pdb=" O5' U I 47 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.48e+00 chirality pdb=" P G G 369 " pdb=" OP1 G G 369 " pdb=" OP2 G G 369 " pdb=" O5' G G 369 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.45e+00 ... (remaining 1834 not shown) Planarity restraints: 1403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " -0.081 2.00e-02 2.50e+03 4.09e-02 3.34e+01 pdb=" CG TYR C 28 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U I 7 " -0.066 2.00e-02 2.50e+03 3.07e-02 2.12e+01 pdb=" N1 U I 7 " 0.032 2.00e-02 2.50e+03 pdb=" C2 U I 7 " 0.021 2.00e-02 2.50e+03 pdb=" O2 U I 7 " 0.007 2.00e-02 2.50e+03 pdb=" N3 U I 7 " 0.010 2.00e-02 2.50e+03 pdb=" C4 U I 7 " -0.013 2.00e-02 2.50e+03 pdb=" O4 U I 7 " -0.034 2.00e-02 2.50e+03 pdb=" C5 U I 7 " 0.009 2.00e-02 2.50e+03 pdb=" C6 U I 7 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 90 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO C 91 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " -0.056 5.00e-02 4.00e+02 ... (remaining 1400 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1821 2.76 - 3.30: 10122 3.30 - 3.83: 21661 3.83 - 4.37: 26817 4.37 - 4.90: 37337 Nonbonded interactions: 97758 Sorted by model distance: nonbonded pdb=" OD2 ASP A 215 " pdb="MG MG A 402 " model vdw 2.230 2.170 nonbonded pdb=" O ILE A 159 " pdb=" N CYS A 161 " model vdw 2.273 3.120 nonbonded pdb=" OD1 ASP A 138 " pdb="MG MG A 402 " model vdw 2.276 2.170 nonbonded pdb=" O ALA E 118 " pdb=" O ASN E 121 " model vdw 2.300 3.040 nonbonded pdb=" O PHE A 139 " pdb="MG MG A 402 " model vdw 2.345 2.170 ... (remaining 97753 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.720 Find NCS groups from input model: 0.130 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 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 : 0.011 0.232 10931 Z= 0.686 Angle : 1.520 12.729 15496 Z= 1.000 Chirality : 0.097 0.600 1837 Planarity : 0.011 0.106 1403 Dihedral : 25.404 175.798 5124 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 2.27 % Allowed : 9.08 % Favored : 88.65 % Rotamer: Outliers : 20.48 % Allowed : 13.92 % Favored : 65.60 % 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: -3.80 (0.24), residues: 881 helix: -1.84 (0.17), residues: 663 sheet: -4.83 (0.91), residues: 24 loop : -3.99 (0.36), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG B 22 TYR 0.081 0.008 TYR C 28 PHE 0.057 0.009 PHE A 231 TRP 0.040 0.008 TRP A 33 HIS 0.018 0.004 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.01088 / 0.69 (10931) covalent geometry : angle 1.52041 / 1.00 (15496) hydrogen bonds : bond 0.18109 / 12.00 ( 595) hydrogen bonds : angle 8.70736 / 6.13 ( 1594) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 154 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7509 (ptm-80) REVERT: A 112 ASP cc_start: 0.8266 (m-30) cc_final: 0.7874 (t70) REVERT: A 222 ASP cc_start: 0.7857 (p0) cc_final: 0.7309 (t0) REVERT: A 223 ASP cc_start: 0.8338 (t70) cc_final: 0.7798 (t0) REVERT: B 75 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7236 (mt) REVERT: B 90 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6794 (tppt) REVERT: B 108 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6996 (tt0) REVERT: C 14 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.5925 (ttt) REVERT: C 90 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6468 (mtpp) REVERT: C 92 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.6862 (m170) REVERT: D 15 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5919 (tp) REVERT: D 19 ARG cc_start: 0.7493 (mmt-90) cc_final: 0.7240 (mmp80) REVERT: D 64 GLN cc_start: 0.6507 (OUTLIER) cc_final: 0.6030 (pm20) REVERT: D 122 ARG cc_start: 0.4726 (OUTLIER) cc_final: 0.4464 (mmp-170) REVERT: E 19 ARG cc_start: 0.7046 (mmm160) cc_final: 0.6777 (mmm160) REVERT: E 50 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6861 (mt) REVERT: E 52 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6770 (tp40) REVERT: E 54 GLU cc_start: 0.7082 (tt0) cc_final: 0.6831 (tt0) REVERT: E 63 ASN cc_start: 0.6692 (OUTLIER) cc_final: 0.6125 (t0) REVERT: E 77 MET cc_start: 0.8196 (tpt) cc_final: 0.7619 (tpp) REVERT: E 89 GLN cc_start: 0.6429 (OUTLIER) cc_final: 0.6151 (mt0) REVERT: E 90 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6484 (ttmm) REVERT: E 94 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8362 (ttm) REVERT: F 13 GLN cc_start: 0.4172 (OUTLIER) cc_final: 0.3437 (mt0) REVERT: F 14 MET cc_start: 0.5244 (OUTLIER) cc_final: 0.3710 (ttp) REVERT: F 19 ARG cc_start: 0.6747 (tpp80) cc_final: 0.6477 (mmm160) REVERT: F 43 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6458 (mp0) REVERT: F 65 VAL cc_start: 0.6832 (OUTLIER) cc_final: 0.6451 (t) REVERT: F 77 MET cc_start: 0.7380 (tpt) cc_final: 0.6831 (tpt) REVERT: F 90 LYS cc_start: 0.5191 (OUTLIER) cc_final: 0.4842 (mtpp) REVERT: F 122 ARG cc_start: 0.5272 (OUTLIER) cc_final: 0.4648 (mtt-85) REVERT: F 123 LYS cc_start: 0.3481 (OUTLIER) cc_final: 0.3246 (mttm) outliers start: 153 outliers final: 46 residues processed: 272 average time/residue: 0.1513 time to fit residues: 51.4409 Evaluate side-chains 195 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 126 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 170 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 208 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 91 PRO Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN C 121 ASN F 13 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.182975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139851 restraints weight = 12820.285| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.39 r_work: 0.3448 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10931 Z= 0.210 Angle : 0.751 8.779 15496 Z= 0.409 Chirality : 0.046 0.243 1837 Planarity : 0.008 0.132 1403 Dihedral : 24.411 179.481 3550 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.72 % Favored : 91.37 % Rotamer: Outliers : 8.84 % Allowed : 18.74 % Favored : 72.42 % 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: -1.79 (0.27), residues: 881 helix: -0.38 (0.19), residues: 668 sheet: -3.99 (0.91), residues: 22 loop : -3.44 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 74 TYR 0.022 0.002 TYR C 28 PHE 0.032 0.003 PHE B 80 TRP 0.016 0.002 TRP D 116 HIS 0.006 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (10931) covalent geometry : angle 0.75147 / 0.41 (15496) hydrogen bonds : bond 0.07231 / 4.69 ( 595) hydrogen bonds : angle 4.86102 / 3.37 ( 1594) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 138 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8989 (t80) cc_final: 0.8764 (t80) REVERT: A 208 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8337 (mpt90) REVERT: A 248 HIS cc_start: 0.7908 (m-70) cc_final: 0.7696 (m-70) REVERT: A 256 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7775 (mtp-110) REVERT: C 14 MET cc_start: 0.7493 (tpt) cc_final: 0.7092 (ttt) REVERT: C 33 SER cc_start: 0.8610 (p) cc_final: 0.8403 (m) REVERT: C 90 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.6871 (mtpp) REVERT: E 50 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7589 (mt) REVERT: E 52 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7368 (tp40) REVERT: E 67 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8464 (mttp) REVERT: F 14 MET cc_start: 0.5647 (mmt) cc_final: 0.5059 (tmm) REVERT: F 33 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8095 (p) REVERT: F 43 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: F 83 ARG cc_start: 0.8119 (ptp90) cc_final: 0.7835 (ptp90) REVERT: F 122 ARG cc_start: 0.4874 (OUTLIER) cc_final: 0.4023 (tmm160) outliers start: 66 outliers final: 24 residues processed: 193 average time/residue: 0.1374 time to fit residues: 34.1793 Evaluate side-chains 150 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 170 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 208 ARG Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 88 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.0670 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN C 92 HIS E 52 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.174434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.134520 restraints weight = 12689.594| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.24 r_work: 0.3319 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10931 Z= 0.161 Angle : 0.619 8.602 15496 Z= 0.345 Chirality : 0.040 0.221 1837 Planarity : 0.007 0.135 1403 Dihedral : 23.813 177.201 3446 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.04 % Favored : 92.17 % Rotamer: Outliers : 6.43 % Allowed : 21.42 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.01 (0.28), residues: 881 helix: 0.16 (0.19), residues: 666 sheet: -3.08 (1.07), residues: 22 loop : -3.12 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 19 TYR 0.017 0.002 TYR F 28 PHE 0.028 0.002 PHE A 231 TRP 0.009 0.001 TRP F 81 HIS 0.013 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (10931) covalent geometry : angle 0.61904 / 0.35 (15496) hydrogen bonds : bond 0.05880 / 3.74 ( 595) hydrogen bonds : angle 4.41533 / 3.07 ( 1594) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7963 (mtpp) REVERT: B 4 ILE cc_start: 0.8980 (mt) cc_final: 0.8741 (mt) REVERT: C 33 SER cc_start: 0.8486 (p) cc_final: 0.8263 (m) REVERT: C 89 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6527 (pp30) REVERT: E 19 ARG cc_start: 0.7052 (mmm160) cc_final: 0.6783 (mmm160) REVERT: E 50 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7656 (mt) REVERT: E 52 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7193 (tp40) REVERT: E 108 GLU cc_start: 0.8109 (tp30) cc_final: 0.7485 (tp30) REVERT: F 14 MET cc_start: 0.5277 (mmp) cc_final: 0.4539 (ttm) REVERT: F 43 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7733 (tp30) REVERT: F 122 ARG cc_start: 0.4615 (OUTLIER) cc_final: 0.3964 (tmm160) outliers start: 48 outliers final: 24 residues processed: 169 average time/residue: 0.1321 time to fit residues: 29.1982 Evaluate side-chains 150 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 94 VAL 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 276 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 58 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 HIS C 13 GLN C 32 GLN C 121 ASN ** F 98 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 = 0.4001 r_free = 0.4001 target = 0.174310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.133705 restraints weight = 12930.273| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.26 r_work: 0.3229 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10931 Z= 0.158 Angle : 0.591 7.833 15496 Z= 0.323 Chirality : 0.039 0.206 1837 Planarity : 0.006 0.125 1403 Dihedral : 23.426 179.226 3412 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.81 % Favored : 92.51 % Rotamer: Outliers : 4.82 % Allowed : 23.96 % Favored : 71.22 % 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: -0.60 (0.28), residues: 881 helix: 0.44 (0.20), residues: 665 sheet: -2.59 (1.19), residues: 22 loop : -2.92 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 122 TYR 0.014 0.002 TYR F 28 PHE 0.026 0.002 PHE A 231 TRP 0.010 0.001 TRP F 116 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (10931) covalent geometry : angle 0.59093 / 0.32 (15496) hydrogen bonds : bond 0.05634 / 3.56 ( 595) hydrogen bonds : angle 4.22031 / 2.95 ( 1594) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7878 (mtpp) REVERT: B 4 ILE cc_start: 0.8860 (mt) cc_final: 0.8623 (mt) REVERT: B 77 MET cc_start: 0.8801 (tpt) cc_final: 0.8503 (tpt) REVERT: E 50 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7361 (mt) REVERT: E 52 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7216 (tp40) REVERT: E 67 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8582 (mmtt) REVERT: E 108 GLU cc_start: 0.7969 (tp30) cc_final: 0.7756 (tp30) REVERT: F 43 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7854 (tp30) outliers start: 36 outliers final: 21 residues processed: 154 average time/residue: 0.1229 time to fit residues: 24.7628 Evaluate side-chains 145 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 94 optimal weight: 40.0000 chunk 18 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS ** F 98 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 = 0.4012 r_free = 0.4012 target = 0.175252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134100 restraints weight = 12943.412| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.23 r_work: 0.3289 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10931 Z= 0.151 Angle : 0.569 9.052 15496 Z= 0.314 Chirality : 0.038 0.238 1837 Planarity : 0.006 0.123 1403 Dihedral : 23.286 179.308 3403 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.68 % Favored : 93.53 % Rotamer: Outliers : 4.95 % Allowed : 23.43 % Favored : 71.62 % 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: -0.27 (0.28), residues: 881 helix: 0.65 (0.20), residues: 664 sheet: -2.53 (1.20), residues: 22 loop : -2.65 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 122 TYR 0.011 0.001 TYR F 28 PHE 0.024 0.002 PHE A 231 TRP 0.008 0.001 TRP A 210 HIS 0.005 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (10931) covalent geometry : angle 0.56887 / 0.31 (15496) hydrogen bonds : bond 0.05326 / 3.33 ( 595) hydrogen bonds : angle 4.08270 / 2.85 ( 1594) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7953 (t70) cc_final: 0.7548 (t70) REVERT: A 283 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7777 (mtpp) REVERT: B 4 ILE cc_start: 0.8788 (mt) cc_final: 0.8573 (mt) REVERT: C 47 LYS cc_start: 0.8594 (mttm) cc_final: 0.8386 (mtpt) REVERT: E 50 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7427 (mt) REVERT: E 52 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7178 (tp40) outliers start: 37 outliers final: 24 residues processed: 155 average time/residue: 0.1186 time to fit residues: 24.3258 Evaluate side-chains 149 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL 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 254 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU 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 69 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 25 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 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 = 0.4022 r_free = 0.4022 target = 0.176121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.136341 restraints weight = 13038.073| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.20 r_work: 0.3267 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 10931 Z= 0.140 Angle : 0.560 10.056 15496 Z= 0.305 Chirality : 0.038 0.189 1837 Planarity : 0.006 0.120 1403 Dihedral : 23.091 178.883 3400 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.45 % Favored : 93.76 % Rotamer: Outliers : 4.42 % Allowed : 23.83 % Favored : 71.75 % 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: -0.12 (0.28), residues: 881 helix: 0.74 (0.20), residues: 666 sheet: -2.42 (1.19), residues: 22 loop : -2.56 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 122 TYR 0.013 0.001 TYR A 35 PHE 0.024 0.002 PHE B 80 TRP 0.007 0.001 TRP A 303 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (10931) covalent geometry : angle 0.56048 / 0.31 (15496) hydrogen bonds : bond 0.05215 / 3.25 ( 595) hydrogen bonds : angle 4.03159 / 2.82 ( 1594) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8727 (t80) cc_final: 0.8473 (t80) REVERT: A 283 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7813 (mtpp) REVERT: C 47 LYS cc_start: 0.8589 (mttm) cc_final: 0.8388 (mtpt) REVERT: D 103 GLN cc_start: 0.8140 (mt0) cc_final: 0.7872 (mm-40) REVERT: E 52 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7143 (tp40) outliers start: 33 outliers final: 20 residues processed: 155 average time/residue: 0.1255 time to fit residues: 25.2186 Evaluate side-chains 143 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL 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 254 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 16 ILE 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 18 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 GLN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS ** F 98 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 = 0.4013 r_free = 0.4013 target = 0.175258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.134282 restraints weight = 12905.491| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.25 r_work: 0.3308 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10931 Z= 0.165 Angle : 0.575 8.673 15496 Z= 0.314 Chirality : 0.038 0.190 1837 Planarity : 0.006 0.119 1403 Dihedral : 22.943 178.541 3393 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.56 % Favored : 93.64 % Rotamer: Outliers : 4.55 % Allowed : 23.83 % Favored : 71.62 % 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: -0.12 (0.28), residues: 881 helix: 0.74 (0.20), residues: 667 sheet: -2.60 (1.12), residues: 24 loop : -2.54 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 36 TYR 0.014 0.001 TYR B 26 PHE 0.024 0.002 PHE B 80 TRP 0.007 0.001 TRP A 249 HIS 0.004 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (10931) covalent geometry : angle 0.57486 / 0.31 (15496) hydrogen bonds : bond 0.05267 / 3.30 ( 595) hydrogen bonds : angle 4.03905 / 2.81 ( 1594) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7967 (t70) cc_final: 0.7491 (t70) REVERT: A 283 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7834 (mtpp) REVERT: C 47 LYS cc_start: 0.8653 (mttm) cc_final: 0.8437 (mtpt) REVERT: D 103 GLN cc_start: 0.8145 (mt0) cc_final: 0.7882 (mm-40) REVERT: E 52 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7313 (tp40) REVERT: F 43 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7553 (tp30) outliers start: 34 outliers final: 26 residues processed: 145 average time/residue: 0.1357 time to fit residues: 25.7026 Evaluate side-chains 148 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 138 ASP 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 200 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 65 VAL 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 22 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 GLN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 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 = 0.4020 r_free = 0.4020 target = 0.175735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.135930 restraints weight = 12838.691| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.16 r_work: 0.3355 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10931 Z= 0.155 Angle : 0.559 9.594 15496 Z= 0.306 Chirality : 0.037 0.206 1837 Planarity : 0.006 0.118 1403 Dihedral : 22.825 178.225 3393 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.79 % Favored : 93.42 % Rotamer: Outliers : 4.15 % Allowed : 24.36 % Favored : 71.49 % 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: -0.01 (0.28), residues: 881 helix: 0.83 (0.20), residues: 664 sheet: -2.26 (1.17), residues: 22 loop : -2.57 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 122 TYR 0.010 0.001 TYR A 35 PHE 0.023 0.002 PHE B 80 TRP 0.007 0.001 TRP A 303 HIS 0.003 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (10931) covalent geometry : angle 0.55942 / 0.31 (15496) hydrogen bonds : bond 0.05203 / 3.25 ( 595) hydrogen bonds : angle 3.99530 / 2.79 ( 1594) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7956 (t70) cc_final: 0.7518 (t70) REVERT: A 283 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7810 (mtpp) REVERT: C 47 LYS cc_start: 0.8630 (mttm) cc_final: 0.8415 (mtpt) REVERT: D 103 GLN cc_start: 0.8117 (mt0) cc_final: 0.7892 (mm-40) REVERT: E 52 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7329 (tp40) REVERT: E 54 GLU cc_start: 0.7403 (tt0) cc_final: 0.7115 (tt0) REVERT: F 43 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7487 (tp30) outliers start: 31 outliers final: 26 residues processed: 146 average time/residue: 0.1270 time to fit residues: 24.4385 Evaluate side-chains 149 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 ILE 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 200 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 87 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 GLN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 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 = 0.4020 r_free = 0.4020 target = 0.175778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.134640 restraints weight = 12865.632| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.20 r_work: 0.3296 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 10931 Z= 0.158 Angle : 0.561 9.742 15496 Z= 0.306 Chirality : 0.037 0.196 1837 Planarity : 0.006 0.118 1403 Dihedral : 22.716 178.176 3393 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.90 % Favored : 93.30 % Rotamer: Outliers : 4.28 % Allowed : 24.23 % Favored : 71.49 % 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: -0.01 (0.28), residues: 881 helix: 0.81 (0.20), residues: 666 sheet: -2.20 (1.15), residues: 22 loop : -2.55 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 19 TYR 0.011 0.001 TYR C 28 PHE 0.024 0.002 PHE B 80 TRP 0.007 0.001 TRP A 249 HIS 0.003 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (10931) covalent geometry : angle 0.56092 / 0.31 (15496) hydrogen bonds : bond 0.05213 / 3.25 ( 595) hydrogen bonds : angle 4.02530 / 2.81 ( 1594) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7971 (t70) cc_final: 0.7568 (t70) REVERT: A 283 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7812 (mtpp) REVERT: C 47 LYS cc_start: 0.8632 (mttm) cc_final: 0.8418 (mtpt) REVERT: D 103 GLN cc_start: 0.8076 (mt0) cc_final: 0.7863 (mm-40) REVERT: E 52 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7266 (tp40) REVERT: E 54 GLU cc_start: 0.7355 (tt0) cc_final: 0.7057 (tt0) REVERT: F 43 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7521 (tp30) outliers start: 32 outliers final: 24 residues processed: 144 average time/residue: 0.1351 time to fit residues: 25.0669 Evaluate side-chains 145 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 95 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 7 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 GLN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 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 = 0.4023 r_free = 0.4023 target = 0.175911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135595 restraints weight = 12824.281| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.20 r_work: 0.3321 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 10931 Z= 0.155 Angle : 0.567 10.223 15496 Z= 0.309 Chirality : 0.037 0.200 1837 Planarity : 0.006 0.118 1403 Dihedral : 22.613 178.037 3391 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.36 % Favored : 92.96 % Rotamer: Outliers : 3.61 % Allowed : 24.90 % Favored : 71.49 % 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: 0.01 (0.28), residues: 881 helix: 0.82 (0.20), residues: 666 sheet: -2.17 (1.13), residues: 22 loop : -2.52 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 36 TYR 0.011 0.001 TYR F 20 PHE 0.025 0.002 PHE B 80 TRP 0.007 0.001 TRP A 249 HIS 0.003 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (10931) covalent geometry : angle 0.56739 / 0.31 (15496) hydrogen bonds : bond 0.05226 / 3.25 ( 595) hydrogen bonds : angle 4.03698 / 2.82 ( 1594) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8719 (t80) cc_final: 0.8355 (t80) REVERT: A 223 ASP cc_start: 0.7665 (t70) cc_final: 0.7226 (t70) REVERT: A 283 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7747 (mtpp) REVERT: C 47 LYS cc_start: 0.8537 (mttm) cc_final: 0.8334 (mtpt) REVERT: D 14 MET cc_start: 0.6921 (mtp) cc_final: 0.6602 (mtt) REVERT: D 18 GLU cc_start: 0.7299 (mp0) cc_final: 0.6966 (mp0) REVERT: E 52 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.7074 (tp40) REVERT: E 54 GLU cc_start: 0.7220 (tt0) cc_final: 0.6927 (tt0) REVERT: F 43 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7240 (tp30) outliers start: 27 outliers final: 23 residues processed: 144 average time/residue: 0.1292 time to fit residues: 24.0151 Evaluate side-chains 145 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 GLN C 32 GLN C 92 HIS ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.187621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148076 restraints weight = 13032.518| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.19 r_work: 0.3533 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 10931 Z= 0.160 Angle : 0.571 11.361 15496 Z= 0.308 Chirality : 0.038 0.202 1837 Planarity : 0.006 0.118 1403 Dihedral : 22.526 178.043 3391 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.90 % Favored : 93.42 % Rotamer: Outliers : 3.75 % Allowed : 25.17 % Favored : 71.08 % 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: 0.04 (0.28), residues: 881 helix: 0.85 (0.19), residues: 665 sheet: -2.17 (1.13), residues: 22 loop : -2.50 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 19 TYR 0.012 0.001 TYR C 28 PHE 0.025 0.002 PHE B 80 TRP 0.011 0.001 TRP A 309 HIS 0.004 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (10931) covalent geometry : angle 0.57126 / 0.31 (15496) hydrogen bonds : bond 0.05223 / 3.24 ( 595) hydrogen bonds : angle 4.02422 / 2.81 ( 1594) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2470.88 seconds wall clock time: 43 minutes 12.31 seconds (2592.31 seconds total)