Starting phenix.real_space_refine on Wed Aug 5 22:16:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo0_43363/08_2026/8vo0_43363.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo0_43363/08_2026/8vo0_43363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vo0_43363/08_2026/8vo0_43363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo0_43363/08_2026/8vo0_43363.map" model { file = "/net/cci-nas-00/data/ceres_data/8vo0_43363/08_2026/8vo0_43363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo0_43363/08_2026/8vo0_43363.cif" } resolution = 3.3 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= 0.039 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 314 5.49 5 S 14 5.16 5 C 6691 2.51 5 N 2285 2.21 5 O 2913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 12217 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 3237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3237 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "I" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 738 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "J" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 672 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 84} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "Q" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "R" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "S" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 689 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3202 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Time building chain proxies: 2.27, per 1000 atoms: 0.19 Number of scatterers: 12217 At special positions: 0 Unit cell: (116.55, 136.5, 122.85, 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 14 16.00 P 314 15.00 O 2913 8.00 N 2285 7.00 C 6691 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: 0.76 Conformation dependent library (CDL) restraints added in 308.8 milliseconds 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1370 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 73.4% alpha, 1.9% beta 156 base pairs and 265 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'I' and resid 46 through 55 removed outlier: 3.552A pdb=" N GLN I 55 " --> pdb=" O ILE I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 76 Processing helix chain 'I' and resid 85 through 114 Processing helix chain 'I' and resid 120 through 132 removed outlier: 3.521A pdb=" N ILE I 124 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 29 Processing helix chain 'J' and resid 30 through 42 Processing helix chain 'J' and resid 49 through 76 removed outlier: 4.290A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 94 removed outlier: 3.535A pdb=" N VAL J 86 " --> pdb=" O THR J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 22 removed outlier: 3.527A pdb=" N ARG K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 45 through 73 removed outlier: 4.398A pdb=" N VAL K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 89 removed outlier: 3.516A pdb=" N ASN K 89 " --> pdb=" O LEU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 97 removed outlier: 3.548A pdb=" N LEU K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 46 Processing helix chain 'M' and resid 53 through 81 removed outlier: 3.555A pdb=" N MET M 59 " --> pdb=" O ALA M 55 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 99 removed outlier: 3.589A pdb=" N ILE M 91 " --> pdb=" O THR M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 121 removed outlier: 3.502A pdb=" N SER M 109 " --> pdb=" O LYS M 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 55 Processing helix chain 'O' and resid 63 through 79 removed outlier: 4.088A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 132 removed outlier: 3.521A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 30 through 42 Processing helix chain 'Q' and resid 49 through 77 removed outlier: 4.202A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG Q 55 " --> pdb=" O TYR Q 51 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP Q 68 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 93 removed outlier: 3.710A pdb=" N VAL Q 86 " --> pdb=" O THR Q 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 22 removed outlier: 3.620A pdb=" N ARG R 20 " --> pdb=" O THR R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 36 Processing helix chain 'R' and resid 45 through 73 removed outlier: 4.265A pdb=" N VAL R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 89 Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'S' and resid 35 through 46 Processing helix chain 'S' and resid 52 through 81 Processing helix chain 'S' and resid 87 through 99 Processing helix chain 'S' and resid 101 through 121 removed outlier: 3.769A pdb=" N LYS S 105 " --> pdb=" O GLY S 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 83 through 84 removed outlier: 7.644A pdb=" N ARG I 83 " --> pdb=" O VAL J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'I' and resid 118 through 119 removed outlier: 4.010A pdb=" N ILE I 119 " --> pdb=" O ARG J 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'J' and resid 97 through 98 removed outlier: 3.537A pdb=" N TYR J 98 " --> pdb=" O THR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'K' and resid 42 through 43 removed outlier: 7.674A pdb=" N ARG K 42 " --> pdb=" O ILE M 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 101 through 102 removed outlier: 6.898A pdb=" N THR K 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.312A pdb=" N ARG R 42 " --> pdb=" O ILE S 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'R' and resid 77 through 78 381 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 396 hydrogen bonds 756 hydrogen bond angles 0 basepair planarities 156 basepair parallelities 265 stacking parallelities Total time for adding SS restraints: 1.82 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: 0.78 - 1.04: 1 1.04 - 1.30: 1246 1.30 - 1.56: 11171 1.56 - 1.82: 654 1.82 - 2.08: 1 Bond restraints: 13073 Sorted by residual: bond pdb=" CG PRO Q 32 " pdb=" CD PRO Q 32 " ideal model delta sigma weight residual 1.503 0.780 0.723 3.40e-02 8.65e+02 4.52e+02 bond pdb=" CB PRO Q 32 " pdb=" CG PRO Q 32 " ideal model delta sigma weight residual 1.492 2.083 -0.591 5.00e-02 4.00e+02 1.40e+02 bond pdb=" N PRO Q 32 " pdb=" CD PRO Q 32 " ideal model delta sigma weight residual 1.473 1.609 -0.136 1.40e-02 5.10e+03 9.46e+01 bond pdb=" C LYS Q 31 " pdb=" N PRO Q 32 " ideal model delta sigma weight residual 1.336 1.447 -0.111 1.25e-02 6.40e+03 7.92e+01 bond pdb=" CZ ARG R 71 " pdb=" NH1 ARG R 71 " ideal model delta sigma weight residual 1.323 1.215 0.108 1.40e-02 5.10e+03 5.90e+01 ... (remaining 13068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 19013 21.21 - 42.42: 2 42.42 - 63.63: 0 63.63 - 84.85: 0 84.85 - 106.06: 1 Bond angle restraints: 19016 Sorted by residual: angle pdb=" CB PRO Q 32 " pdb=" CG PRO Q 32 " pdb=" CD PRO Q 32 " ideal model delta sigma weight residual 106.10 0.04 106.06 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO Q 32 " pdb=" N PRO Q 32 " pdb=" CD PRO Q 32 " ideal model delta sigma weight residual 112.00 79.95 32.05 1.40e+00 5.10e-01 5.24e+02 angle pdb=" C LYS Q 31 " pdb=" N PRO Q 32 " pdb=" CA PRO Q 32 " ideal model delta sigma weight residual 119.56 106.85 12.71 1.01e+00 9.80e-01 1.58e+02 angle pdb=" N PRO Q 32 " pdb=" CD PRO Q 32 " pdb=" CG PRO Q 32 " ideal model delta sigma weight residual 103.20 85.19 18.01 1.50e+00 4.44e-01 1.44e+02 angle pdb=" CA LYS Q 31 " pdb=" C LYS Q 31 " pdb=" N PRO Q 32 " ideal model delta sigma weight residual 120.77 131.96 -11.19 9.70e-01 1.06e+00 1.33e+02 ... (remaining 19011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 5575 35.89 - 71.78: 1379 71.78 - 107.68: 22 107.68 - 143.57: 9 143.57 - 179.46: 24 Dihedral angle restraints: 7009 sinusoidal: 4885 harmonic: 2124 Sorted by residual: dihedral pdb=" CA PRO Q 32 " pdb=" CB PRO Q 32 " pdb=" CG PRO Q 32 " pdb=" CD PRO Q 32 " ideal model delta sinusoidal sigma weight residual -38.00 -169.25 131.25 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" C LYS Q 31 " pdb=" N LYS Q 31 " pdb=" CA LYS Q 31 " pdb=" CB LYS Q 31 " ideal model delta harmonic sigma weight residual -122.60 -132.93 10.33 0 2.50e+00 1.60e-01 1.71e+01 dihedral pdb=" N PRO Q 32 " pdb=" C PRO Q 32 " pdb=" CA PRO Q 32 " pdb=" CB PRO Q 32 " ideal model delta harmonic sigma weight residual 115.10 104.83 10.27 0 2.50e+00 1.60e-01 1.69e+01 ... (remaining 7006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1893 0.074 - 0.147: 260 0.147 - 0.221: 15 0.221 - 0.295: 2 0.295 - 0.369: 2 Chirality restraints: 2172 Sorted by residual: chirality pdb=" CG LEU Q 62 " pdb=" CB LEU Q 62 " pdb=" CD1 LEU Q 62 " pdb=" CD2 LEU Q 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA ASN R 68 " pdb=" N ASN R 68 " pdb=" C ASN R 68 " pdb=" CB ASN R 68 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA PRO Q 32 " pdb=" N PRO Q 32 " pdb=" C PRO Q 32 " pdb=" CB PRO Q 32 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2169 not shown) Planarity restraints: 1319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 54 " -0.070 2.00e-02 2.50e+03 4.88e-02 4.76e+01 pdb=" CG TYR O 54 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR O 54 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR O 54 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR O 54 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR O 54 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR O 54 " 0.042 2.00e-02 2.50e+03 pdb=" OH TYR O 54 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 116 " -0.105 5.00e-02 4.00e+02 1.56e-01 3.92e+01 pdb=" N PRO R 117 " 0.270 5.00e-02 4.00e+02 pdb=" CA PRO R 117 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO R 117 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 88 " -0.006 2.00e-02 2.50e+03 4.40e-02 3.88e+01 pdb=" CG TYR Q 88 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 88 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 88 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 88 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 88 " 0.093 2.00e-02 2.50e+03 pdb=" CZ TYR Q 88 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR Q 88 " -0.043 2.00e-02 2.50e+03 ... (remaining 1316 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 89 2.50 - 3.10: 8287 3.10 - 3.70: 22408 3.70 - 4.30: 30327 4.30 - 4.90: 42804 Nonbonded interactions: 103915 Sorted by model distance: nonbonded pdb=" O VAL O 101 " pdb=" OE1 GLU O 105 " model vdw 1.905 3.040 nonbonded pdb=" O GLU S 102 " pdb=" ND1 HIS S 106 " model vdw 2.049 3.120 nonbonded pdb=" N2 DG H 94 " pdb=" O2 DC D 221 " model vdw 2.074 2.496 nonbonded pdb=" N GLU O 105 " pdb=" OE1 GLU O 105 " model vdw 2.074 3.120 nonbonded pdb=" N2 DG H 124 " pdb=" O2 DC D 191 " model vdw 2.089 2.496 ... (remaining 103910 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 'I' selection = (chain 'O' and resid 46 through 135) } ncs_group { reference = chain 'J' selection = (chain 'Q' and resid 25 through 102) } ncs_group { reference = chain 'K' selection = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 119)) } ncs_group { reference = chain 'M' selection = (chain 'S' and resid 36 through 122) } 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=1.00 max=1.00 mean=1.00 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: 3.600 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.190 Find NCS groups from input model: 0.090 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:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 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 0.723 13073 Z= 0.607 Angle : 1.257 106.057 19016 Z= 0.805 Chirality : 0.050 0.369 2172 Planarity : 0.008 0.156 1319 Dihedral : 31.014 179.458 5639 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.83 % Allowed : 33.33 % Favored : 65.84 % Cbeta Deviations : 0.29 % 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: 0.90 (0.31), residues: 718 helix: 1.36 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.37 (0.39), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG Q 40 TYR 0.095 0.005 TYR O 54 PHE 0.048 0.003 PHE I 78 HIS 0.035 0.003 HIS S 106 Details of bonding type rmsd/Z covalent geometry : bond 0.01087 / 0.61 (13073) covalent geometry : angle 1.25721 / 0.81 (19016) hydrogen bonds : bond 0.11105 / 11.93 ( 777) hydrogen bonds : angle 3.99959 / 5.34 ( 1887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 114 average time/residue: 0.1039 time to fit residues: 16.9930 Evaluate side-chains 112 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain S residue 56 MET Chi-restraints excluded: chain S residue 110 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN S 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.100545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.082644 restraints weight = 82752.558| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 4.01 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.175 13073 Z= 0.184 Angle : 0.738 12.426 19016 Z= 0.425 Chirality : 0.053 0.378 2172 Planarity : 0.006 0.091 1319 Dihedral : 33.795 179.143 4234 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.98 % Allowed : 27.69 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.31), residues: 718 helix: 1.59 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.39 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 67 TYR 0.039 0.002 TYR S 80 PHE 0.013 0.002 PHE Q 61 HIS 0.007 0.001 HIS S 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 (13073) covalent geometry : angle 0.73752 / 0.42 (19016) hydrogen bonds : bond 0.07357 / 8.13 ( 777) hydrogen bonds : angle 3.47043 / 4.73 ( 1887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 59 LYS cc_start: 0.9056 (tppt) cc_final: 0.8559 (tppt) REVERT: Q 78 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8042 (ptt90) REVERT: S 68 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7825 (pp20) outliers start: 24 outliers final: 10 residues processed: 138 average time/residue: 0.0946 time to fit residues: 18.6698 Evaluate side-chains 121 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 79 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 0.0270 chunk 53 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 20.0000 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN ** S 79 HIS ** 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 = 0.4420 r_free = 0.4420 target = 0.081251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.070910 restraints weight = 96934.276| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 3.75 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13073 Z= 0.194 Angle : 0.725 7.518 19016 Z= 0.420 Chirality : 0.052 0.387 2172 Planarity : 0.006 0.071 1319 Dihedral : 33.917 179.387 4226 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.81 % Allowed : 27.03 % Favored : 68.16 % 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: 1.21 (0.31), residues: 718 helix: 1.62 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.45 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 92 TYR 0.047 0.003 TYR S 80 PHE 0.026 0.003 PHE O 78 HIS 0.027 0.003 HIS S 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.19 (13073) covalent geometry : angle 0.72494 / 0.42 (19016) hydrogen bonds : bond 0.07502 / 8.22 ( 777) hydrogen bonds : angle 3.41042 / 4.75 ( 1887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 59 LYS cc_start: 0.9152 (tppt) cc_final: 0.8650 (tppt) REVERT: Q 74 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8372 (pp20) REVERT: R 64 GLU cc_start: 0.7775 (tp30) cc_final: 0.7572 (tp30) outliers start: 29 outliers final: 15 residues processed: 136 average time/residue: 0.1082 time to fit residues: 20.8157 Evaluate side-chains 120 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain O residue 84 PHE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 79 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 73 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 ASN O 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.092004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.077301 restraints weight = 85995.970| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 3.97 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13073 Z= 0.176 Angle : 0.719 12.900 19016 Z= 0.411 Chirality : 0.053 0.385 2172 Planarity : 0.005 0.070 1319 Dihedral : 33.954 178.904 4223 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.15 % Allowed : 26.20 % Favored : 69.65 % 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: 1.31 (0.31), residues: 718 helix: 1.66 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -1.22 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 92 TYR 0.041 0.002 TYR S 80 PHE 0.023 0.002 PHE Q 61 HIS 0.017 0.002 HIS S 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.18 (13073) covalent geometry : angle 0.71873 / 0.41 (19016) hydrogen bonds : bond 0.06942 / 7.69 ( 777) hydrogen bonds : angle 3.33444 / 4.74 ( 1887) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 59 LYS cc_start: 0.9228 (tppt) cc_final: 0.8668 (tppp) REVERT: J 84 MET cc_start: 0.8443 (mmm) cc_final: 0.7980 (mmm) REVERT: K 36 LYS cc_start: 0.8998 (tppt) cc_final: 0.8514 (mppt) REVERT: K 95 LYS cc_start: 0.8787 (tmmt) cc_final: 0.8552 (tmmt) REVERT: Q 78 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8207 (ptt90) REVERT: S 68 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8050 (tp30) REVERT: S 99 LEU cc_start: 0.8692 (mm) cc_final: 0.8476 (mm) outliers start: 25 outliers final: 14 residues processed: 138 average time/residue: 0.1149 time to fit residues: 22.5827 Evaluate side-chains 118 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain O residue 84 PHE Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 79 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 31 optimal weight: 0.0980 chunk 7 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 overall best weight: 5.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN R 31 HIS S 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.059967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.048474 restraints weight = 92394.323| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.49 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.194 13073 Z= 0.454 Angle : 1.151 15.279 19016 Z= 0.626 Chirality : 0.072 0.521 2172 Planarity : 0.010 0.089 1319 Dihedral : 34.717 179.373 4223 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 41.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 10.78 % Allowed : 25.87 % Favored : 63.35 % 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: -1.11 (0.28), residues: 718 helix: -0.37 (0.20), residues: 523 sheet: None (None), residues: 0 loop : -1.38 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG Q 92 TYR 0.132 0.006 TYR Q 88 PHE 0.036 0.006 PHE Q 61 HIS 0.017 0.005 HIS I 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00918 / 0.45 (13073) covalent geometry : angle 1.15145 / 0.63 (19016) hydrogen bonds : bond 0.18568 / 20.39 ( 777) hydrogen bonds : angle 5.01530 / 6.98 ( 1887) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 120 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 31 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8875 (tttm) REVERT: K 25 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7034 (t80) REVERT: K 95 LYS cc_start: 0.8898 (tmmt) cc_final: 0.8428 (mmmm) REVERT: O 125 GLN cc_start: 0.9263 (mm-40) cc_final: 0.9049 (mm-40) REVERT: Q 59 LYS cc_start: 0.9237 (pttt) cc_final: 0.9035 (pttm) REVERT: Q 79 LYS cc_start: 0.8076 (mttt) cc_final: 0.7836 (mptt) REVERT: R 71 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.6612 (ptt-90) REVERT: R 112 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7906 (tm-30) outliers start: 65 outliers final: 29 residues processed: 164 average time/residue: 0.1150 time to fit residues: 26.1863 Evaluate side-chains 128 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 108 ASN Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 31 LYS Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 44 LYS Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 79 HIS Chi-restraints excluded: chain S residue 99 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 14 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.064658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.052412 restraints weight = 86698.136| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.47 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.6727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13073 Z= 0.181 Angle : 0.851 12.195 19016 Z= 0.467 Chirality : 0.060 0.382 2172 Planarity : 0.006 0.065 1319 Dihedral : 34.699 179.469 4223 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.97 % Allowed : 30.51 % Favored : 63.52 % 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 are not related in a simple way. whole: 0.18 (0.30), residues: 718 helix: 0.70 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -1.30 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG R 77 TYR 0.039 0.003 TYR S 80 PHE 0.038 0.003 PHE I 104 HIS 0.005 0.002 HIS M 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.18 (13073) covalent geometry : angle 0.85113 / 0.47 (19016) hydrogen bonds : bond 0.07672 / 8.42 ( 777) hydrogen bonds : angle 3.86986 / 5.49 ( 1887) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 25 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7021 (t80) REVERT: M 48 ASP cc_start: 0.8598 (p0) cc_final: 0.8353 (p0) REVERT: O 100 LEU cc_start: 0.8205 (pp) cc_final: 0.7781 (pp) REVERT: Q 63 GLU cc_start: 0.9226 (pt0) cc_final: 0.8960 (pt0) REVERT: Q 78 ARG cc_start: 0.9402 (OUTLIER) cc_final: 0.8514 (ptt180) REVERT: S 90 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7726 (mm-30) outliers start: 36 outliers final: 15 residues processed: 156 average time/residue: 0.1161 time to fit residues: 25.7106 Evaluate side-chains 125 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 110 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN ** R 112 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 = 0.4060 r_free = 0.4060 target = 0.063240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.052282 restraints weight = 100863.011| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 3.48 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.7555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13073 Z= 0.283 Angle : 0.899 11.884 19016 Z= 0.494 Chirality : 0.061 0.752 2172 Planarity : 0.007 0.058 1319 Dihedral : 34.695 179.949 4223 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 26.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.80 % Allowed : 31.51 % Favored : 62.69 % 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: 0.24 (0.30), residues: 718 helix: 0.64 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -0.92 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG K 99 TYR 0.041 0.003 TYR S 80 PHE 0.024 0.003 PHE M 62 HIS 0.008 0.002 HIS M 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.28 (13073) covalent geometry : angle 0.89866 / 0.49 (19016) hydrogen bonds : bond 0.10598 / 11.55 ( 777) hydrogen bonds : angle 4.16305 / 5.76 ( 1887) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 59 LYS cc_start: 0.9424 (tppt) cc_final: 0.9128 (tppp) REVERT: K 25 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7404 (t80) REVERT: M 97 LEU cc_start: 0.9361 (mt) cc_final: 0.9062 (mt) REVERT: O 100 LEU cc_start: 0.8405 (pp) cc_final: 0.8043 (pp) REVERT: Q 44 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8707 (mmmm) REVERT: Q 59 LYS cc_start: 0.9229 (pttt) cc_final: 0.8986 (pttm) REVERT: Q 63 GLU cc_start: 0.9174 (pt0) cc_final: 0.8688 (pt0) REVERT: Q 78 ARG cc_start: 0.9377 (OUTLIER) cc_final: 0.9078 (ptt90) REVERT: S 90 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7758 (mm-30) REVERT: S 106 HIS cc_start: 0.8744 (m90) cc_final: 0.8216 (m-70) outliers start: 35 outliers final: 20 residues processed: 141 average time/residue: 0.1133 time to fit residues: 22.5464 Evaluate side-chains 133 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 108 ASN Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain Q residue 44 LYS Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 79 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 74 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 3 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN ** R 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.065269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.054306 restraints weight = 99937.375| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 3.48 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.7625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13073 Z= 0.178 Angle : 0.836 11.202 19016 Z= 0.458 Chirality : 0.058 0.399 2172 Planarity : 0.006 0.060 1319 Dihedral : 34.674 179.166 4223 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.81 % Allowed : 32.50 % Favored : 62.69 % 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: 0.65 (0.31), residues: 718 helix: 1.00 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -0.92 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 77 TYR 0.065 0.003 TYR S 80 PHE 0.027 0.003 PHE M 62 HIS 0.006 0.001 HIS M 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.18 (13073) covalent geometry : angle 0.83625 / 0.46 (19016) hydrogen bonds : bond 0.07189 / 7.87 ( 777) hydrogen bonds : angle 3.84074 / 5.41 ( 1887) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: J 59 LYS cc_start: 0.9416 (tppt) cc_final: 0.9154 (tppp) REVERT: K 25 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.6975 (t80) REVERT: O 79 LYS cc_start: 0.8408 (tppt) cc_final: 0.8141 (tppt) REVERT: Q 44 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8613 (mmmm) REVERT: Q 59 LYS cc_start: 0.9182 (pttt) cc_final: 0.8965 (pttm) REVERT: Q 63 GLU cc_start: 0.9216 (pt0) cc_final: 0.9003 (pt0) REVERT: Q 78 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.9085 (ptt90) REVERT: S 90 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7731 (mm-30) outliers start: 29 outliers final: 18 residues processed: 142 average time/residue: 0.0979 time to fit residues: 20.2146 Evaluate side-chains 133 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 44 LYS Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain S residue 79 HIS Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 14 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN ** R 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.064423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.053525 restraints weight = 99582.845| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.48 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.7870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13073 Z= 0.194 Angle : 0.848 13.709 19016 Z= 0.462 Chirality : 0.057 0.404 2172 Planarity : 0.006 0.065 1319 Dihedral : 34.594 179.436 4223 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.48 % Allowed : 33.00 % Favored : 62.52 % 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 are not related in a simple way. whole: 0.78 (0.30), residues: 718 helix: 1.07 (0.22), residues: 517 sheet: None (None), residues: 0 loop : -0.78 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 129 TYR 0.060 0.003 TYR S 80 PHE 0.024 0.002 PHE M 62 HIS 0.007 0.002 HIS M 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.19 (13073) covalent geometry : angle 0.84803 / 0.46 (19016) hydrogen bonds : bond 0.07756 / 8.48 ( 777) hydrogen bonds : angle 3.90176 / 5.45 ( 1887) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 54 TYR cc_start: 0.7893 (m-80) cc_final: 0.7674 (m-80) REVERT: J 59 LYS cc_start: 0.9445 (tppt) cc_final: 0.9217 (tppp) REVERT: Q 44 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8673 (mmmm) REVERT: Q 59 LYS cc_start: 0.9165 (pttt) cc_final: 0.8881 (pttm) REVERT: Q 63 GLU cc_start: 0.9194 (pt0) cc_final: 0.8988 (pt0) outliers start: 27 outliers final: 15 residues processed: 133 average time/residue: 0.0997 time to fit residues: 18.7613 Evaluate side-chains 127 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain Q residue 44 LYS Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain S residue 79 HIS Chi-restraints excluded: chain S residue 80 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 4 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.0770 chunk 9 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.063570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.052806 restraints weight = 101238.904| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.49 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.8272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13073 Z= 0.199 Angle : 0.849 11.035 19016 Z= 0.462 Chirality : 0.059 0.576 2172 Planarity : 0.006 0.065 1319 Dihedral : 34.609 179.714 4223 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.81 % Allowed : 34.33 % Favored : 61.86 % 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: 0.82 (0.31), residues: 718 helix: 1.05 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -0.63 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 129 TYR 0.055 0.003 TYR S 80 PHE 0.067 0.004 PHE I 104 HIS 0.007 0.002 HIS M 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.20 (13073) covalent geometry : angle 0.84935 / 0.46 (19016) hydrogen bonds : bond 0.07454 / 8.15 ( 777) hydrogen bonds : angle 3.95510 / 5.48 ( 1887) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 54 TYR cc_start: 0.8015 (m-80) cc_final: 0.7789 (m-80) REVERT: J 59 LYS cc_start: 0.9512 (tppt) cc_final: 0.9270 (tppp) REVERT: O 79 LYS cc_start: 0.8487 (tppt) cc_final: 0.8261 (tppt) REVERT: O 80 THR cc_start: 0.7104 (m) cc_final: 0.6894 (m) REVERT: O 100 LEU cc_start: 0.8542 (pp) cc_final: 0.8337 (pp) REVERT: Q 44 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8662 (mmmm) REVERT: Q 59 LYS cc_start: 0.9162 (pttt) cc_final: 0.8875 (pttm) REVERT: S 99 LEU cc_start: 0.8727 (mm) cc_final: 0.8521 (mm) REVERT: S 102 GLU cc_start: 0.8414 (pm20) cc_final: 0.7677 (pm20) REVERT: S 106 HIS cc_start: 0.8771 (m90) cc_final: 0.8017 (m90) outliers start: 23 outliers final: 16 residues processed: 133 average time/residue: 0.1108 time to fit residues: 21.2607 Evaluate side-chains 128 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 44 LYS Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain S residue 79 HIS Chi-restraints excluded: chain S residue 80 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 90 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 24 optimal weight: 0.0970 chunk 75 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN R 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.064534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.053691 restraints weight = 100805.150| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.56 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.8358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13073 Z= 0.169 Angle : 0.850 17.237 19016 Z= 0.458 Chirality : 0.058 0.546 2172 Planarity : 0.005 0.062 1319 Dihedral : 34.531 179.385 4221 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.32 % Allowed : 35.49 % Favored : 61.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.31), residues: 718 helix: 1.16 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -0.59 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 129 TYR 0.050 0.002 TYR S 80 PHE 0.026 0.003 PHE M 62 HIS 0.006 0.001 HIS M 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 (13073) covalent geometry : angle 0.84988 / 0.46 (19016) hydrogen bonds : bond 0.06969 / 7.65 ( 777) hydrogen bonds : angle 3.87500 / 5.37 ( 1887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2566.87 seconds wall clock time: 44 minutes 39.06 seconds (2679.06 seconds total)