Starting phenix.real_space_refine on Wed May 14 16:58:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo0_43363/05_2025/8vo0_43363.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo0_43363/05_2025/8vo0_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_43363/05_2025/8vo0_43363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo0_43363/05_2025/8vo0_43363.map" model { file = "/net/cci-nas-00/data/ceres_data/8vo0_43363/05_2025/8vo0_43363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo0_43363/05_2025/8vo0_43363.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.05, per 1000 atoms: 0.66 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: 3.01 Conformation dependent library (CDL) restraints added in 914.0 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: 6.22 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: 4.89 Time building geometry restraints manager: 3.56 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: 2025 0.074 - 0.147: 136 0.147 - 0.221: 7 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: 5.730 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.130 Set scattering table: 0.380 Process input model: 35.150 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.840 ------------------------------------------------------------------------------- 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 : 0.010 0.723 13073 Z= 0.356 Angle : 1.154 106.057 19016 Z= 0.550 Chirality : 0.040 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 : 21.04 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.035 0.003 HIS S 106 PHE 0.048 0.003 PHE I 78 TYR 0.095 0.005 TYR O 54 ARG 0.018 0.001 ARG Q 40 Details of bonding type rmsd hydrogen bonds : bond 0.11105 ( 777) hydrogen bonds : angle 3.99959 ( 1887) covalent geometry : bond 0.00997 (13073) covalent geometry : angle 1.15400 (19016) *********************** 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 : 0.793 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: 0.2630 time to fit residues: 41.6436 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 : 0.849 ------------------------------------------------------------------------------- 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 82 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 0.2980 chunk 29 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN ** K 82 HIS ** 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 = 0.4467 r_free = 0.4467 target = 0.083975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.074084 restraints weight = 95760.279| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 3.67 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13073 Z= 0.177 Angle : 0.656 10.425 19016 Z= 0.377 Chirality : 0.038 0.212 2172 Planarity : 0.006 0.089 1319 Dihedral : 33.534 179.525 4234 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.32 % Allowed : 27.86 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.31), residues: 718 helix: 1.69 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.39 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS S 79 PHE 0.015 0.002 PHE Q 61 TYR 0.041 0.002 TYR Q 88 ARG 0.010 0.000 ARG R 71 Details of bonding type rmsd hydrogen bonds : bond 0.06677 ( 777) hydrogen bonds : angle 3.21263 ( 1887) covalent geometry : bond 0.00391 (13073) covalent geometry : angle 0.65645 (19016) *********************** 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 160 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 59 LYS cc_start: 0.9130 (tppt) cc_final: 0.8568 (tppt) REVERT: K 104 GLN cc_start: 0.8050 (mm110) cc_final: 0.7500 (mm-40) REVERT: O 133 GLU cc_start: 0.6175 (mp0) cc_final: 0.5617 (pm20) REVERT: Q 44 LYS cc_start: 0.8678 (mmmm) cc_final: 0.8242 (mmtt) REVERT: Q 74 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8384 (pp20) REVERT: R 102 ILE cc_start: 0.6709 (mm) cc_final: 0.6441 (tp) REVERT: S 68 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7972 (pp20) outliers start: 20 outliers final: 10 residues processed: 147 average time/residue: 0.2735 time to fit residues: 54.8311 Evaluate side-chains 122 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain O residue 108 ASN Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 53 SER 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 82 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.080203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.067039 restraints weight = 89019.233| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.59 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 13073 Z= 0.280 Angle : 0.819 15.028 19016 Z= 0.462 Chirality : 0.046 0.327 2172 Planarity : 0.008 0.086 1319 Dihedral : 34.350 179.801 4223 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 25.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 6.63 % Allowed : 26.87 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.30), residues: 718 helix: 1.05 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.34 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.003 HIS S 79 PHE 0.025 0.003 PHE M 62 TYR 0.032 0.003 TYR K 57 ARG 0.007 0.001 ARG R 81 Details of bonding type rmsd hydrogen bonds : bond 0.08672 ( 777) hydrogen bonds : angle 4.06241 ( 1887) covalent geometry : bond 0.00622 (13073) covalent geometry : angle 0.81870 (19016) *********************** 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 192 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 104 PHE cc_start: 0.8822 (m-80) cc_final: 0.8536 (m-80) REVERT: J 59 LYS cc_start: 0.9353 (tppt) cc_final: 0.9011 (tmtt) REVERT: K 25 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.6695 (t80) REVERT: K 95 LYS cc_start: 0.8855 (tmmt) cc_final: 0.8616 (tmmt) REVERT: M 48 ASP cc_start: 0.8501 (p0) cc_final: 0.8179 (p0) REVERT: M 54 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8629 (tttt) REVERT: O 104 PHE cc_start: 0.8904 (m-10) cc_final: 0.8677 (m-10) REVERT: O 133 GLU cc_start: 0.7518 (mp0) cc_final: 0.7237 (pm20) REVERT: R 84 GLN cc_start: 0.9185 (tp40) cc_final: 0.8479 (tm-30) REVERT: R 85 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8076 (mt) REVERT: S 90 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7657 (mm-30) outliers start: 40 outliers final: 18 residues processed: 171 average time/residue: 0.2686 time to fit residues: 63.0750 Evaluate side-chains 137 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 108 ASN 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 114 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 88 SER Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 59 MET Chi-restraints excluded: chain S residue 66 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.069655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.058636 restraints weight = 97490.424| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 3.53 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13073 Z= 0.179 Angle : 0.690 12.161 19016 Z= 0.392 Chirality : 0.039 0.204 2172 Planarity : 0.005 0.065 1319 Dihedral : 34.073 179.484 4223 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.98 % Allowed : 28.69 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.31), residues: 718 helix: 1.44 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.18 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS M 46 PHE 0.023 0.002 PHE M 62 TYR 0.042 0.002 TYR S 80 ARG 0.006 0.001 ARG I 129 Details of bonding type rmsd hydrogen bonds : bond 0.06304 ( 777) hydrogen bonds : angle 3.40237 ( 1887) covalent geometry : bond 0.00401 (13073) covalent geometry : angle 0.68988 (19016) *********************** 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 154 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 104 PHE cc_start: 0.8731 (m-80) cc_final: 0.8345 (m-80) REVERT: J 59 LYS cc_start: 0.9395 (tppt) cc_final: 0.9165 (tppp) REVERT: K 95 LYS cc_start: 0.8838 (tmmt) cc_final: 0.8556 (ttpt) REVERT: M 48 ASP cc_start: 0.8523 (p0) cc_final: 0.8289 (p0) REVERT: M 68 GLU cc_start: 0.9039 (tp30) cc_final: 0.8805 (mm-30) REVERT: M 97 LEU cc_start: 0.9316 (mt) cc_final: 0.9094 (mt) REVERT: O 125 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8801 (mm-40) REVERT: S 79 HIS cc_start: 0.8108 (OUTLIER) cc_final: 0.7846 (p90) REVERT: S 99 LEU cc_start: 0.8850 (mm) cc_final: 0.8558 (mm) outliers start: 24 outliers final: 9 residues processed: 145 average time/residue: 0.2556 time to fit residues: 51.4888 Evaluate side-chains 122 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 92 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 114 VAL Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain O residue 124 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 70 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 GLN S 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.068745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.057932 restraints weight = 98174.362| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 3.41 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13073 Z= 0.180 Angle : 0.682 9.972 19016 Z= 0.388 Chirality : 0.038 0.170 2172 Planarity : 0.005 0.057 1319 Dihedral : 33.987 179.518 4221 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.64 % Allowed : 28.03 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.31), residues: 718 helix: 1.41 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.11 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS Q 75 PHE 0.020 0.002 PHE M 62 TYR 0.044 0.002 TYR Q 98 ARG 0.006 0.000 ARG I 129 Details of bonding type rmsd hydrogen bonds : bond 0.06379 ( 777) hydrogen bonds : angle 3.40065 ( 1887) covalent geometry : bond 0.00403 (13073) covalent geometry : angle 0.68202 (19016) *********************** 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 165 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: J 59 LYS cc_start: 0.9433 (tppt) cc_final: 0.9218 (tppp) REVERT: K 95 LYS cc_start: 0.8876 (tmmt) cc_final: 0.8623 (tmmt) REVERT: M 68 GLU cc_start: 0.9052 (tp30) cc_final: 0.8821 (mm-30) REVERT: M 110 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8269 (tm-30) REVERT: O 79 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8318 (tppt) REVERT: O 125 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8899 (mm-40) REVERT: S 99 LEU cc_start: 0.8783 (mm) cc_final: 0.8528 (mm) outliers start: 28 outliers final: 10 residues processed: 154 average time/residue: 0.2713 time to fit residues: 57.6408 Evaluate side-chains 127 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU 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 68 ASP Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain O residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN R 68 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 = 0.4152 r_free = 0.4152 target = 0.067262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.056276 restraints weight = 101104.516| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.57 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.7506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13073 Z= 0.191 Angle : 0.715 15.570 19016 Z= 0.400 Chirality : 0.041 0.459 2172 Planarity : 0.005 0.056 1319 Dihedral : 34.005 178.928 4221 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.48 % Allowed : 31.67 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.31), residues: 718 helix: 1.30 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.85 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS M 46 PHE 0.033 0.003 PHE Q 61 TYR 0.041 0.002 TYR S 80 ARG 0.006 0.000 ARG I 129 Details of bonding type rmsd hydrogen bonds : bond 0.06432 ( 777) hydrogen bonds : angle 3.52842 ( 1887) covalent geometry : bond 0.00428 (13073) covalent geometry : angle 0.71510 (19016) *********************** 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 149 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 95 LYS cc_start: 0.8920 (tmmt) cc_final: 0.8646 (tmmt) REVERT: M 68 GLU cc_start: 0.9032 (tp30) cc_final: 0.8830 (mm-30) REVERT: M 110 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8250 (tm-30) REVERT: O 125 GLN cc_start: 0.9292 (mm-40) cc_final: 0.9086 (mm-40) REVERT: Q 59 LYS cc_start: 0.9154 (pttt) cc_final: 0.8487 (pttm) REVERT: S 99 LEU cc_start: 0.8749 (mm) cc_final: 0.8476 (mm) REVERT: S 102 GLU cc_start: 0.8610 (pm20) cc_final: 0.8236 (pm20) outliers start: 21 outliers final: 14 residues processed: 140 average time/residue: 0.2477 time to fit residues: 49.3009 Evaluate side-chains 124 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 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 79 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 98 LEU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 108 ASN Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 62 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN S 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.067660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.054552 restraints weight = 92522.364| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.69 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 1.0156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 13073 Z= 0.333 Angle : 0.860 16.116 19016 Z= 0.484 Chirality : 0.047 0.184 2172 Planarity : 0.007 0.069 1319 Dihedral : 34.788 179.678 4221 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 28.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.30 % Allowed : 29.68 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.30), residues: 718 helix: 0.50 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.86 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.003 HIS S 46 PHE 0.026 0.004 PHE O 104 TYR 0.065 0.004 TYR S 80 ARG 0.008 0.001 ARG R 77 Details of bonding type rmsd hydrogen bonds : bond 0.10095 ( 777) hydrogen bonds : angle 4.30338 ( 1887) covalent geometry : bond 0.00744 (13073) covalent geometry : angle 0.85996 (19016) *********************** 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 178 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 85 ASP cc_start: 0.8281 (m-30) cc_final: 0.7960 (m-30) REVERT: K 95 LYS cc_start: 0.8982 (tmmt) cc_final: 0.8695 (tmmt) REVERT: M 110 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8161 (tm-30) REVERT: O 99 TYR cc_start: 0.8470 (t80) cc_final: 0.8193 (t80) REVERT: Q 59 LYS cc_start: 0.9293 (pttt) cc_final: 0.9080 (pttm) REVERT: Q 78 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.8830 (ptt90) REVERT: S 102 GLU cc_start: 0.8571 (pm20) cc_final: 0.8135 (pm20) outliers start: 38 outliers final: 22 residues processed: 159 average time/residue: 0.2635 time to fit residues: 58.4635 Evaluate side-chains 145 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 60 LEU 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 79 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 108 ASN Chi-restraints excluded: chain O residue 112 ILE 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 59 MET Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 79 HIS Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 93 GLN ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 HIS K 82 HIS ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 68 ASN ** 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 = 0.4031 r_free = 0.4031 target = 0.062144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.051423 restraints weight = 99293.259| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.45 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 1.0160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13073 Z= 0.202 Angle : 0.773 10.823 19016 Z= 0.432 Chirality : 0.042 0.237 2172 Planarity : 0.005 0.054 1319 Dihedral : 34.563 178.896 4221 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.65 % Allowed : 34.66 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 718 helix: 1.00 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -0.96 (0.39), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS R 82 PHE 0.066 0.003 PHE I 104 TYR 0.028 0.002 TYR Q 98 ARG 0.013 0.001 ARG O 134 Details of bonding type rmsd hydrogen bonds : bond 0.06463 ( 777) hydrogen bonds : angle 3.86387 ( 1887) covalent geometry : bond 0.00458 (13073) covalent geometry : angle 0.77286 (19016) *********************** 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 163 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 85 ASP cc_start: 0.8375 (m-30) cc_final: 0.8103 (m-30) REVERT: M 68 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8765 (mm-30) REVERT: M 110 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8208 (tm-30) REVERT: O 133 GLU cc_start: 0.7691 (pm20) cc_final: 0.7465 (mp0) REVERT: Q 59 LYS cc_start: 0.9266 (pttt) cc_final: 0.9023 (pttm) REVERT: S 59 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7901 (tmm) REVERT: S 99 LEU cc_start: 0.8637 (mm) cc_final: 0.8375 (mm) REVERT: S 102 GLU cc_start: 0.8616 (pm20) cc_final: 0.8215 (pm20) outliers start: 22 outliers final: 15 residues processed: 152 average time/residue: 0.2475 time to fit residues: 53.1279 Evaluate side-chains 140 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 88 SER Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain S residue 59 MET Chi-restraints excluded: chain S residue 79 HIS Chi-restraints excluded: chain S residue 90 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 29 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 93 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 93 GLN ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN ** Q 75 HIS ** 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 = 0.3998 r_free = 0.3998 target = 0.059301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.048386 restraints weight = 81750.455| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.15 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 1.0290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13073 Z= 0.190 Angle : 0.758 10.173 19016 Z= 0.423 Chirality : 0.042 0.263 2172 Planarity : 0.005 0.053 1319 Dihedral : 34.433 179.737 4221 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.65 % Allowed : 34.66 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.30), residues: 718 helix: 0.98 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -0.90 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 46 PHE 0.023 0.002 PHE M 62 TYR 0.027 0.002 TYR S 80 ARG 0.007 0.001 ARG I 129 Details of bonding type rmsd hydrogen bonds : bond 0.06438 ( 777) hydrogen bonds : angle 3.82106 ( 1887) covalent geometry : bond 0.00431 (13073) covalent geometry : angle 0.75789 (19016) *********************** 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 151 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 85 ASP cc_start: 0.8380 (m-30) cc_final: 0.8139 (m-30) REVERT: J 91 LYS cc_start: 0.9108 (ttpp) cc_final: 0.8873 (ttmm) REVERT: M 68 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8716 (mm-30) REVERT: M 110 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8214 (tm-30) REVERT: O 67 PHE cc_start: 0.8836 (t80) cc_final: 0.8611 (t80) REVERT: O 125 GLN cc_start: 0.9485 (mm-40) cc_final: 0.9261 (mm-40) REVERT: O 133 GLU cc_start: 0.7711 (pm20) cc_final: 0.7419 (mp0) REVERT: Q 59 LYS cc_start: 0.9215 (pttt) cc_final: 0.8955 (pttm) REVERT: R 110 ASN cc_start: 0.8872 (t0) cc_final: 0.8608 (p0) REVERT: S 59 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7962 (tmm) REVERT: S 99 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8278 (mm) REVERT: S 102 GLU cc_start: 0.8483 (pm20) cc_final: 0.8099 (pm20) outliers start: 22 outliers final: 13 residues processed: 140 average time/residue: 0.2545 time to fit residues: 51.6652 Evaluate side-chains 135 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 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 M residue 49 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 88 SER Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 59 MET Chi-restraints excluded: chain S residue 79 HIS Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 99 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 42 optimal weight: 0.4980 chunk 1 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 74 optimal weight: 0.0040 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.059481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.048615 restraints weight = 82160.698| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.19 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 1.0426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13073 Z= 0.189 Angle : 0.779 11.561 19016 Z= 0.431 Chirality : 0.042 0.275 2172 Planarity : 0.005 0.052 1319 Dihedral : 34.390 179.552 4221 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.99 % Allowed : 35.32 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.30), residues: 718 helix: 1.04 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -0.86 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 82 PHE 0.070 0.003 PHE I 104 TYR 0.049 0.002 TYR S 80 ARG 0.005 0.000 ARG J 67 Details of bonding type rmsd hydrogen bonds : bond 0.06330 ( 777) hydrogen bonds : angle 3.79067 ( 1887) covalent geometry : bond 0.00431 (13073) covalent geometry : angle 0.77909 (19016) ********************** 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 151 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 85 ASP cc_start: 0.8396 (m-30) cc_final: 0.8108 (m-30) REVERT: K 95 LYS cc_start: 0.9058 (tttp) cc_final: 0.8513 (tmmt) REVERT: M 68 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8678 (mm-30) REVERT: M 110 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8204 (tm-30) REVERT: O 67 PHE cc_start: 0.8807 (t80) cc_final: 0.8566 (t80) REVERT: O 125 GLN cc_start: 0.9486 (mm-40) cc_final: 0.9258 (mm-40) REVERT: O 133 GLU cc_start: 0.7768 (pm20) cc_final: 0.7458 (mp0) REVERT: Q 59 LYS cc_start: 0.9206 (pttt) cc_final: 0.8954 (pttm) REVERT: R 110 ASN cc_start: 0.8920 (t0) cc_final: 0.8669 (p0) REVERT: S 99 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8212 (mm) REVERT: S 102 GLU cc_start: 0.8480 (pm20) cc_final: 0.8138 (pm20) outliers start: 18 outliers final: 14 residues processed: 142 average time/residue: 0.2423 time to fit residues: 48.7325 Evaluate side-chains 140 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 108 ASN 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 76 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 88 SER Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 79 HIS Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 99 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 75 HIS ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 ASN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 24 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 = 0.3980 r_free = 0.3980 target = 0.057757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.046410 restraints weight = 86601.112| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.25 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 1.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13073 Z= 0.213 Angle : 0.775 11.595 19016 Z= 0.433 Chirality : 0.042 0.266 2172 Planarity : 0.005 0.052 1319 Dihedral : 34.510 179.531 4221 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.15 % Allowed : 35.82 % Favored : 61.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.30), residues: 718 helix: 1.01 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 46 PHE 0.022 0.003 PHE M 62 TYR 0.087 0.003 TYR S 80 ARG 0.008 0.001 ARG Q 45 Details of bonding type rmsd hydrogen bonds : bond 0.06607 ( 777) hydrogen bonds : angle 3.86846 ( 1887) covalent geometry : bond 0.00485 (13073) covalent geometry : angle 0.77475 (19016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5777.75 seconds wall clock time: 100 minutes 40.94 seconds (6040.94 seconds total)