Starting phenix.real_space_refine on Wed Sep 17 23:01:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo0_43363/09_2025/8vo0_43363.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo0_43363/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vo0_43363/09_2025/8vo0_43363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo0_43363/09_2025/8vo0_43363.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vo0_43363/09_2025/8vo0_43363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo0_43363/09_2025/8vo0_43363.map" } 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-2.0-5805/lib/python3.9/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: 3.19, per 1000 atoms: 0.26 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: 1.11 Conformation dependent library (CDL) restraints added in 405.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.18 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: 2.59 Time building geometry restraints manager: 1.46 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.870 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.530 ------------------------------------------------------------------------------- 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 : 21.00 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 aren 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 covalent geometry : bond 0.00997 (13073) covalent geometry : angle 1.15400 (19016) hydrogen bonds : bond 0.11105 ( 777) hydrogen bonds : angle 3.99959 ( 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 : 0.327 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: 0.1325 time to fit residues: 21.1659 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 : 0.299 ------------------------------------------------------------------------------- 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: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 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: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4568 r_free = 0.4568 target = 0.099244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.081460 restraints weight = 82178.590| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 3.94 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13073 Z= 0.177 Angle : 0.655 8.278 19016 Z= 0.378 Chirality : 0.038 0.211 2172 Planarity : 0.006 0.090 1319 Dihedral : 33.544 179.556 4234 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.15 % Allowed : 28.36 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.31), residues: 718 helix: 1.68 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.39 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 71 TYR 0.045 0.002 TYR Q 88 PHE 0.015 0.002 PHE Q 61 HIS 0.004 0.001 HIS S 79 Details of bonding type rmsd covalent geometry : bond 0.00391 (13073) covalent geometry : angle 0.65546 (19016) hydrogen bonds : bond 0.06574 ( 777) hydrogen bonds : angle 3.22124 ( 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 159 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 59 LYS cc_start: 0.9015 (tppt) cc_final: 0.8546 (tppt) REVERT: K 104 GLN cc_start: 0.7850 (mm110) cc_final: 0.7451 (mm-40) REVERT: O 133 GLU cc_start: 0.6078 (mp0) cc_final: 0.5683 (pm20) REVERT: Q 44 LYS cc_start: 0.8506 (mmmm) cc_final: 0.8219 (mmtt) REVERT: Q 74 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8310 (pp20) REVERT: R 102 ILE cc_start: 0.6551 (mm) cc_final: 0.6258 (tp) REVERT: S 68 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7813 (pp20) outliers start: 19 outliers final: 10 residues processed: 147 average time/residue: 0.1405 time to fit residues: 28.3509 Evaluate side-chains 120 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 15 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 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 = 0.4058 r_free = 0.4058 target = 0.061988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.049758 restraints weight = 89521.741| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.64 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.7306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 13073 Z= 0.344 Angle : 0.887 14.408 19016 Z= 0.499 Chirality : 0.049 0.358 2172 Planarity : 0.008 0.077 1319 Dihedral : 34.623 179.270 4223 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 29.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 7.46 % Allowed : 26.87 % Favored : 65.67 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.30), residues: 718 helix: 0.73 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.38 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 35 TYR 0.056 0.004 TYR Q 88 PHE 0.030 0.004 PHE M 62 HIS 0.018 0.003 HIS S 79 Details of bonding type rmsd covalent geometry : bond 0.00759 (13073) covalent geometry : angle 0.88673 (19016) hydrogen bonds : bond 0.10298 ( 777) hydrogen bonds : angle 4.28986 ( 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 204 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 100 LEU cc_start: 0.9454 (mm) cc_final: 0.9226 (tp) REVERT: I 104 PHE cc_start: 0.8802 (m-80) cc_final: 0.8452 (m-80) REVERT: J 59 LYS cc_start: 0.9433 (tppt) cc_final: 0.9080 (tptt) REVERT: J 85 ASP cc_start: 0.8354 (m-30) cc_final: 0.8125 (m-30) REVERT: K 25 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7277 (t80) REVERT: K 64 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8910 (tm-30) REVERT: K 95 LYS cc_start: 0.8916 (tmmt) cc_final: 0.8641 (tmmt) REVERT: M 48 ASP cc_start: 0.8650 (p0) cc_final: 0.8330 (p0) REVERT: M 54 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8616 (tttt) REVERT: M 97 LEU cc_start: 0.9439 (mt) cc_final: 0.9207 (mt) REVERT: Q 78 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.8906 (ptt90) REVERT: R 84 GLN cc_start: 0.9185 (tp40) cc_final: 0.8831 (tm-30) REVERT: S 90 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7627 (mm-30) outliers start: 45 outliers final: 19 residues processed: 181 average time/residue: 0.1433 time to fit residues: 35.1043 Evaluate side-chains 143 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 62 ILE 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 34 ILE Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain K residue 25 PHE 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 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 65 LEU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain S residue 53 SER 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 48 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.067018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.056015 restraints weight = 99607.954| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.55 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.7462 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= 0.191 Angle : 0.708 11.230 19016 Z= 0.401 Chirality : 0.040 0.213 2172 Planarity : 0.005 0.069 1319 Dihedral : 34.270 179.927 4223 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.64 % Allowed : 27.53 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.30), residues: 718 helix: 1.30 (0.22), residues: 517 sheet: None (None), residues: 0 loop : -1.25 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 129 TYR 0.040 0.002 TYR S 80 PHE 0.021 0.002 PHE M 62 HIS 0.006 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00430 (13073) covalent geometry : angle 0.70753 (19016) hydrogen bonds : bond 0.06445 ( 777) hydrogen bonds : angle 3.52082 ( 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 166 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 104 PHE cc_start: 0.8699 (m-80) cc_final: 0.8237 (m-80) REVERT: J 52 GLU cc_start: 0.8896 (pm20) cc_final: 0.8670 (pm20) REVERT: J 85 ASP cc_start: 0.8379 (m-30) cc_final: 0.8174 (m-30) REVERT: K 25 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7281 (t80) REVERT: K 64 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8803 (tm-30) REVERT: K 95 LYS cc_start: 0.8916 (tmmt) cc_final: 0.8599 (tmmt) REVERT: O 125 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8715 (mm-40) REVERT: S 58 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7205 (mt) REVERT: S 99 LEU cc_start: 0.8881 (mm) cc_final: 0.8581 (mm) REVERT: S 103 LEU cc_start: 0.8959 (mt) cc_final: 0.8577 (mp) REVERT: S 106 HIS cc_start: 0.8840 (m90) cc_final: 0.8119 (m90) outliers start: 28 outliers final: 10 residues processed: 152 average time/residue: 0.1353 time to fit residues: 28.1314 Evaluate side-chains 129 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 62 ILE 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 54 TYR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain S residue 58 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.061970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.049399 restraints weight = 93431.336| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.71 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.9359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 13073 Z= 0.305 Angle : 0.795 11.887 19016 Z= 0.450 Chirality : 0.044 0.220 2172 Planarity : 0.006 0.064 1319 Dihedral : 34.638 179.707 4223 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 25.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 6.14 % Allowed : 27.03 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.30), residues: 718 helix: 0.93 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -0.93 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 89 TYR 0.048 0.003 TYR S 80 PHE 0.019 0.003 PHE M 62 HIS 0.006 0.002 HIS M 46 Details of bonding type rmsd covalent geometry : bond 0.00681 (13073) covalent geometry : angle 0.79472 (19016) hydrogen bonds : bond 0.08729 ( 777) hydrogen bonds : angle 3.94007 ( 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 172 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 104 PHE cc_start: 0.8651 (m-80) cc_final: 0.8356 (m-80) REVERT: J 85 ASP cc_start: 0.8463 (m-30) cc_final: 0.8116 (m-30) REVERT: K 25 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: K 95 LYS cc_start: 0.8971 (tmmt) cc_final: 0.8479 (mmmm) REVERT: M 97 LEU cc_start: 0.9378 (mt) cc_final: 0.9146 (mt) REVERT: S 102 GLU cc_start: 0.8706 (pm20) cc_final: 0.8235 (pm20) outliers start: 37 outliers final: 22 residues processed: 157 average time/residue: 0.1323 time to fit residues: 28.7458 Evaluate side-chains 146 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 63 GLU 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 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 65 LEU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 66 VAL 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: 4.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 85 GLN O 108 ASN Q 25 ASN ** R 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.065755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.053416 restraints weight = 93293.266| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.82 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.9470 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= 0.187 Angle : 0.718 8.741 19016 Z= 0.404 Chirality : 0.040 0.241 2172 Planarity : 0.005 0.058 1319 Dihedral : 34.418 179.262 4223 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.15 % Allowed : 32.17 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.31), residues: 718 helix: 1.29 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -0.79 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 129 TYR 0.039 0.002 TYR S 80 PHE 0.009 0.001 PHE O 84 HIS 0.004 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00423 (13073) covalent geometry : angle 0.71837 (19016) hydrogen bonds : bond 0.06371 ( 777) hydrogen bonds : angle 3.55992 ( 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 163 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 104 PHE cc_start: 0.8784 (m-80) cc_final: 0.8372 (m-80) REVERT: J 58 LEU cc_start: 0.9501 (tp) cc_final: 0.9262 (pp) REVERT: J 85 ASP cc_start: 0.8396 (m-30) cc_final: 0.8079 (m-30) REVERT: K 25 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: O 104 PHE cc_start: 0.8996 (m-10) cc_final: 0.8631 (m-10) REVERT: S 56 MET cc_start: 0.8563 (tpp) cc_final: 0.8245 (tpt) REVERT: S 99 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8461 (mm) REVERT: S 106 HIS cc_start: 0.8924 (m90) cc_final: 0.8562 (m90) outliers start: 19 outliers final: 11 residues processed: 154 average time/residue: 0.1222 time to fit residues: 26.3982 Evaluate side-chains 138 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 K residue 25 PHE 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 O residue 54 TYR Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain S residue 79 HIS Chi-restraints excluded: chain S residue 99 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 80 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 85 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.060198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.049460 restraints weight = 100968.415| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.50 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 1.0186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13073 Z= 0.261 Angle : 0.768 13.913 19016 Z= 0.432 Chirality : 0.043 0.455 2172 Planarity : 0.005 0.056 1319 Dihedral : 34.617 179.730 4223 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.81 % Allowed : 31.01 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.31), residues: 718 helix: 1.18 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -0.71 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 129 TYR 0.048 0.003 TYR S 80 PHE 0.030 0.003 PHE I 67 HIS 0.005 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00587 (13073) covalent geometry : angle 0.76848 (19016) hydrogen bonds : bond 0.07731 ( 777) hydrogen bonds : angle 3.80834 ( 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 165 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 54 TYR cc_start: 0.8339 (m-80) cc_final: 0.8107 (m-80) REVERT: I 104 PHE cc_start: 0.8755 (m-80) cc_final: 0.8368 (m-80) REVERT: J 85 ASP cc_start: 0.8524 (m-30) cc_final: 0.8239 (m-30) REVERT: K 64 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8886 (tm-30) REVERT: K 95 LYS cc_start: 0.8942 (tmmt) cc_final: 0.8671 (tmmt) REVERT: O 133 GLU cc_start: 0.8048 (mp0) cc_final: 0.7708 (pm20) REVERT: R 110 ASN cc_start: 0.8892 (t0) cc_final: 0.8444 (p0) REVERT: S 106 HIS cc_start: 0.8783 (m90) cc_final: 0.8542 (m-70) outliers start: 29 outliers final: 20 residues processed: 152 average time/residue: 0.1231 time to fit residues: 25.9139 Evaluate side-chains 141 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 M residue 98 LEU Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain Q residue 44 LYS Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 79 HIS Chi-restraints excluded: chain S residue 99 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 74 optimal weight: 0.9990 chunk 42 optimal weight: 0.0770 chunk 71 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 69 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- 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** Q 25 ASN R 68 ASN ** R 112 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 = 0.4051 r_free = 0.4051 target = 0.062745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.052200 restraints weight = 99161.473| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.43 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 1.0180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13073 Z= 0.179 Angle : 0.749 16.695 19016 Z= 0.414 Chirality : 0.042 0.538 2172 Planarity : 0.005 0.054 1319 Dihedral : 34.424 178.988 4221 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.65 % Allowed : 33.50 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.30), residues: 718 helix: 1.41 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -0.86 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 49 TYR 0.017 0.002 TYR S 80 PHE 0.025 0.002 PHE I 67 HIS 0.004 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00408 (13073) covalent geometry : angle 0.74867 (19016) hydrogen bonds : bond 0.06278 ( 777) hydrogen bonds : angle 3.60095 ( 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 157 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 100 LEU cc_start: 0.9560 (tp) cc_final: 0.8959 (tp) REVERT: I 104 PHE cc_start: 0.8654 (m-80) cc_final: 0.8197 (m-80) REVERT: J 85 ASP cc_start: 0.8490 (m-30) cc_final: 0.8162 (m-30) REVERT: K 64 GLU cc_start: 0.9266 (tm-30) cc_final: 0.8976 (tm-30) REVERT: O 60 LEU cc_start: 0.8281 (mt) cc_final: 0.8057 (mp) REVERT: R 110 ASN cc_start: 0.8991 (t0) cc_final: 0.8689 (p0) REVERT: S 99 LEU cc_start: 0.8611 (mm) cc_final: 0.8321 (mm) REVERT: S 106 HIS cc_start: 0.8845 (m90) cc_final: 0.8463 (m-70) outliers start: 16 outliers final: 11 residues processed: 150 average time/residue: 0.1171 time to fit residues: 24.9269 Evaluate side-chains 141 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 M residue 57 SER Chi-restraints excluded: chain M residue 88 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain S residue 79 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 14 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 66 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 0.0570 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 75 HIS M 81 ASN Q 25 ASN R 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.060091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.048684 restraints weight = 86341.840| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.29 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 1.0226 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= 0.177 Angle : 0.766 14.675 19016 Z= 0.417 Chirality : 0.042 0.486 2172 Planarity : 0.005 0.054 1319 Dihedral : 34.316 179.415 4221 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.32 % Allowed : 34.16 % 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 aren not related in a simple way. whole: 1.04 (0.30), residues: 718 helix: 1.30 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -0.84 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 67 TYR 0.064 0.002 TYR Q 88 PHE 0.021 0.002 PHE O 67 HIS 0.004 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00402 (13073) covalent geometry : angle 0.76598 (19016) hydrogen bonds : bond 0.06237 ( 777) hydrogen bonds : angle 3.63987 ( 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 153 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 104 PHE cc_start: 0.8624 (m-80) cc_final: 0.8299 (m-80) REVERT: J 85 ASP cc_start: 0.8490 (m-30) cc_final: 0.8243 (m-30) REVERT: K 64 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8958 (tm-30) REVERT: K 104 GLN cc_start: 0.8990 (mm110) cc_final: 0.8732 (tp40) REVERT: S 102 GLU cc_start: 0.8445 (pm20) cc_final: 0.7974 (pm20) outliers start: 20 outliers final: 15 residues processed: 143 average time/residue: 0.1071 time to fit residues: 22.4399 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 : 0.304 ------------------------------------------------------------------------------- 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 K residue 76 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 79 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 0.0060 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 25 ASN ** Q 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.063773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.053436 restraints weight = 98445.656| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.45 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 1.0264 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 : 0.765 14.407 19016 Z= 0.419 Chirality : 0.042 0.509 2172 Planarity : 0.005 0.053 1319 Dihedral : 34.258 179.307 4221 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.15 % Allowed : 34.99 % 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 aren not related in a simple way. whole: 0.90 (0.30), residues: 718 helix: 1.24 (0.22), residues: 512 sheet: None (None), residues: 0 loop : -0.95 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 83 TYR 0.054 0.002 TYR S 80 PHE 0.026 0.002 PHE O 67 HIS 0.004 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00403 (13073) covalent geometry : angle 0.76480 (19016) hydrogen bonds : bond 0.06218 ( 777) hydrogen bonds : angle 3.72025 ( 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 148 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 104 PHE cc_start: 0.8655 (m-80) cc_final: 0.8331 (m-80) REVERT: J 85 ASP cc_start: 0.8500 (m-30) cc_final: 0.8183 (m-30) REVERT: K 64 GLU cc_start: 0.9265 (tm-30) cc_final: 0.8953 (tm-30) REVERT: K 104 GLN cc_start: 0.9011 (mm110) cc_final: 0.8781 (tp40) REVERT: S 44 GLN cc_start: 0.8610 (pt0) cc_final: 0.8406 (pp30) REVERT: S 102 GLU cc_start: 0.8377 (pm20) cc_final: 0.7995 (pm20) outliers start: 19 outliers final: 14 residues processed: 137 average time/residue: 0.1119 time to fit residues: 22.2441 Evaluate side-chains 138 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 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 O residue 124 ILE Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 79 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 0.0170 chunk 75 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.057155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.045892 restraints weight = 87281.017| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.25 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 1.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 13073 Z= 0.252 Angle : 0.797 13.800 19016 Z= 0.440 Chirality : 0.045 0.514 2172 Planarity : 0.005 0.055 1319 Dihedral : 34.468 179.697 4221 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.99 % Allowed : 34.66 % Favored : 62.35 % 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 aren not related in a simple way. whole: 0.87 (0.30), residues: 718 helix: 1.16 (0.22), residues: 512 sheet: None (None), residues: 0 loop : -0.78 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 67 TYR 0.090 0.003 TYR S 80 PHE 0.042 0.003 PHE R 25 HIS 0.004 0.001 HIS M 46 Details of bonding type rmsd covalent geometry : bond 0.00566 (13073) covalent geometry : angle 0.79654 (19016) hydrogen bonds : bond 0.07350 ( 777) hydrogen bonds : angle 3.97258 ( 1887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2890.32 seconds wall clock time: 50 minutes 18.80 seconds (3018.80 seconds total)