Starting phenix.real_space_refine on Wed Jul 30 05:21:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo0_43363/07_2025/8vo0_43363.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo0_43363/07_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_43363/07_2025/8vo0_43363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo0_43363/07_2025/8vo0_43363.map" model { file = "/net/cci-nas-00/data/ceres_data/8vo0_43363/07_2025/8vo0_43363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo0_43363/07_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-5711/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: 8.56, per 1000 atoms: 0.70 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: 3.21 Conformation dependent library (CDL) restraints added in 981.4 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: 6.20 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: 5.15 Time building geometry restraints manager: 3.85 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: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.910 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.160 ------------------------------------------------------------------------------- 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 : 0.888 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: 0.2761 time to fit residues: 43.5853 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 : 0.901 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.074084 restraints weight = 95760.238| |-----------------------------------------------------------------------------| 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 : 0.836 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: 0.7501 (mm-40) REVERT: O 133 GLU cc_start: 0.6174 (mp0) cc_final: 0.5616 (pm20) REVERT: Q 44 LYS cc_start: 0.8678 (mmmm) cc_final: 0.8242 (mmtt) REVERT: Q 74 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8383 (pp20) REVERT: R 102 ILE cc_start: 0.6709 (mm) cc_final: 0.6441 (tp) REVERT: S 68 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7973 (pp20) outliers start: 20 outliers final: 10 residues processed: 147 average time/residue: 0.2741 time to fit residues: 55.0419 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 : 0.833 ------------------------------------------------------------------------------- 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: 2.9990 chunk 71 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 82 HIS ** 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 = 0.4249 r_free = 0.4249 target = 0.071668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.060717 restraints weight = 99105.357| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 3.51 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 13073 Z= 0.261 Angle : 0.751 11.184 19016 Z= 0.430 Chirality : 0.043 0.373 2172 Planarity : 0.007 0.072 1319 Dihedral : 34.038 179.209 4223 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 5.14 % Allowed : 26.53 % Favored : 68.33 % Cbeta Deviations : 0.15 % 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: 0.99 (0.30), residues: 718 helix: 1.35 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.25 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.026 0.003 HIS S 79 PHE 0.029 0.003 PHE M 62 TYR 0.031 0.003 TYR Q 88 ARG 0.006 0.001 ARG R 81 Details of bonding type rmsd hydrogen bonds : bond 0.07645 ( 777) hydrogen bonds : angle 3.68647 ( 1887) covalent geometry : bond 0.00559 (13073) covalent geometry : angle 0.75082 (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 175 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 100 LEU cc_start: 0.9418 (mm) cc_final: 0.9085 (tp) REVERT: I 104 PHE cc_start: 0.8693 (m-80) cc_final: 0.8321 (m-80) REVERT: J 59 LYS cc_start: 0.9315 (tppt) cc_final: 0.8827 (tppp) REVERT: J 85 ASP cc_start: 0.8248 (m-30) cc_final: 0.8039 (m-30) REVERT: K 25 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6370 (t80) REVERT: K 95 LYS cc_start: 0.8896 (tmmt) cc_final: 0.8646 (tmmt) REVERT: K 104 GLN cc_start: 0.8914 (mm110) cc_final: 0.8635 (mm-40) REVERT: M 48 ASP cc_start: 0.8336 (p0) cc_final: 0.8064 (p0) REVERT: O 79 LYS cc_start: 0.8447 (mmmt) cc_final: 0.8162 (tppt) REVERT: Q 100 PHE cc_start: 0.8235 (m-80) cc_final: 0.8033 (m-10) outliers start: 31 outliers final: 14 residues processed: 157 average time/residue: 0.2822 time to fit residues: 60.7510 Evaluate side-chains 129 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 O residue 107 THR 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: 4.9990 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.070154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.059391 restraints weight = 97363.431| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.36 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.6074 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= 0.195 Angle : 0.679 11.974 19016 Z= 0.388 Chirality : 0.039 0.201 2172 Planarity : 0.005 0.067 1319 Dihedral : 33.956 179.742 4223 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.64 % Allowed : 28.69 % Favored : 66.67 % 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: 1.23 (0.31), residues: 718 helix: 1.54 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -1.10 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS S 79 PHE 0.021 0.002 PHE M 62 TYR 0.035 0.002 TYR Q 88 ARG 0.006 0.000 ARG I 129 Details of bonding type rmsd hydrogen bonds : bond 0.06386 ( 777) hydrogen bonds : angle 3.38084 ( 1887) covalent geometry : bond 0.00436 (13073) covalent geometry : angle 0.67932 (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 168 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: I 104 PHE cc_start: 0.8708 (m-80) cc_final: 0.8373 (m-80) REVERT: J 59 LYS cc_start: 0.9380 (tppt) cc_final: 0.9000 (tppp) REVERT: K 95 LYS cc_start: 0.8920 (tmmt) cc_final: 0.8668 (tmmt) REVERT: M 48 ASP cc_start: 0.8459 (p0) cc_final: 0.8179 (p0) REVERT: M 54 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8563 (tttt) REVERT: O 79 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8226 (tppt) REVERT: R 102 ILE cc_start: 0.7602 (mm) cc_final: 0.7392 (tp) REVERT: S 99 LEU cc_start: 0.8828 (mm) cc_final: 0.8562 (mm) REVERT: S 106 HIS cc_start: 0.8897 (m90) cc_final: 0.8255 (m90) outliers start: 28 outliers final: 15 residues processed: 156 average time/residue: 0.2510 time to fit residues: 55.3224 Evaluate side-chains 129 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 79 ILE 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 86 ILE Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain S residue 53 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 70 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.066427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.055641 restraints weight = 100113.566| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.42 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.7481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13073 Z= 0.213 Angle : 0.715 11.493 19016 Z= 0.403 Chirality : 0.041 0.224 2172 Planarity : 0.005 0.068 1319 Dihedral : 34.092 179.972 4221 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.31 % Allowed : 28.36 % Favored : 66.33 % 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: 1.00 (0.31), residues: 718 helix: 1.28 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -0.98 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS S 46 PHE 0.026 0.002 PHE M 62 TYR 0.042 0.002 TYR S 80 ARG 0.005 0.001 ARG I 129 Details of bonding type rmsd hydrogen bonds : bond 0.06876 ( 777) hydrogen bonds : angle 3.56768 ( 1887) covalent geometry : bond 0.00477 (13073) covalent geometry : angle 0.71512 (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 171 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 100 LEU cc_start: 0.9537 (tp) cc_final: 0.9059 (tp) REVERT: I 104 PHE cc_start: 0.8687 (m-80) cc_final: 0.8278 (m-80) REVERT: K 95 LYS cc_start: 0.8949 (tmmt) cc_final: 0.8656 (tmmt) REVERT: M 68 GLU cc_start: 0.8939 (tp30) cc_final: 0.8684 (mm-30) REVERT: Q 59 LYS cc_start: 0.9162 (pttt) cc_final: 0.8903 (pttm) REVERT: S 59 MET cc_start: 0.7290 (tmm) cc_final: 0.7086 (tmm) REVERT: S 99 LEU cc_start: 0.8839 (mm) cc_final: 0.8599 (mm) outliers start: 32 outliers final: 16 residues processed: 158 average time/residue: 0.2770 time to fit residues: 59.7523 Evaluate side-chains 132 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 74 ILE 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 34 LEU Chi-restraints excluded: chain K residue 65 LEU 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 M residue 98 LEU 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 S residue 66 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 68 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.063993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.053143 restraints weight = 101265.633| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.57 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.8647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13073 Z= 0.226 Angle : 0.742 14.358 19016 Z= 0.415 Chirality : 0.041 0.315 2172 Planarity : 0.006 0.056 1319 Dihedral : 34.209 179.862 4221 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.64 % Allowed : 30.85 % Favored : 64.51 % 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: 1.02 (0.31), residues: 718 helix: 1.29 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS M 46 PHE 0.037 0.003 PHE Q 61 TYR 0.040 0.003 TYR S 80 ARG 0.007 0.001 ARG I 129 Details of bonding type rmsd hydrogen bonds : bond 0.06741 ( 777) hydrogen bonds : angle 3.63942 ( 1887) covalent geometry : bond 0.00505 (13073) covalent geometry : angle 0.74203 (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 163 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 100 LEU cc_start: 0.9579 (tp) cc_final: 0.9083 (tp) REVERT: I 104 PHE cc_start: 0.8695 (m-80) cc_final: 0.8264 (m-80) REVERT: K 95 LYS cc_start: 0.8974 (tmmt) cc_final: 0.8672 (tmmt) REVERT: Q 59 LYS cc_start: 0.9223 (pttt) cc_final: 0.8913 (pttm) REVERT: R 64 GLU cc_start: 0.8536 (tp30) cc_final: 0.8333 (mm-30) REVERT: S 59 MET cc_start: 0.7406 (tmm) cc_final: 0.7204 (tmm) REVERT: S 99 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8624 (mm) REVERT: S 106 HIS cc_start: 0.8831 (m90) cc_final: 0.8101 (m90) outliers start: 28 outliers final: 18 residues processed: 149 average time/residue: 0.3039 time to fit residues: 61.7981 Evaluate side-chains 138 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 68 ASP Chi-restraints excluded: chain K residue 34 LEU 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 M residue 98 LEU Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain S residue 53 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 66 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 GLN O 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.062860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.052186 restraints weight = 99990.708| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.50 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.9481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13073 Z= 0.215 Angle : 0.739 13.450 19016 Z= 0.414 Chirality : 0.041 0.304 2172 Planarity : 0.005 0.052 1319 Dihedral : 34.341 179.849 4221 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.81 % Allowed : 31.18 % 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: 1.16 (0.31), residues: 718 helix: 1.36 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -0.73 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 46 PHE 0.028 0.003 PHE M 62 TYR 0.039 0.002 TYR S 80 ARG 0.009 0.001 ARG J 67 Details of bonding type rmsd hydrogen bonds : bond 0.06593 ( 777) hydrogen bonds : angle 3.67910 ( 1887) covalent geometry : bond 0.00489 (13073) covalent geometry : angle 0.73867 (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 163 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 104 PHE cc_start: 0.8680 (m-80) cc_final: 0.8363 (m-80) REVERT: J 58 LEU cc_start: 0.9437 (tp) cc_final: 0.9136 (pp) REVERT: K 95 LYS cc_start: 0.9007 (tmmt) cc_final: 0.8714 (tmmt) REVERT: M 54 LYS cc_start: 0.8841 (ttmt) cc_final: 0.8632 (tttt) REVERT: Q 44 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8666 (mmmm) REVERT: Q 59 LYS cc_start: 0.9225 (pttt) cc_final: 0.9005 (pttm) REVERT: Q 91 LYS cc_start: 0.9391 (pptt) cc_final: 0.9043 (pptt) REVERT: S 56 MET cc_start: 0.8739 (tpp) cc_final: 0.8450 (tpt) REVERT: S 102 GLU cc_start: 0.8603 (pm20) cc_final: 0.8120 (pm20) outliers start: 29 outliers final: 18 residues processed: 153 average time/residue: 0.2811 time to fit residues: 59.5952 Evaluate side-chains 141 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain K residue 65 LEU 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 88 SER Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 44 LYS Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 79 HIS Chi-restraints excluded: chain S residue 99 LEU 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: 5.9990 chunk 7 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN ** R 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.052118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.041063 restraints weight = 95142.153| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.26 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 1.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 13073 Z= 0.421 Angle : 0.926 13.595 19016 Z= 0.519 Chirality : 0.054 0.733 2172 Planarity : 0.007 0.074 1319 Dihedral : 35.351 179.196 4221 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 30.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 6.63 % Allowed : 30.18 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.31 (0.30), residues: 718 helix: 0.59 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -0.56 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS J 75 PHE 0.029 0.004 PHE Q 61 TYR 0.053 0.003 TYR S 80 ARG 0.014 0.001 ARG J 67 Details of bonding type rmsd hydrogen bonds : bond 0.10495 ( 777) hydrogen bonds : angle 4.54410 ( 1887) covalent geometry : bond 0.00931 (13073) covalent geometry : angle 0.92590 (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 168 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 100 LEU cc_start: 0.9638 (tp) cc_final: 0.9161 (tp) REVERT: I 104 PHE cc_start: 0.8693 (m-80) cc_final: 0.8325 (m-80) REVERT: K 95 LYS cc_start: 0.9036 (tmmt) cc_final: 0.8557 (mmmm) REVERT: M 110 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8245 (tm-30) REVERT: S 59 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8151 (ppp) REVERT: S 102 GLU cc_start: 0.8650 (pm20) cc_final: 0.8289 (pm20) outliers start: 40 outliers final: 27 residues processed: 150 average time/residue: 0.3399 time to fit residues: 73.0555 Evaluate side-chains 144 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 76 THR 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 87 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 71 THR 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 59 MET Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 79 HIS Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN ** 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 = 0.3920 r_free = 0.3920 target = 0.055541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.044664 restraints weight = 83588.830| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.15 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 1.1453 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= 0.217 Angle : 0.814 17.997 19016 Z= 0.447 Chirality : 0.046 0.567 2172 Planarity : 0.005 0.050 1319 Dihedral : 35.072 179.033 4221 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.48 % Allowed : 32.50 % Favored : 63.02 % 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: 0.80 (0.30), residues: 718 helix: 1.06 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -0.72 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS S 79 PHE 0.023 0.003 PHE M 62 TYR 0.052 0.003 TYR S 80 ARG 0.012 0.001 ARG Q 92 Details of bonding type rmsd hydrogen bonds : bond 0.06604 ( 777) hydrogen bonds : angle 3.98654 ( 1887) covalent geometry : bond 0.00489 (13073) covalent geometry : angle 0.81446 (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 164 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 104 PHE cc_start: 0.8671 (m-80) cc_final: 0.8247 (m-80) REVERT: K 91 GLU cc_start: 0.8541 (mp0) cc_final: 0.8288 (mp0) REVERT: K 95 LYS cc_start: 0.9009 (tmmt) cc_final: 0.8432 (mmmm) REVERT: M 89 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8541 (ptm-80) REVERT: Q 91 LYS cc_start: 0.9359 (pptt) cc_final: 0.9056 (pptt) REVERT: S 59 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7864 (tmm) REVERT: S 106 HIS cc_start: 0.8745 (m90) cc_final: 0.8447 (m90) outliers start: 27 outliers final: 19 residues processed: 153 average time/residue: 0.3098 time to fit residues: 65.7271 Evaluate side-chains 142 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 74 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 76 THR 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 89 ARG 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 Q residue 43 VAL Chi-restraints excluded: chain Q residue 86 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 99 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 42 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 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: 1.9586 ------------------------------------------------------------------------------- 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** I 93 GLN ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN S 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.058685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.048415 restraints weight = 100983.864| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.21 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 1.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13073 Z= 0.237 Angle : 0.814 15.877 19016 Z= 0.445 Chirality : 0.045 0.507 2172 Planarity : 0.005 0.059 1319 Dihedral : 35.002 179.678 4221 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 22.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.81 % Allowed : 33.67 % 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 (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: 0.82 (0.30), residues: 718 helix: 1.09 (0.22), residues: 517 sheet: None (None), residues: 0 loop : -0.76 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS S 79 PHE 0.028 0.003 PHE O 67 TYR 0.041 0.002 TYR S 80 ARG 0.013 0.001 ARG Q 92 Details of bonding type rmsd hydrogen bonds : bond 0.07178 ( 777) hydrogen bonds : angle 4.05555 ( 1887) covalent geometry : bond 0.00536 (13073) covalent geometry : angle 0.81440 (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 150 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 104 PHE cc_start: 0.8727 (m-80) cc_final: 0.8303 (m-80) REVERT: K 95 LYS cc_start: 0.9032 (tmmt) cc_final: 0.8710 (tmmt) REVERT: Q 58 LEU cc_start: 0.9734 (mt) cc_final: 0.9436 (mt) REVERT: Q 91 LYS cc_start: 0.9381 (pptt) cc_final: 0.9076 (pptt) REVERT: Q 92 ARG cc_start: 0.9287 (ttp80) cc_final: 0.9065 (ttp80) REVERT: S 102 GLU cc_start: 0.8473 (pm20) cc_final: 0.8097 (pm20) outliers start: 23 outliers final: 20 residues processed: 141 average time/residue: 0.2497 time to fit residues: 51.1716 Evaluate side-chains 143 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 K residue 65 LEU Chi-restraints excluded: chain K residue 76 THR 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 88 SER Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 87 SER 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 79 HIS 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: 5.9990 chunk 14 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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** S 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.058079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.047888 restraints weight = 101391.399| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.20 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 1.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 13073 Z= 0.260 Angle : 0.830 16.225 19016 Z= 0.453 Chirality : 0.046 0.482 2172 Planarity : 0.006 0.055 1319 Dihedral : 35.042 179.426 4221 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.65 % Allowed : 33.67 % Favored : 62.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.31), residues: 718 helix: 1.04 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -0.78 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS S 79 PHE 0.025 0.003 PHE O 67 TYR 0.037 0.003 TYR S 80 ARG 0.012 0.001 ARG Q 92 Details of bonding type rmsd hydrogen bonds : bond 0.07342 ( 777) hydrogen bonds : angle 4.07799 ( 1887) covalent geometry : bond 0.00588 (13073) covalent geometry : angle 0.82988 (19016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6324.62 seconds wall clock time: 112 minutes 49.99 seconds (6769.99 seconds total)