Starting phenix.real_space_refine on Wed Aug 5 23:48:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vob_43373/08_2026/8vob_43373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vob_43373/08_2026/8vob_43373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vob_43373/08_2026/8vob_43373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vob_43373/08_2026/8vob_43373.map" model { file = "/net/cci-nas-00/data/ceres_data/8vob_43373/08_2026/8vob_43373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vob_43373/08_2026/8vob_43373.cif" } resolution = 3.1 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= 0.042 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 6897 2.51 5 N 2356 2.21 5 O 2969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12550 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: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 835 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} 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: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Q" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 667 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 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: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3202 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Time building chain proxies: 2.81, per 1000 atoms: 0.22 Number of scatterers: 12550 At special positions: 0 Unit cell: (112.35, 136.5, 119.7, 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 2969 8.00 N 2356 7.00 C 6897 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: 1.04 Conformation dependent library (CDL) restraints added in 358.4 milliseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1454 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 71.2% alpha, 2.3% beta 155 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'I' and resid 45 through 56 removed outlier: 3.504A pdb=" N LYS I 56 " --> pdb=" O ARG I 52 " (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 131 Processing helix chain 'J' and resid 24 through 29 Processing helix chain 'J' and resid 30 through 42 Processing helix chain 'J' and resid 50 through 76 removed outlier: 3.840A pdb=" N ASP J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 94 removed outlier: 3.664A pdb=" N VAL J 86 " --> pdb=" O THR J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 21 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 45 through 73 removed outlier: 4.320A pdb=" N VAL K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 88 Processing helix chain 'K' and resid 90 through 98 removed outlier: 3.994A pdb=" N LEU K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 116 Processing helix chain 'M' and resid 34 through 46 Processing helix chain 'M' and resid 52 through 81 Processing helix chain 'M' and resid 87 through 99 removed outlier: 3.809A pdb=" N ILE M 91 " --> pdb=" O THR M 87 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU M 99 " --> pdb=" O VAL M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 121 removed outlier: 3.726A pdb=" N ALA M 121 " --> pdb=" O LYS M 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 55 Processing helix chain 'O' and resid 63 through 79 removed outlier: 3.983A pdb=" N PHE O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) removed outlier: 3.734A 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: 3.714A 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 76 removed outlier: 4.387A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG Q 55 " --> pdb=" O TYR Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 93 removed outlier: 3.609A pdb=" N VAL Q 86 " --> pdb=" O THR Q 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 21 removed outlier: 3.649A pdb=" N ARG R 20 " --> pdb=" O THR R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 37 Processing helix chain 'R' and resid 45 through 73 removed outlier: 4.296A pdb=" N VAL R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 90 Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'R' and resid 112 through 116 Processing helix chain 'S' and resid 34 through 46 Processing helix chain 'S' and resid 52 through 81 Processing helix chain 'S' and resid 87 through 99 removed outlier: 3.514A pdb=" N ILE S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 121 removed outlier: 4.038A 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: 7.590A 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: 3.515A 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 96 through 97 removed outlier: 6.336A pdb=" N THR J 96 " --> 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: 7.566A 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'K' and resid 101 through 102 removed outlier: 7.048A pdb=" N THR K 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.767A pdb=" N ARG O 83 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.333A pdb=" N ARG R 42 " --> pdb=" O ILE S 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'R' and resid 77 through 78 396 hydrogen bonds defined for protein. 1161 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 395 hydrogen bonds 758 hydrogen bond angles 0 basepair planarities 155 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2633 1.33 - 1.46: 4388 1.46 - 1.58: 5741 1.58 - 1.70: 627 1.70 - 1.82: 24 Bond restraints: 13413 Sorted by residual: bond pdb=" CG PRO Q 32 " pdb=" CD PRO Q 32 " ideal model delta sigma weight residual 1.503 1.300 0.203 3.40e-02 8.65e+02 3.55e+01 bond pdb=" N PRO Q 32 " pdb=" CD PRO Q 32 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.40e+01 bond pdb=" C3' DT H 16 " pdb=" C2' DT H 16 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' DG D 239 " pdb=" C2' DG D 239 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DG D 244 " pdb=" C2' DG D 244 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 ... (remaining 13408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 19376 3.74 - 7.48: 89 7.48 - 11.21: 8 11.21 - 14.95: 1 14.95 - 18.69: 1 Bond angle restraints: 19475 Sorted by residual: angle pdb=" CA PRO Q 32 " pdb=" N PRO Q 32 " pdb=" CD PRO Q 32 " ideal model delta sigma weight residual 112.00 93.31 18.69 1.40e+00 5.10e-01 1.78e+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 90.45 12.75 1.50e+00 4.44e-01 7.23e+01 angle pdb=" N VAL I 117 " pdb=" CA VAL I 117 " pdb=" C VAL I 117 " ideal model delta sigma weight residual 113.71 109.03 4.68 9.50e-01 1.11e+00 2.42e+01 angle pdb=" CA PRO Q 32 " pdb=" CB PRO Q 32 " pdb=" CG PRO Q 32 " ideal model delta sigma weight residual 104.50 95.21 9.29 1.90e+00 2.77e-01 2.39e+01 angle pdb=" O4' DA H 18 " pdb=" C4' DA H 18 " pdb=" C3' DA H 18 " ideal model delta sigma weight residual 106.00 103.15 2.85 6.00e-01 2.78e+00 2.25e+01 ... (remaining 19470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 5759 35.96 - 71.93: 1405 71.93 - 107.89: 30 107.89 - 143.86: 8 143.86 - 179.82: 24 Dihedral angle restraints: 7226 sinusoidal: 4973 harmonic: 2253 Sorted by residual: dihedral pdb=" C4' DT D 225 " pdb=" C3' DT D 225 " pdb=" O3' DT D 225 " pdb=" P DT D 226 " ideal model delta sinusoidal sigma weight residual 220.00 40.18 179.82 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC D 162 " pdb=" C3' DC D 162 " pdb=" O3' DC D 162 " pdb=" P DC D 163 " ideal model delta sinusoidal sigma weight residual -140.00 39.60 -179.60 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG D 231 " pdb=" C3' DG D 231 " pdb=" O3' DG D 231 " pdb=" P DC D 232 " ideal model delta sinusoidal sigma weight residual 220.00 40.77 179.23 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1917 0.070 - 0.140: 277 0.140 - 0.209: 24 0.209 - 0.279: 1 0.279 - 0.349: 1 Chirality restraints: 2220 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 -2.24 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB ILE O 62 " pdb=" CA ILE O 62 " pdb=" CG1 ILE O 62 " pdb=" CG2 ILE O 62 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C3' DG H 135 " pdb=" C4' DG H 135 " pdb=" O3' DG H 135 " pdb=" C2' DG H 135 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.15e-01 ... (remaining 2217 not shown) Planarity restraints: 1378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS Q 31 " -0.108 5.00e-02 4.00e+02 1.47e-01 3.43e+01 pdb=" N PRO Q 32 " 0.252 5.00e-02 4.00e+02 pdb=" CA PRO Q 32 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO Q 32 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU Q 63 " 0.013 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" CD GLU Q 63 " -0.048 2.00e-02 2.50e+03 pdb=" OE1 GLU Q 63 " 0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU Q 63 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC H 114 " 0.002 2.00e-02 2.50e+03 1.65e-02 6.12e+00 pdb=" N1 DC H 114 " -0.011 2.00e-02 2.50e+03 pdb=" C2 DC H 114 " 0.041 2.00e-02 2.50e+03 pdb=" O2 DC H 114 " -0.022 2.00e-02 2.50e+03 pdb=" N3 DC H 114 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC H 114 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC H 114 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DC H 114 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC H 114 " -0.003 2.00e-02 2.50e+03 ... (remaining 1375 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 269 2.63 - 3.20: 10907 3.20 - 3.77: 25129 3.77 - 4.33: 30746 4.33 - 4.90: 43494 Nonbonded interactions: 110545 Sorted by model distance: nonbonded pdb=" N2 DG H 137 " pdb=" O2 DC D 178 " model vdw 2.066 2.496 nonbonded pdb=" O2 DC H 110 " pdb=" N2 DG D 205 " model vdw 2.123 2.496 nonbonded pdb=" N2 DG H 135 " pdb=" O2 DC D 180 " model vdw 2.137 2.496 nonbonded pdb=" O2 DC H 154 " pdb=" N2 DG D 161 " model vdw 2.144 2.496 nonbonded pdb=" N2 DG H 93 " pdb=" O2 DC D 222 " model vdw 2.153 2.496 ... (remaining 110540 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' and resid 37 through 135) selection = chain 'O' } ncs_group { reference = (chain 'J' and ((resid 20 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 102)) selection = (chain 'Q' and resid 20 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 28 through 122) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.550 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.006 0.203 13413 Z= 0.529 Angle : 0.905 18.688 19475 Z= 0.740 Chirality : 0.049 0.349 2220 Planarity : 0.006 0.147 1378 Dihedral : 31.207 179.822 5772 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.79 % Allowed : 31.80 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.31), residues: 759 helix: 1.49 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.50 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 76 TYR 0.023 0.002 TYR K 57 PHE 0.012 0.002 PHE M 67 HIS 0.003 0.001 HIS J 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.53 (13413) covalent geometry : angle 0.90475 / 0.74 (19475) hydrogen bonds : bond 0.10427 / 11.31 ( 791) hydrogen bonds : angle 3.77246 / 5.02 ( 1919) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 161 average time/residue: 0.1334 time to fit residues: 30.1578 Evaluate side-chains 155 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 105 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 68 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 = 0.3998 r_free = 0.3998 target = 0.067326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.054362 restraints weight = 67648.305| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.94 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13413 Z= 0.177 Angle : 0.742 8.551 19475 Z= 0.426 Chirality : 0.053 0.349 2220 Planarity : 0.005 0.061 1378 Dihedral : 34.056 179.953 4280 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.53 % Allowed : 26.42 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.31), residues: 759 helix: 1.51 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -1.43 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 63 TYR 0.048 0.002 TYR Q 88 PHE 0.009 0.001 PHE M 62 HIS 0.003 0.001 HIS I 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.18 (13413) covalent geometry : angle 0.74174 / 0.43 (19475) hydrogen bonds : bond 0.07610 / 8.37 ( 791) hydrogen bonds : angle 3.40689 / 4.44 ( 1919) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9359 (pt0) cc_final: 0.9033 (pt0) REVERT: K 64 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7884 (mm-30) REVERT: K 73 ASN cc_start: 0.8912 (t0) cc_final: 0.8694 (t0) REVERT: M 32 GLU cc_start: 0.7938 (tp30) cc_final: 0.7660 (tp30) REVERT: M 92 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8251 (tm-30) REVERT: O 90 MET cc_start: 0.8388 (mpp) cc_final: 0.8090 (mmm) REVERT: Q 59 LYS cc_start: 0.8388 (mtmm) cc_final: 0.7993 (mttt) REVERT: Q 63 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8535 (mp0) REVERT: Q 93 GLN cc_start: 0.8623 (mm110) cc_final: 0.8313 (mm110) REVERT: R 84 GLN cc_start: 0.8843 (tp40) cc_final: 0.8487 (tp40) REVERT: S 44 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8674 (mm110) outliers start: 16 outliers final: 8 residues processed: 176 average time/residue: 0.1308 time to fit residues: 32.4001 Evaluate side-chains 159 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 74 ILE Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 64 ASN Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 113 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 44 optimal weight: 0.0870 chunk 100 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 GLN ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.065859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.052944 restraints weight = 68511.043| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.92 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13413 Z= 0.206 Angle : 0.745 7.904 19475 Z= 0.427 Chirality : 0.052 0.353 2220 Planarity : 0.005 0.060 1378 Dihedral : 34.100 179.781 4276 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.32 % Allowed : 26.90 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.30), residues: 759 helix: 1.41 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.41 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 92 TYR 0.032 0.002 TYR Q 88 PHE 0.011 0.002 PHE I 67 HIS 0.005 0.001 HIS I 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.21 (13413) covalent geometry : angle 0.74457 / 0.43 (19475) hydrogen bonds : bond 0.07611 / 8.31 ( 791) hydrogen bonds : angle 3.41091 / 4.45 ( 1919) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9399 (pt0) cc_final: 0.9116 (pt0) REVERT: K 64 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7964 (mm-30) REVERT: K 73 ASN cc_start: 0.8982 (t0) cc_final: 0.8738 (t0) REVERT: M 92 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8346 (tm-30) REVERT: O 90 MET cc_start: 0.8486 (mpp) cc_final: 0.8048 (mmm) REVERT: Q 59 LYS cc_start: 0.8402 (mtmm) cc_final: 0.8036 (mttt) REVERT: Q 63 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8257 (mp0) REVERT: Q 84 MET cc_start: 0.8686 (mmp) cc_final: 0.8262 (mmp) REVERT: R 84 GLN cc_start: 0.8835 (tp40) cc_final: 0.8435 (tp40) outliers start: 21 outliers final: 12 residues processed: 174 average time/residue: 0.1020 time to fit residues: 25.1175 Evaluate side-chains 159 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain Q residue 64 ASN Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 31 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 94 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 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 = 0.3975 r_free = 0.3975 target = 0.066343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.053317 restraints weight = 67026.935| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.91 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13413 Z= 0.171 Angle : 0.718 6.887 19475 Z= 0.412 Chirality : 0.052 0.360 2220 Planarity : 0.005 0.060 1378 Dihedral : 34.097 179.879 4276 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.16 % Allowed : 28.01 % Favored : 68.83 % 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 are not related in a simple way. whole: 0.85 (0.30), residues: 759 helix: 1.48 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.44 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 76 TYR 0.023 0.002 TYR S 80 PHE 0.012 0.001 PHE M 62 HIS 0.005 0.001 HIS J 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 (13413) covalent geometry : angle 0.71807 / 0.41 (19475) hydrogen bonds : bond 0.06960 / 7.71 ( 791) hydrogen bonds : angle 3.28598 / 4.29 ( 1919) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9363 (pt0) cc_final: 0.9074 (pt0) REVERT: I 120 MET cc_start: 0.5829 (mtt) cc_final: 0.5621 (mtt) REVERT: K 64 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7888 (mm-30) REVERT: K 73 ASN cc_start: 0.9017 (t0) cc_final: 0.8719 (t0) REVERT: M 54 LYS cc_start: 0.8719 (pttm) cc_final: 0.8319 (ptmt) REVERT: M 92 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8294 (tm-30) REVERT: O 90 MET cc_start: 0.8475 (tpp) cc_final: 0.7956 (mmm) REVERT: R 84 GLN cc_start: 0.8807 (tp40) cc_final: 0.8377 (tp40) outliers start: 20 outliers final: 9 residues processed: 176 average time/residue: 0.1062 time to fit residues: 26.1496 Evaluate side-chains 155 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 88 optimal weight: 50.0000 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 GLN ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.066761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.053789 restraints weight = 68230.910| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.97 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13413 Z= 0.162 Angle : 0.715 8.119 19475 Z= 0.410 Chirality : 0.051 0.355 2220 Planarity : 0.005 0.060 1378 Dihedral : 34.078 179.311 4276 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.48 % Allowed : 28.48 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.30), residues: 759 helix: 1.47 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.42 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG I 134 TYR 0.023 0.002 TYR Q 88 PHE 0.008 0.001 PHE I 67 HIS 0.005 0.001 HIS J 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.16 (13413) covalent geometry : angle 0.71524 / 0.41 (19475) hydrogen bonds : bond 0.06861 / 7.61 ( 791) hydrogen bonds : angle 3.26542 / 4.28 ( 1919) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9382 (pt0) cc_final: 0.9139 (pt0) REVERT: K 64 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7916 (mm-30) REVERT: K 73 ASN cc_start: 0.9054 (t0) cc_final: 0.8757 (t0) REVERT: M 54 LYS cc_start: 0.8684 (pttm) cc_final: 0.8311 (ptmt) REVERT: M 92 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: O 90 MET cc_start: 0.8494 (tpp) cc_final: 0.7991 (mmm) REVERT: Q 59 LYS cc_start: 0.8237 (mttt) cc_final: 0.7865 (mtmm) REVERT: R 84 GLN cc_start: 0.8802 (tp40) cc_final: 0.8357 (tp40) outliers start: 22 outliers final: 13 residues processed: 176 average time/residue: 0.0999 time to fit residues: 25.2152 Evaluate side-chains 162 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 74 ILE Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain S residue 31 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 0.0670 chunk 100 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 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 = 0.3986 r_free = 0.3986 target = 0.066909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.054032 restraints weight = 67226.789| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.90 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13413 Z= 0.160 Angle : 0.722 9.206 19475 Z= 0.411 Chirality : 0.052 0.352 2220 Planarity : 0.005 0.060 1378 Dihedral : 34.066 178.739 4276 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.48 % Allowed : 28.32 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.30), residues: 759 helix: 1.53 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.43 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 129 TYR 0.031 0.002 TYR Q 88 PHE 0.013 0.001 PHE O 67 HIS 0.002 0.001 HIS I 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.16 (13413) covalent geometry : angle 0.72211 / 0.41 (19475) hydrogen bonds : bond 0.06819 / 7.55 ( 791) hydrogen bonds : angle 3.24257 / 4.26 ( 1919) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9361 (pt0) cc_final: 0.9120 (pt0) REVERT: K 64 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7902 (mm-30) REVERT: K 73 ASN cc_start: 0.9080 (t0) cc_final: 0.8820 (t0) REVERT: M 42 LEU cc_start: 0.9344 (pp) cc_final: 0.8965 (tp) REVERT: M 54 LYS cc_start: 0.8640 (pttm) cc_final: 0.8270 (ptmt) REVERT: M 59 MET cc_start: 0.8391 (mmt) cc_final: 0.8161 (mmt) REVERT: M 92 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8308 (tm-30) REVERT: O 54 TYR cc_start: 0.7423 (t80) cc_final: 0.7122 (t80) REVERT: O 81 ASP cc_start: 0.8104 (t0) cc_final: 0.7891 (t0) REVERT: O 90 MET cc_start: 0.8446 (tpp) cc_final: 0.7992 (mmm) REVERT: Q 59 LYS cc_start: 0.8144 (mttt) cc_final: 0.7765 (mtmm) REVERT: R 84 GLN cc_start: 0.8809 (tp40) cc_final: 0.8347 (tp40) REVERT: S 42 LEU cc_start: 0.8552 (mt) cc_final: 0.8114 (tp) REVERT: S 103 LEU cc_start: 0.9434 (mt) cc_final: 0.9206 (mt) outliers start: 22 outliers final: 14 residues processed: 172 average time/residue: 0.1030 time to fit residues: 25.1302 Evaluate side-chains 166 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 74 ILE Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain S residue 31 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 16 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 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 = 0.3953 r_free = 0.3953 target = 0.065420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.052428 restraints weight = 67317.187| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.92 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13413 Z= 0.193 Angle : 0.748 9.558 19475 Z= 0.424 Chirality : 0.052 0.357 2220 Planarity : 0.005 0.062 1378 Dihedral : 34.135 178.925 4276 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.01 % Allowed : 29.59 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.30), residues: 759 helix: 1.48 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.50 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 76 TYR 0.028 0.002 TYR Q 88 PHE 0.016 0.002 PHE M 62 HIS 0.004 0.001 HIS I 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.19 (13413) covalent geometry : angle 0.74773 / 0.42 (19475) hydrogen bonds : bond 0.07252 / 7.96 ( 791) hydrogen bonds : angle 3.32872 / 4.36 ( 1919) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 64 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7851 (mm-30) REVERT: K 73 ASN cc_start: 0.9108 (t0) cc_final: 0.8829 (t0) REVERT: M 54 LYS cc_start: 0.8725 (pttm) cc_final: 0.8374 (ptpt) REVERT: M 92 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8409 (tm-30) REVERT: O 54 TYR cc_start: 0.7577 (t80) cc_final: 0.7360 (t80) REVERT: O 81 ASP cc_start: 0.8218 (t0) cc_final: 0.8011 (t0) REVERT: O 90 MET cc_start: 0.8506 (tpp) cc_final: 0.8227 (mmm) REVERT: O 120 MET cc_start: 0.7388 (mmt) cc_final: 0.7141 (mmt) REVERT: R 84 GLN cc_start: 0.8841 (tp40) cc_final: 0.8062 (tm-30) REVERT: S 103 LEU cc_start: 0.9451 (mt) cc_final: 0.9231 (mt) outliers start: 19 outliers final: 15 residues processed: 168 average time/residue: 0.1051 time to fit residues: 24.5700 Evaluate side-chains 161 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain S residue 58 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 0.0270 chunk 48 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.065452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.052498 restraints weight = 67143.286| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.92 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13413 Z= 0.183 Angle : 0.749 8.794 19475 Z= 0.425 Chirality : 0.052 0.363 2220 Planarity : 0.005 0.061 1378 Dihedral : 34.165 179.430 4276 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.01 % Allowed : 30.22 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.30), residues: 759 helix: 1.45 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.53 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 92 TYR 0.027 0.002 TYR S 80 PHE 0.010 0.001 PHE O 104 HIS 0.003 0.001 HIS M 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.18 (13413) covalent geometry : angle 0.74858 / 0.42 (19475) hydrogen bonds : bond 0.06957 / 7.70 ( 791) hydrogen bonds : angle 3.36484 / 4.43 ( 1919) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9348 (pt0) cc_final: 0.9073 (pt0) REVERT: K 64 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7941 (mm-30) REVERT: K 73 ASN cc_start: 0.9124 (t0) cc_final: 0.8829 (t0) REVERT: M 54 LYS cc_start: 0.8694 (pttm) cc_final: 0.8380 (ptmt) REVERT: M 92 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: O 54 TYR cc_start: 0.7659 (t80) cc_final: 0.7312 (t80) REVERT: O 90 MET cc_start: 0.8491 (tpp) cc_final: 0.8016 (mmm) REVERT: O 120 MET cc_start: 0.7404 (mmt) cc_final: 0.7156 (mmt) REVERT: Q 59 LYS cc_start: 0.8369 (mttt) cc_final: 0.7903 (mtmm) REVERT: R 84 GLN cc_start: 0.8851 (tp40) cc_final: 0.8391 (tp40) REVERT: S 103 LEU cc_start: 0.9446 (mt) cc_final: 0.9204 (mt) outliers start: 19 outliers final: 13 residues processed: 171 average time/residue: 0.0996 time to fit residues: 24.0342 Evaluate side-chains 160 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 31 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 68 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 = 0.3967 r_free = 0.3967 target = 0.066010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.053018 restraints weight = 67047.785| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.00 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13413 Z= 0.167 Angle : 0.756 11.347 19475 Z= 0.426 Chirality : 0.052 0.359 2220 Planarity : 0.005 0.060 1378 Dihedral : 34.139 179.438 4276 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.53 % Allowed : 31.01 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.30), residues: 759 helix: 1.47 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.56 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 76 TYR 0.025 0.002 TYR M 80 PHE 0.014 0.001 PHE M 62 HIS 0.003 0.001 HIS O 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.17 (13413) covalent geometry : angle 0.75563 / 0.43 (19475) hydrogen bonds : bond 0.06748 / 7.51 ( 791) hydrogen bonds : angle 3.33670 / 4.41 ( 1919) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 64 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7969 (mm-30) REVERT: K 73 ASN cc_start: 0.9120 (t0) cc_final: 0.8834 (t0) REVERT: M 54 LYS cc_start: 0.8662 (pttm) cc_final: 0.8347 (ptmt) REVERT: M 92 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8379 (tm-30) REVERT: O 54 TYR cc_start: 0.7586 (t80) cc_final: 0.7308 (t80) REVERT: O 90 MET cc_start: 0.8515 (tpp) cc_final: 0.8068 (mmm) REVERT: O 120 MET cc_start: 0.7357 (mmt) cc_final: 0.7094 (mmt) REVERT: Q 59 LYS cc_start: 0.8310 (mttt) cc_final: 0.7883 (mtmm) REVERT: R 84 GLN cc_start: 0.8828 (tp40) cc_final: 0.8361 (tp40) REVERT: S 103 LEU cc_start: 0.9447 (mt) cc_final: 0.9194 (mt) outliers start: 16 outliers final: 13 residues processed: 167 average time/residue: 0.1075 time to fit residues: 25.6618 Evaluate side-chains 163 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 31 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 68 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 = 0.3909 r_free = 0.3909 target = 0.063487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.050755 restraints weight = 68904.440| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.91 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13413 Z= 0.246 Angle : 0.823 11.095 19475 Z= 0.460 Chirality : 0.055 0.371 2220 Planarity : 0.006 0.065 1378 Dihedral : 34.250 179.810 4276 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.53 % Allowed : 31.33 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.30), residues: 759 helix: 1.34 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.86 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 92 TYR 0.031 0.003 TYR Q 88 PHE 0.012 0.002 PHE O 67 HIS 0.007 0.002 HIS S 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.25 (13413) covalent geometry : angle 0.82275 / 0.46 (19475) hydrogen bonds : bond 0.08154 / 8.90 ( 791) hydrogen bonds : angle 3.57325 / 4.73 ( 1919) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 64 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7965 (mm-30) REVERT: K 73 ASN cc_start: 0.9131 (t0) cc_final: 0.8808 (t0) REVERT: M 54 LYS cc_start: 0.8787 (pttm) cc_final: 0.8491 (ptmt) REVERT: M 92 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8456 (tm-30) REVERT: O 54 TYR cc_start: 0.7785 (t80) cc_final: 0.7461 (t80) REVERT: O 120 MET cc_start: 0.7422 (mmt) cc_final: 0.7198 (mmt) REVERT: Q 59 LYS cc_start: 0.8363 (mttt) cc_final: 0.7928 (mtmm) REVERT: R 84 GLN cc_start: 0.8891 (tp40) cc_final: 0.8089 (tm-30) REVERT: S 103 LEU cc_start: 0.9437 (mt) cc_final: 0.9227 (mt) outliers start: 16 outliers final: 12 residues processed: 158 average time/residue: 0.1015 time to fit residues: 22.7543 Evaluate side-chains 157 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 74 ILE Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 31 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 102 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 84 optimal weight: 0.0770 chunk 94 optimal weight: 20.0000 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.064987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.052078 restraints weight = 67805.886| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.98 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13413 Z= 0.172 Angle : 0.780 11.930 19475 Z= 0.439 Chirality : 0.054 0.370 2220 Planarity : 0.005 0.059 1378 Dihedral : 34.206 179.994 4276 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.22 % Allowed : 31.65 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.30), residues: 759 helix: 1.38 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.69 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 92 TYR 0.054 0.002 TYR M 80 PHE 0.016 0.002 PHE M 62 HIS 0.002 0.001 HIS J 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (13413) covalent geometry : angle 0.77970 / 0.44 (19475) hydrogen bonds : bond 0.06802 / 7.58 ( 791) hydrogen bonds : angle 3.43901 / 4.55 ( 1919) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.95 seconds wall clock time: 44 minutes 3.80 seconds (2643.80 seconds total)