Starting phenix.real_space_refine on Mon Jul 6 14:54:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqd_61728/07_2026/9jqd_61728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqd_61728/07_2026/9jqd_61728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jqd_61728/07_2026/9jqd_61728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqd_61728/07_2026/9jqd_61728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jqd_61728/07_2026/9jqd_61728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqd_61728/07_2026/9jqd_61728.map" } resolution = 1.81 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= 0.001 sd= 0.080 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 Fe 48 7.16 5 S 168 5.16 5 C 21480 2.51 5 N 6048 2.21 5 O 9600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37344 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1415 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'MHS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Conformer: "B" Number of residues, atoms: 172, 1415 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'MHS:plan-2': 2} Unresolved non-hydrogen planarities: 2 bond proxies already assigned to first conformer: 1434 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 2} Chain breaks: 2 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "I" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "J" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "K" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "L" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "M" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "N" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "O" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "P" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "Q" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "R" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "S" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "T" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "U" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "V" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "W" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "X" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N AHIS A 60 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 60 " occ=0.50 residue: pdb=" N AHIS B 60 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 60 " occ=0.50 residue: pdb=" N AHIS C 60 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 60 " occ=0.50 residue: pdb=" N AHIS D 60 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 60 " occ=0.50 residue: pdb=" N AHIS E 60 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS E 60 " occ=0.50 residue: pdb=" N AHIS F 60 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS F 60 " occ=0.50 residue: pdb=" N AHIS G 60 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS G 60 " occ=0.50 residue: pdb=" N AHIS H 60 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS H 60 " occ=0.50 residue: pdb=" N AHIS I 60 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS I 60 " occ=0.50 residue: pdb=" N AHIS J 60 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS J 60 " occ=0.50 residue: pdb=" N AHIS K 60 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS K 60 " occ=0.50 residue: pdb=" N AHIS L 60 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS L 60 " occ=0.50 ... (remaining 12 not shown) Time building chain proxies: 4.76, per 1000 atoms: 0.13 Number of scatterers: 37344 At special positions: 0 Unit cell: (132.932, 132.932, 132.932, 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) Fe 48 26.01 S 168 16.00 O 9600 8.00 N 6048 7.00 C 21480 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: 3.64 Conformation dependent library (CDL) restraints added in 2.8 seconds 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU E 167 " --> pdb=" O SER E 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU G 167 " --> pdb=" O SER G 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 removed outlier: 3.509A pdb=" N GLU H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 removed outlier: 3.509A pdb=" N GLU I 167 " --> pdb=" O SER I 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU J 167 " --> pdb=" O SER J 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU K 167 " --> pdb=" O SER K 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU L 167 " --> pdb=" O SER L 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU M 167 " --> pdb=" O SER M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU N 167 " --> pdb=" O SER N 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU O 167 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU P 167 " --> pdb=" O SER P 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU Q 167 " --> pdb=" O SER Q 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU R 167 " --> pdb=" O SER R 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU S 167 " --> pdb=" O SER S 163 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU T 167 " --> pdb=" O SER T 163 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU U 167 " --> pdb=" O SER U 163 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU V 167 " --> pdb=" O SER V 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU W 167 " --> pdb=" O SER W 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 removed outlier: 3.508A pdb=" N GLU X 167 " --> pdb=" O SER X 163 " (cutoff:3.500A) 2712 hydrogen bonds defined for protein. 8160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.89 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6073 1.31 - 1.44: 9479 1.44 - 1.56: 19176 1.56 - 1.68: 0 1.68 - 1.81: 264 Bond restraints: 34992 Sorted by residual: bond pdb=" CG MHS M 67 " pdb=" ND1 MHS M 67 " ideal model delta sigma weight residual 1.373 1.312 0.061 2.00e-02 2.50e+03 9.19e+00 bond pdb=" CG MHS N 67 " pdb=" ND1 MHS N 67 " ideal model delta sigma weight residual 1.373 1.312 0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" CG MHS U 67 " pdb=" ND1 MHS U 67 " ideal model delta sigma weight residual 1.373 1.313 0.060 2.00e-02 2.50e+03 9.04e+00 bond pdb=" CG MHS H 67 " pdb=" ND1 MHS H 67 " ideal model delta sigma weight residual 1.373 1.313 0.060 2.00e-02 2.50e+03 9.04e+00 bond pdb=" CG MHS R 67 " pdb=" ND1 MHS R 67 " ideal model delta sigma weight residual 1.373 1.313 0.060 2.00e-02 2.50e+03 9.04e+00 ... (remaining 34987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 45417 1.18 - 2.36: 1168 2.36 - 3.54: 449 3.54 - 4.72: 102 4.72 - 5.90: 96 Bond angle restraints: 47232 Sorted by residual: angle pdb=" CA AHIS J 60 " pdb=" C AHIS J 60 " pdb=" O AHIS J 60 " ideal model delta sigma weight residual 120.82 117.81 3.01 1.05e+00 9.07e-01 8.22e+00 angle pdb=" CA AHIS X 60 " pdb=" C AHIS X 60 " pdb=" O AHIS X 60 " ideal model delta sigma weight residual 120.82 117.81 3.01 1.05e+00 9.07e-01 8.22e+00 angle pdb=" CA AHIS W 60 " pdb=" C AHIS W 60 " pdb=" O AHIS W 60 " ideal model delta sigma weight residual 120.82 117.81 3.01 1.05e+00 9.07e-01 8.20e+00 angle pdb=" CA AHIS F 60 " pdb=" C AHIS F 60 " pdb=" O AHIS F 60 " ideal model delta sigma weight residual 120.82 117.83 2.99 1.05e+00 9.07e-01 8.13e+00 angle pdb=" CA AHIS E 60 " pdb=" C AHIS E 60 " pdb=" O AHIS E 60 " ideal model delta sigma weight residual 120.82 117.85 2.97 1.05e+00 9.07e-01 8.00e+00 ... (remaining 47227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 19560 17.88 - 35.75: 984 35.75 - 53.63: 144 53.63 - 71.51: 192 71.51 - 89.38: 48 Dihedral angle restraints: 20928 sinusoidal: 8592 harmonic: 12336 Sorted by residual: dihedral pdb=" CA TRP T 93 " pdb=" C TRP T 93 " pdb=" N GLU T 94 " pdb=" CA GLU T 94 " ideal model delta harmonic sigma weight residual 180.00 160.44 19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TRP J 93 " pdb=" C TRP J 93 " pdb=" N GLU J 94 " pdb=" CA GLU J 94 " ideal model delta harmonic sigma weight residual 180.00 160.46 19.54 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TRP O 93 " pdb=" C TRP O 93 " pdb=" N GLU O 94 " pdb=" CA GLU O 94 " ideal model delta harmonic sigma weight residual 180.00 160.46 19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 20925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3468 0.026 - 0.052: 778 0.052 - 0.079: 410 0.079 - 0.105: 166 0.105 - 0.131: 98 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA TYR B 39 " pdb=" N TYR B 39 " pdb=" C TYR B 39 " pdb=" CB TYR B 39 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA TYR G 39 " pdb=" N TYR G 39 " pdb=" C TYR G 39 " pdb=" CB TYR G 39 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA TYR R 39 " pdb=" N TYR R 39 " pdb=" C TYR R 39 " pdb=" CB TYR R 39 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 4917 not shown) Planarity restraints: 6216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BHIS W 60 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C BHIS W 60 " 0.031 2.00e-02 2.50e+03 pdb=" O BHIS W 60 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU W 61 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BHIS P 60 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C BHIS P 60 " -0.031 2.00e-02 2.50e+03 pdb=" O BHIS P 60 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU P 61 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BHIS I 60 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C BHIS I 60 " -0.031 2.00e-02 2.50e+03 pdb=" O BHIS I 60 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU I 61 " 0.011 2.00e-02 2.50e+03 ... (remaining 6213 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 4008 2.73 - 3.27: 41508 3.27 - 3.82: 79446 3.82 - 4.36: 92748 4.36 - 4.90: 150225 Nonbonded interactions: 367935 Sorted by model distance: nonbonded pdb=" OE1 GLU O 27 " pdb="FE FE O 201 " model vdw 2.190 3.000 nonbonded pdb=" OE1 GLU C 27 " pdb="FE FE C 201 " model vdw 2.190 3.000 nonbonded pdb=" OE1 GLU I 27 " pdb="FE FE I 201 " model vdw 2.190 3.000 nonbonded pdb=" OE1 GLU B 27 " pdb="FE FE B 201 " model vdw 2.190 3.000 nonbonded pdb=" OE1 GLU X 27 " pdb="FE FE X 201 " model vdw 2.190 3.000 ... (remaining 367930 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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=0.50 max=1.00 mean=0.99 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: 7.110 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: 0.030 Extract box with map and model: 0.750 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 33.460 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.100 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:10.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 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 : 0.004 0.061 34992 Z= 0.248 Angle : 0.581 5.901 47232 Z= 0.319 Chirality : 0.035 0.131 4920 Planarity : 0.003 0.021 6216 Dihedral : 13.731 89.382 12960 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.98 (0.13), residues: 4008 helix: 3.90 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : 0.49 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 22 TYR 0.030 0.002 TYR O 32 PHE 0.015 0.002 PHE G 41 TRP 0.012 0.002 TRP R 93 HIS 0.004 0.001 HIS E 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.25 (34992) covalent geometry : angle 0.58130 / 0.32 (47232) hydrogen bonds : bond 0.07929 / 5.40 ( 2712) hydrogen bonds : angle 3.75004 / 2.80 ( 8160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1032 time to evaluate : 1.434 Fit side-chains REVERT: A 119 LYS cc_start: 0.8726 (tttt) cc_final: 0.8274 (mmtp) REVERT: B 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8881 (mtp) REVERT: C 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8873 (mtp) REVERT: C 119 LYS cc_start: 0.8727 (tttt) cc_final: 0.8275 (mmtp) REVERT: D 119 LYS cc_start: 0.8734 (tttt) cc_final: 0.8273 (mmtp) REVERT: E 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8873 (mtp) REVERT: F 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8875 (mtp) REVERT: F 119 LYS cc_start: 0.8742 (tttt) cc_final: 0.8281 (mmtp) REVERT: G 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8869 (mtp) REVERT: G 119 LYS cc_start: 0.8730 (tttt) cc_final: 0.8277 (mmtp) REVERT: H 70 MET cc_start: 0.9100 (mtp) cc_final: 0.8881 (mtp) REVERT: H 119 LYS cc_start: 0.8739 (tttt) cc_final: 0.8277 (mmtp) REVERT: I 70 MET cc_start: 0.9095 (mtp) cc_final: 0.8877 (mtp) REVERT: J 70 MET cc_start: 0.9096 (mtp) cc_final: 0.8881 (mtp) REVERT: L 119 LYS cc_start: 0.8731 (tttt) cc_final: 0.8265 (mmtp) REVERT: M 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8873 (mtp) REVERT: N 119 LYS cc_start: 0.8724 (tttt) cc_final: 0.8267 (mmtp) REVERT: O 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8869 (mtp) REVERT: O 119 LYS cc_start: 0.8732 (tttt) cc_final: 0.8271 (mmtp) REVERT: P 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8876 (mtp) REVERT: R 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8873 (mtp) REVERT: U 70 MET cc_start: 0.9103 (mtp) cc_final: 0.8882 (mtp) REVERT: U 119 LYS cc_start: 0.8740 (tttt) cc_final: 0.8277 (mmtp) REVERT: V 119 LYS cc_start: 0.8732 (tttt) cc_final: 0.8276 (mmtp) REVERT: W 119 LYS cc_start: 0.8726 (tttt) cc_final: 0.8263 (mmtp) REVERT: X 70 MET cc_start: 0.9096 (mtp) cc_final: 0.8873 (mtp) REVERT: X 119 LYS cc_start: 0.8734 (tttt) cc_final: 0.8268 (mmtp) outliers start: 0 outliers final: 0 residues processed: 1032 average time/residue: 0.9542 time to fit residues: 1130.0841 Evaluate side-chains 590 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 590 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A B 60 HIS A C 60 HIS A D 60 HIS A E 60 HIS A F 60 HIS A G 60 HIS A H 60 HIS A I 60 HIS A J 60 HIS A K 60 HIS A L 60 HIS A M 60 HIS A N 60 HIS A O 60 HIS A P 60 HIS A Q 60 HIS A R 60 HIS A S 60 HIS A T 60 HIS A U 60 HIS A V 60 HIS A W 60 HIS A X 60 HIS A Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.145358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.121908 restraints weight = 53300.365| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 0.80 r_work: 0.3092 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work: 0.2703 rms_B_bonded: 4.95 restraints_weight: 0.1250 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34992 Z= 0.160 Angle : 0.576 6.922 47232 Z= 0.322 Chirality : 0.037 0.147 4920 Planarity : 0.004 0.026 6216 Dihedral : 7.844 88.619 4560 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.91 (0.13), residues: 4008 helix: 3.86 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : 0.47 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 79 TYR 0.033 0.003 TYR H 32 PHE 0.017 0.003 PHE A 41 TRP 0.011 0.002 TRP R 93 HIS 0.006 0.001 HIS K 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (34992) covalent geometry : angle 0.57629 / 0.32 (47232) hydrogen bonds : bond 0.05781 / 3.90 ( 2712) hydrogen bonds : angle 3.57867 / 2.67 ( 8160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 602 time to evaluate : 1.343 Fit side-chains REVERT: A 70 MET cc_start: 0.9226 (mtp) cc_final: 0.8984 (mtp) REVERT: B 70 MET cc_start: 0.9227 (mtp) cc_final: 0.8986 (mtp) REVERT: C 70 MET cc_start: 0.9226 (mtp) cc_final: 0.8984 (mtp) REVERT: D 70 MET cc_start: 0.9227 (mtp) cc_final: 0.8987 (mtp) REVERT: E 70 MET cc_start: 0.9226 (mtp) cc_final: 0.8987 (mtp) REVERT: F 70 MET cc_start: 0.9225 (mtp) cc_final: 0.8987 (mtp) REVERT: G 70 MET cc_start: 0.9225 (mtp) cc_final: 0.8985 (mtp) REVERT: H 70 MET cc_start: 0.9224 (mtp) cc_final: 0.8982 (mtp) REVERT: I 70 MET cc_start: 0.9229 (mtp) cc_final: 0.8990 (mtp) REVERT: J 70 MET cc_start: 0.9226 (mtp) cc_final: 0.8983 (mtp) REVERT: K 70 MET cc_start: 0.9225 (mtp) cc_final: 0.8984 (mtp) REVERT: L 70 MET cc_start: 0.9225 (mtp) cc_final: 0.8985 (mtp) REVERT: M 70 MET cc_start: 0.9226 (mtp) cc_final: 0.8988 (mtp) REVERT: N 70 MET cc_start: 0.9223 (mtp) cc_final: 0.8981 (mtp) REVERT: O 70 MET cc_start: 0.9227 (mtp) cc_final: 0.8988 (mtp) REVERT: P 70 MET cc_start: 0.9224 (mtp) cc_final: 0.8982 (mtp) REVERT: Q 70 MET cc_start: 0.9227 (mtp) cc_final: 0.8985 (mtp) REVERT: R 70 MET cc_start: 0.9227 (mtp) cc_final: 0.8987 (mtp) REVERT: S 70 MET cc_start: 0.9223 (mtp) cc_final: 0.8982 (mtp) REVERT: T 70 MET cc_start: 0.9225 (mtp) cc_final: 0.8983 (mtp) REVERT: U 70 MET cc_start: 0.9226 (mtp) cc_final: 0.8987 (mtp) REVERT: V 70 MET cc_start: 0.9225 (mtp) cc_final: 0.8984 (mtp) REVERT: W 70 MET cc_start: 0.9225 (mtp) cc_final: 0.8982 (mtp) REVERT: X 70 MET cc_start: 0.9227 (mtp) cc_final: 0.8989 (mtp) outliers start: 0 outliers final: 0 residues processed: 602 average time/residue: 0.9658 time to fit residues: 664.2697 Evaluate side-chains 588 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 588 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 36 optimal weight: 6.9990 chunk 389 optimal weight: 1.9990 chunk 398 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 170 optimal weight: 7.9990 chunk 290 optimal weight: 2.9990 chunk 347 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 332 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 58 GLN T 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.147183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.121832 restraints weight = 57103.594| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 0.92 r_work: 0.3090 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work: 0.2727 rms_B_bonded: 4.79 restraints_weight: 0.1250 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 34992 Z= 0.133 Angle : 0.530 6.318 47232 Z= 0.294 Chirality : 0.036 0.143 4920 Planarity : 0.003 0.022 6216 Dihedral : 7.845 88.997 4560 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.09 (0.13), residues: 4008 helix: 4.01 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : 0.42 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG M 79 TYR 0.021 0.002 TYR R 32 PHE 0.016 0.002 PHE K 41 TRP 0.011 0.002 TRP R 93 HIS 0.005 0.001 HIS K 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (34992) covalent geometry : angle 0.52956 / 0.29 (47232) hydrogen bonds : bond 0.05243 / 3.54 ( 2712) hydrogen bonds : angle 3.41429 / 2.55 ( 8160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 588 time to evaluate : 1.500 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 588 average time/residue: 0.9849 time to fit residues: 660.9219 Evaluate side-chains 544 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 9.9990 chunk 342 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 282 optimal weight: 0.5980 chunk 194 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 307 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 299 optimal weight: 0.5980 chunk 195 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.149607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.124983 restraints weight = 47817.318| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 0.78 r_work: 0.3151 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 34992 Z= 0.120 Angle : 0.509 6.709 47232 Z= 0.281 Chirality : 0.036 0.143 4920 Planarity : 0.003 0.023 6216 Dihedral : 7.801 88.894 4560 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.28 (0.13), residues: 4008 helix: 4.15 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : 0.44 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG T 79 TYR 0.018 0.002 TYR E 39 PHE 0.014 0.002 PHE B 41 TRP 0.010 0.002 TRP O 93 HIS 0.004 0.001 HIS K 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 (34992) covalent geometry : angle 0.50948 / 0.28 (47232) hydrogen bonds : bond 0.04841 / 3.27 ( 2712) hydrogen bonds : angle 3.31034 / 2.47 ( 8160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 1.394 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 1.0230 time to fit residues: 643.2575 Evaluate side-chains 544 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 342 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 337 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 265 optimal weight: 0.5980 chunk 383 optimal weight: 9.9990 chunk 379 optimal weight: 0.6980 chunk 184 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN E 58 GLN J 58 GLN K 58 GLN M 58 GLN N 58 GLN O 58 GLN T 58 GLN U 58 GLN V 58 GLN X 58 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.147188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.123652 restraints weight = 53001.294| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 0.78 r_work: 0.3120 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work: 0.2753 rms_B_bonded: 4.41 restraints_weight: 0.1250 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34992 Z= 0.141 Angle : 0.556 7.511 47232 Z= 0.308 Chirality : 0.037 0.161 4920 Planarity : 0.003 0.023 6216 Dihedral : 7.793 88.302 4560 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.16 (0.13), residues: 4008 helix: 4.05 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : 0.47 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 79 TYR 0.019 0.002 TYR K 39 PHE 0.016 0.002 PHE E 41 TRP 0.009 0.002 TRP K 93 HIS 0.005 0.001 HIS O 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (34992) covalent geometry : angle 0.55576 / 0.31 (47232) hydrogen bonds : bond 0.05365 / 3.62 ( 2712) hydrogen bonds : angle 3.44231 / 2.57 ( 8160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 1.520 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 1.0093 time to fit residues: 630.4480 Evaluate side-chains 544 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 307 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 356 optimal weight: 3.9990 chunk 397 optimal weight: 4.9990 chunk 282 optimal weight: 0.6980 chunk 218 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 290 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN B 58 GLN D 58 GLN E 58 GLN I 58 GLN J 58 GLN K 58 GLN M 58 GLN N 58 GLN O 58 GLN T 58 GLN U 58 GLN V 58 GLN X 58 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.145978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.123380 restraints weight = 60280.701| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 0.84 r_work: 0.3109 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work: 0.2745 rms_B_bonded: 4.26 restraints_weight: 0.1250 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 34992 Z= 0.161 Angle : 0.588 7.826 47232 Z= 0.327 Chirality : 0.038 0.162 4920 Planarity : 0.004 0.023 6216 Dihedral : 7.792 87.856 4560 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.03 (0.13), residues: 4008 helix: 3.95 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : 0.48 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 79 TYR 0.021 0.003 TYR K 39 PHE 0.018 0.003 PHE H 41 TRP 0.009 0.002 TRP N 93 HIS 0.006 0.001 HIS P 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (34992) covalent geometry : angle 0.58797 / 0.33 (47232) hydrogen bonds : bond 0.05699 / 3.84 ( 2712) hydrogen bonds : angle 3.54930 / 2.64 ( 8160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 1.441 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 540 average time/residue: 0.9521 time to fit residues: 589.9949 Evaluate side-chains 528 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 120 optimal weight: 4.9990 chunk 351 optimal weight: 6.9990 chunk 320 optimal weight: 6.9990 chunk 329 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 349 optimal weight: 9.9990 chunk 323 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 367 optimal weight: 0.9980 chunk 309 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN C 58 GLN E 58 GLN F 58 GLN G 58 GLN H 58 GLN J 58 GLN K 58 GLN L 58 GLN M 58 GLN N 58 GLN O 58 GLN P 58 GLN Q 58 GLN R 58 GLN S 58 GLN T 58 GLN U 58 GLN V 58 GLN W 58 GLN X 58 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.144981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.121874 restraints weight = 58068.525| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 0.82 r_work: 0.3093 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work: 0.2706 rms_B_bonded: 4.68 restraints_weight: 0.1250 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 34992 Z= 0.189 Angle : 0.626 8.112 47232 Z= 0.349 Chirality : 0.039 0.173 4920 Planarity : 0.004 0.027 6216 Dihedral : 7.787 87.395 4560 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.84 (0.13), residues: 4008 helix: 3.80 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.51 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 79 TYR 0.022 0.003 TYR V 39 PHE 0.020 0.003 PHE J 41 TRP 0.010 0.002 TRP G 93 HIS 0.007 0.002 HIS K 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (34992) covalent geometry : angle 0.62612 / 0.35 (47232) hydrogen bonds : bond 0.06003 / 4.05 ( 2712) hydrogen bonds : angle 3.65516 / 2.72 ( 8160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.590 Fit side-chains REVERT: A 70 MET cc_start: 0.9226 (mtp) cc_final: 0.8971 (mtp) REVERT: B 70 MET cc_start: 0.9226 (mtp) cc_final: 0.8973 (mtp) REVERT: C 70 MET cc_start: 0.9224 (mtp) cc_final: 0.8969 (mtp) REVERT: D 70 MET cc_start: 0.9225 (mtp) cc_final: 0.8972 (mtp) REVERT: E 70 MET cc_start: 0.9224 (mtp) cc_final: 0.8969 (mtp) REVERT: G 70 MET cc_start: 0.9222 (mtp) cc_final: 0.8966 (mtp) REVERT: H 70 MET cc_start: 0.9222 (mtp) cc_final: 0.8967 (mtp) REVERT: I 70 MET cc_start: 0.9228 (mtp) cc_final: 0.8976 (mtp) REVERT: J 70 MET cc_start: 0.9224 (mtp) cc_final: 0.8970 (mtp) REVERT: K 70 MET cc_start: 0.9223 (mtp) cc_final: 0.8968 (mtp) REVERT: L 70 MET cc_start: 0.9229 (mtp) cc_final: 0.8978 (mtp) REVERT: M 70 MET cc_start: 0.9228 (mtp) cc_final: 0.8976 (mtp) REVERT: N 70 MET cc_start: 0.9222 (mtp) cc_final: 0.8966 (mtp) REVERT: O 70 MET cc_start: 0.9225 (mtp) cc_final: 0.8969 (mtp) REVERT: P 70 MET cc_start: 0.9224 (mtp) cc_final: 0.8970 (mtp) REVERT: Q 70 MET cc_start: 0.9228 (mtp) cc_final: 0.8974 (mtp) REVERT: R 70 MET cc_start: 0.9223 (mtp) cc_final: 0.8967 (mtp) REVERT: S 70 MET cc_start: 0.9225 (mtp) cc_final: 0.8973 (mtp) REVERT: T 70 MET cc_start: 0.9225 (mtp) cc_final: 0.8969 (mtp) REVERT: U 70 MET cc_start: 0.9226 (mtp) cc_final: 0.8972 (mtp) REVERT: V 70 MET cc_start: 0.9222 (mtp) cc_final: 0.8965 (mtp) REVERT: W 70 MET cc_start: 0.9223 (mtp) cc_final: 0.8967 (mtp) REVERT: X 70 MET cc_start: 0.9223 (mtp) cc_final: 0.8969 (mtp) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 1.0240 time to fit residues: 619.9176 Evaluate side-chains 540 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 34 optimal weight: 20.0000 chunk 251 optimal weight: 2.9990 chunk 404 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 371 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 368 optimal weight: 6.9990 chunk 277 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.146996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.124294 restraints weight = 55627.430| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 0.77 r_work: 0.3115 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work: 0.2748 rms_B_bonded: 4.40 restraints_weight: 0.1250 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 34992 Z= 0.144 Angle : 0.564 7.668 47232 Z= 0.313 Chirality : 0.037 0.161 4920 Planarity : 0.003 0.023 6216 Dihedral : 7.817 88.319 4560 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.08 (0.13), residues: 4008 helix: 4.00 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.42 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 79 TYR 0.021 0.002 TYR E 39 PHE 0.018 0.002 PHE H 41 TRP 0.011 0.002 TRP N 93 HIS 0.005 0.001 HIS D 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (34992) covalent geometry : angle 0.56412 / 0.31 (47232) hydrogen bonds : bond 0.05404 / 3.64 ( 2712) hydrogen bonds : angle 3.47920 / 2.59 ( 8160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 1.580 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 542 average time/residue: 1.0531 time to fit residues: 653.2660 Evaluate side-chains 528 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 241 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 372 optimal weight: 9.9990 chunk 325 optimal weight: 10.0000 chunk 376 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 chunk 264 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.145927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.121808 restraints weight = 55495.895| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 0.84 r_work: 0.3082 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work: 0.2725 rms_B_bonded: 4.46 restraints_weight: 0.1250 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 34992 Z= 0.163 Angle : 0.593 7.940 47232 Z= 0.330 Chirality : 0.038 0.167 4920 Planarity : 0.004 0.023 6216 Dihedral : 7.799 87.766 4560 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.95 (0.13), residues: 4008 helix: 3.89 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.47 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 79 TYR 0.021 0.002 TYR G 39 PHE 0.019 0.003 PHE G 41 TRP 0.010 0.002 TRP N 93 HIS 0.006 0.001 HIS U 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (34992) covalent geometry : angle 0.59291 / 0.33 (47232) hydrogen bonds : bond 0.05712 / 3.85 ( 2712) hydrogen bonds : angle 3.56763 / 2.66 ( 8160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.499 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 1.0053 time to fit residues: 606.6605 Evaluate side-chains 528 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 72 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 332 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 263 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 335 optimal weight: 2.9990 chunk 367 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.151542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.125276 restraints weight = 54017.971| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 0.82 r_work: 0.3140 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 34992 Z= 0.113 Angle : 0.505 7.407 47232 Z= 0.276 Chirality : 0.036 0.151 4920 Planarity : 0.003 0.024 6216 Dihedral : 7.783 89.071 4560 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.46 (0.13), residues: 4008 helix: 4.29 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.46 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 22 TYR 0.019 0.002 TYR S 39 PHE 0.014 0.002 PHE U 41 TRP 0.011 0.002 TRP P 93 HIS 0.003 0.001 HIS F 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 (34992) covalent geometry : angle 0.50545 / 0.28 (47232) hydrogen bonds : bond 0.04504 / 3.04 ( 2712) hydrogen bonds : angle 3.24164 / 2.42 ( 8160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.457 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.9825 time to fit residues: 594.9251 Evaluate side-chains 544 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 359 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 327 optimal weight: 0.0770 chunk 294 optimal weight: 0.3980 chunk 247 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 overall best weight: 2.0942 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.146656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.123777 restraints weight = 48295.780| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 0.74 r_work: 0.3117 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34992 Z= 0.148 Angle : 0.575 7.964 47232 Z= 0.318 Chirality : 0.037 0.171 4920 Planarity : 0.003 0.023 6216 Dihedral : 7.774 88.026 4560 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.24 (0.13), residues: 4008 helix: 4.10 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : 0.50 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 79 TYR 0.020 0.002 TYR B 39 PHE 0.017 0.002 PHE I 41 TRP 0.010 0.002 TRP P 93 HIS 0.005 0.001 HIS G 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (34992) covalent geometry : angle 0.57492 / 0.32 (47232) hydrogen bonds : bond 0.05466 / 3.69 ( 2712) hydrogen bonds : angle 3.48142 / 2.59 ( 8160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22367.14 seconds wall clock time: 380 minutes 16.77 seconds (22816.77 seconds total)