Starting phenix.real_space_refine on Tue Aug 26 11:29:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqd_61728/08_2025/9jqd_61728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqd_61728/08_2025/9jqd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jqd_61728/08_2025/9jqd_61728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqd_61728/08_2025/9jqd_61728.map" model { file = "/net/cci-nas-00/data/ceres_data/9jqd_61728/08_2025/9jqd_61728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqd_61728/08_2025/9jqd_61728.cif" } 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-2.0-5787/lib/python3.9/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, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 3.45, per 1000 atoms: 0.09 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: 2.66 Conformation dependent library (CDL) restraints added in 2.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.65 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: 5.92 Time building geometry restraints manager: 3.48 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 2.260 nonbonded pdb=" OE1 GLU C 27 " pdb="FE FE C 201 " model vdw 2.190 2.260 nonbonded pdb=" OE1 GLU I 27 " pdb="FE FE I 201 " model vdw 2.190 2.260 nonbonded pdb=" OE1 GLU B 27 " pdb="FE FE B 201 " model vdw 2.190 2.260 nonbonded pdb=" OE1 GLU X 27 " pdb="FE FE X 201 " model vdw 2.190 2.260 ... (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: 0.07 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: 6.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.880 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 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 aren 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 covalent geometry : bond 0.00449 (34992) covalent geometry : angle 0.58130 (47232) hydrogen bonds : bond 0.07929 ( 2712) hydrogen bonds : angle 3.75004 ( 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 : 1.512 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: 0.8880 (mtp) REVERT: C 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8872 (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: 0.8741 (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: 0.8880 (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: 0.8272 (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: 0.8872 (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: 0.8264 (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: 0.9278 time to fit residues: 1096.2809 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 : 1.283 ------------------------------------------------------------------------------- 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: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3539 r_free = 0.3539 target = 0.144556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.121755 restraints weight = 51845.136| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 0.76 r_work: 0.3093 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work: 0.2718 rms_B_bonded: 4.46 restraints_weight: 0.1250 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1505 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= 0.166 Angle : 0.586 6.973 47232 Z= 0.327 Chirality : 0.037 0.148 4920 Planarity : 0.004 0.027 6216 Dihedral : 7.858 88.653 4560 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.64 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 aren not related in a simple way. whole: 4.87 (0.13), residues: 4008 helix: 3.82 (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 L 79 TYR 0.034 0.003 TYR O 32 PHE 0.018 0.003 PHE K 41 TRP 0.011 0.002 TRP R 93 HIS 0.006 0.001 HIS S 128 Details of bonding type rmsd covalent geometry : bond 0.00320 (34992) covalent geometry : angle 0.58611 (47232) hydrogen bonds : bond 0.05866 ( 2712) hydrogen bonds : angle 3.61095 ( 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 : 1.319 Fit side-chains REVERT: A 70 MET cc_start: 0.9219 (mtp) cc_final: 0.8974 (mtp) REVERT: B 70 MET cc_start: 0.9220 (mtp) cc_final: 0.8977 (mtp) REVERT: C 70 MET cc_start: 0.9218 (mtp) cc_final: 0.8973 (mtp) REVERT: D 70 MET cc_start: 0.9220 (mtp) cc_final: 0.8975 (mtp) REVERT: E 70 MET cc_start: 0.9217 (mtp) cc_final: 0.8973 (mtp) REVERT: G 70 MET cc_start: 0.9218 (mtp) cc_final: 0.8974 (mtp) REVERT: H 70 MET cc_start: 0.9216 (mtp) cc_final: 0.8970 (mtp) REVERT: I 70 MET cc_start: 0.9220 (mtp) cc_final: 0.8976 (mtp) REVERT: J 70 MET cc_start: 0.9216 (mtp) cc_final: 0.8969 (mtp) REVERT: K 70 MET cc_start: 0.9215 (mtp) cc_final: 0.8970 (mtp) REVERT: L 70 MET cc_start: 0.9221 (mtp) cc_final: 0.8976 (mtp) REVERT: M 70 MET cc_start: 0.9218 (mtp) cc_final: 0.8973 (mtp) REVERT: N 70 MET cc_start: 0.9215 (mtp) cc_final: 0.8969 (mtp) REVERT: O 70 MET cc_start: 0.9217 (mtp) cc_final: 0.8971 (mtp) REVERT: P 70 MET cc_start: 0.9215 (mtp) cc_final: 0.8969 (mtp) REVERT: Q 70 MET cc_start: 0.9220 (mtp) cc_final: 0.8974 (mtp) REVERT: R 70 MET cc_start: 0.9220 (mtp) cc_final: 0.8975 (mtp) REVERT: S 70 MET cc_start: 0.9216 (mtp) cc_final: 0.8970 (mtp) REVERT: T 70 MET cc_start: 0.9220 (mtp) cc_final: 0.8974 (mtp) REVERT: U 70 MET cc_start: 0.9218 (mtp) cc_final: 0.8974 (mtp) REVERT: V 70 MET cc_start: 0.9215 (mtp) cc_final: 0.8970 (mtp) REVERT: W 70 MET cc_start: 0.9216 (mtp) cc_final: 0.8968 (mtp) REVERT: X 70 MET cc_start: 0.9218 (mtp) cc_final: 0.8974 (mtp) outliers start: 0 outliers final: 0 residues processed: 602 average time/residue: 0.9536 time to fit residues: 654.9201 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 : 1.185 ------------------------------------------------------------------------------- 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: 5.9990 chunk 398 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 290 optimal weight: 2.9990 chunk 347 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 332 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3563 r_free = 0.3563 target = 0.146936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.122650 restraints weight = 55882.230| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 0.88 r_work: 0.3103 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work: 0.2741 rms_B_bonded: 4.54 restraints_weight: 0.1250 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 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 = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1530 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= 0.132 Angle : 0.529 6.325 47232 Z= 0.294 Chirality : 0.036 0.144 4920 Planarity : 0.003 0.023 6216 Dihedral : 7.864 89.221 4560 Min Nonbonded Distance : 2.222 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 aren 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 J 79 TYR 0.020 0.002 TYR H 32 PHE 0.016 0.002 PHE F 41 TRP 0.011 0.002 TRP R 93 HIS 0.004 0.001 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00246 (34992) covalent geometry : angle 0.52934 (47232) hydrogen bonds : bond 0.05237 ( 2712) hydrogen bonds : angle 3.42012 ( 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 : 1.193 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 588 average time/residue: 0.9843 time to fit residues: 659.3385 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 : 1.007 ------------------------------------------------------------------------------- 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: 3.9990 chunk 68 optimal weight: 20.0000 chunk 282 optimal weight: 0.5980 chunk 194 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 307 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 299 optimal weight: 0.5980 chunk 195 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.150996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.127099 restraints weight = 48166.743| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 0.78 r_work: 0.3175 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1591 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= 0.111 Angle : 0.488 6.650 47232 Z= 0.269 Chirality : 0.035 0.140 4920 Planarity : 0.003 0.023 6216 Dihedral : 7.816 89.630 4560 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.18 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 aren not related in a simple way. whole: 5.42 (0.13), residues: 4008 helix: 4.25 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.47 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 79 TYR 0.017 0.002 TYR U 39 PHE 0.013 0.002 PHE X 41 TRP 0.010 0.002 TRP W 93 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00202 (34992) covalent geometry : angle 0.48813 (47232) hydrogen bonds : bond 0.04453 ( 2712) hydrogen bonds : angle 3.21487 ( 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 540 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 1.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 540 average time/residue: 0.9812 time to fit residues: 603.5935 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 : 1.029 ------------------------------------------------------------------------------- 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: 10.0000 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: 0.7980 chunk 383 optimal weight: 10.0000 chunk 379 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN B 58 GLN C 58 GLN D 58 GLN E 58 GLN F 58 GLN G 58 GLN H 58 GLN I 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.145136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.121849 restraints weight = 51291.521| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 0.78 r_work: 0.3081 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work: 0.2709 rms_B_bonded: 4.64 restraints_weight: 0.1250 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1632 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= 0.172 Angle : 0.604 7.831 47232 Z= 0.336 Chirality : 0.038 0.172 4920 Planarity : 0.004 0.024 6216 Dihedral : 7.782 87.823 4560 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % 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 aren 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 : 0.47 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 79 TYR 0.021 0.003 TYR E 39 PHE 0.018 0.003 PHE F 41 TRP 0.009 0.002 TRP G 93 HIS 0.007 0.002 HIS T 128 Details of bonding type rmsd covalent geometry : bond 0.00339 (34992) covalent geometry : angle 0.60431 (47232) hydrogen bonds : bond 0.05813 ( 2712) hydrogen bonds : angle 3.58480 ( 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 540 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 1.454 Fit side-chains REVERT: C 70 MET cc_start: 0.9219 (mtp) cc_final: 0.8972 (mtp) REVERT: H 70 MET cc_start: 0.9217 (mtp) cc_final: 0.8970 (mtp) REVERT: O 70 MET cc_start: 0.9219 (mtp) cc_final: 0.8972 (mtp) REVERT: V 70 MET cc_start: 0.9218 (mtp) cc_final: 0.8971 (mtp) outliers start: 0 outliers final: 0 residues processed: 540 average time/residue: 0.9597 time to fit residues: 591.2487 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 : 1.316 ------------------------------------------------------------------------------- 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: 0.7980 chunk 66 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 307 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 356 optimal weight: 5.9990 chunk 397 optimal weight: 4.9990 chunk 282 optimal weight: 0.6980 chunk 218 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 290 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN B 58 GLN D 58 GLN E 58 GLN G 58 GLN I 58 GLN J 58 GLN K 58 GLN L 58 GLN M 58 GLN N 58 GLN O 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.145437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.121209 restraints weight = 58151.206| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 0.87 r_work: 0.3073 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work: 0.2721 rms_B_bonded: 4.45 restraints_weight: 0.1250 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1610 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= 0.164 Angle : 0.591 7.740 47232 Z= 0.329 Chirality : 0.038 0.158 4920 Planarity : 0.004 0.023 6216 Dihedral : 7.816 87.931 4560 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % 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 aren not related in a simple way. whole: 4.94 (0.13), residues: 4008 helix: 3.89 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.43 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 79 TYR 0.021 0.003 TYR V 39 PHE 0.018 0.003 PHE M 41 TRP 0.010 0.002 TRP G 93 HIS 0.007 0.001 HIS J 128 Details of bonding type rmsd covalent geometry : bond 0.00320 (34992) covalent geometry : angle 0.59109 (47232) hydrogen bonds : bond 0.05736 ( 2712) hydrogen bonds : angle 3.57662 ( 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 528 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.464 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.9607 time to fit residues: 580.6624 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 : 1.252 ------------------------------------------------------------------------------- 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: 4.9990 chunk 78 optimal weight: 3.9990 chunk 349 optimal weight: 10.0000 chunk 323 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 367 optimal weight: 0.6980 chunk 309 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN N 58 GLN O 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.145296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.120726 restraints weight = 56377.395| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 0.87 r_work: 0.3072 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work: 0.2715 rms_B_bonded: 4.50 restraints_weight: 0.1250 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 34992 Z= 0.165 Angle : 0.596 8.009 47232 Z= 0.332 Chirality : 0.038 0.164 4920 Planarity : 0.004 0.023 6216 Dihedral : 7.817 87.899 4560 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.55 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 aren 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 : 0.46 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 79 TYR 0.022 0.003 TYR V 39 PHE 0.019 0.003 PHE J 41 TRP 0.010 0.002 TRP P 93 HIS 0.007 0.001 HIS W 128 Details of bonding type rmsd covalent geometry : bond 0.00322 (34992) covalent geometry : angle 0.59605 (47232) hydrogen bonds : bond 0.05753 ( 2712) hydrogen bonds : angle 3.58101 ( 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 : 1.381 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.9410 time to fit residues: 568.4518 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 : 1.055 ------------------------------------------------------------------------------- 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: 3.9990 chunk 404 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 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: 0.8980 chunk 79 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.146530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.122441 restraints weight = 53817.797| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 0.85 r_work: 0.3099 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work: 0.2731 rms_B_bonded: 4.56 restraints_weight: 0.1250 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 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 = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1563 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= 0.142 Angle : 0.561 7.754 47232 Z= 0.311 Chirality : 0.037 0.158 4920 Planarity : 0.003 0.023 6216 Dihedral : 7.826 88.388 4560 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.06 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 aren not related in a simple way. whole: 5.10 (0.13), residues: 4008 helix: 4.02 (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 M 79 TYR 0.020 0.002 TYR V 39 PHE 0.017 0.002 PHE I 41 TRP 0.010 0.002 TRP N 93 HIS 0.005 0.001 HIS K 128 Details of bonding type rmsd covalent geometry : bond 0.00270 (34992) covalent geometry : angle 0.56149 (47232) hydrogen bonds : bond 0.05384 ( 2712) hydrogen bonds : angle 3.48056 ( 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 528 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.197 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.9791 time to fit residues: 590.3456 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 : 1.034 ------------------------------------------------------------------------------- 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: 9.9990 chunk 376 optimal weight: 10.0000 chunk 165 optimal weight: 0.6980 chunk 264 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 chunk 270 optimal weight: 0.0670 chunk 74 optimal weight: 9.9990 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.146133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.122269 restraints weight = 53699.234| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 0.84 r_work: 0.3100 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work: 0.2732 rms_B_bonded: 4.49 restraints_weight: 0.1250 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 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 = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1599 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= 0.144 Angle : 0.568 7.758 47232 Z= 0.315 Chirality : 0.037 0.162 4920 Planarity : 0.003 0.023 6216 Dihedral : 7.831 88.400 4560 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.03 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 aren 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 E 79 TYR 0.020 0.002 TYR J 39 PHE 0.017 0.002 PHE G 41 TRP 0.010 0.002 TRP R 93 HIS 0.005 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00276 (34992) covalent geometry : angle 0.56828 (47232) hydrogen bonds : bond 0.05436 ( 2712) hydrogen bonds : angle 3.48283 ( 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 : 1.478 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.9927 time to fit residues: 598.4515 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 : 1.204 ------------------------------------------------------------------------------- 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: 0.8980 chunk 203 optimal weight: 10.0000 chunk 332 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 335 optimal weight: 2.9990 chunk 367 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.150612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.126284 restraints weight = 54538.226| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 0.86 r_work: 0.3153 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work: 0.2802 rms_B_bonded: 4.48 restraints_weight: 0.1250 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 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 0.025 34992 Z= 0.113 Angle : 0.504 7.398 47232 Z= 0.276 Chirality : 0.036 0.152 4920 Planarity : 0.003 0.024 6216 Dihedral : 7.818 89.479 4560 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % 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 aren not related in a simple way. whole: 5.45 (0.13), residues: 4008 helix: 4.28 (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 E 22 TYR 0.018 0.002 TYR V 39 PHE 0.014 0.002 PHE G 41 TRP 0.010 0.002 TRP J 93 HIS 0.003 0.001 HIS Q 128 Details of bonding type rmsd covalent geometry : bond 0.00207 (34992) covalent geometry : angle 0.50448 (47232) hydrogen bonds : bond 0.04516 ( 2712) hydrogen bonds : angle 3.24544 ( 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 : 1.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.9562 time to fit residues: 577.6544 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 : 1.393 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 9.9990 chunk 359 optimal weight: 7.9990 chunk 258 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 327 optimal weight: 0.9990 chunk 294 optimal weight: 0.9980 chunk 247 optimal weight: 10.0000 chunk 136 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.145958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.122961 restraints weight = 46566.031| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 0.66 r_work: 0.3108 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work: 0.2706 rms_B_bonded: 4.81 restraints_weight: 0.1250 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1622 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= 0.157 Angle : 0.589 8.025 47232 Z= 0.326 Chirality : 0.038 0.173 4920 Planarity : 0.004 0.023 6216 Dihedral : 7.782 87.980 4560 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % 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 aren not related in a simple way. whole: 5.17 (0.13), residues: 4008 helix: 4.06 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : 0.46 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 79 TYR 0.020 0.002 TYR E 39 PHE 0.018 0.002 PHE G 41 TRP 0.010 0.002 TRP J 93 HIS 0.006 0.001 HIS R 128 Details of bonding type rmsd covalent geometry : bond 0.00305 (34992) covalent geometry : angle 0.58861 (47232) hydrogen bonds : bond 0.05606 ( 2712) hydrogen bonds : angle 3.52436 ( 8160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21602.03 seconds wall clock time: 366 minutes 28.18 seconds (21988.18 seconds total)