Starting phenix.real_space_refine (version: 1.19rc7) on Tue Jan 5 11:27:55 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/01_2021/6wx6_21951.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/01_2021/6wx6_21951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/01_2021/6wx6_21951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/01_2021/6wx6_21951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/01_2021/6wx6_21951.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/01_2021/6wx6_21951.pdb" } resolution = 2.0 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 ------------------------------------------------------------------------------- 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= -0.005 sd= 0.431 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 68332 Number of models: 1 Model: "" Number of chains: 56 Chain: "A" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "B" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "C" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "D" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "E" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "F" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "G" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "H" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "I" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "J" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "K" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "L" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "M" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "N" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "O" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "P" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "Q" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "R" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "S" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "T" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "U" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "V" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "W" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "X" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "C" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "E" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "F" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "G" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "H" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "I" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "J" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "K" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "L" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "N" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "O" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "P" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "Q" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "R" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "S" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "T" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "U" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "V" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "W" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "X" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Time building chain proxies: 23.10, per 1000 atoms: 0.34 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 176) selection = (chain 'B' and resid 5 through 176) selection = (chain 'C' and resid 5 through 176) selection = (chain 'D' and resid 5 through 176) 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' and resid 5 through 176) selection = (chain 'N' and resid 5 through 176) selection = (chain 'O' and resid 5 through 176) selection = (chain 'P' and resid 5 through 176) selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Number of scatterers: 68332 At special positions: 0 Unit cell: (139.536, 139.536, 139.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 120 16.00 O 8732 8.00 N 5808 7.00 C 21000 6.00 H 32664 1.00 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 - 3.50 Amimo acid : False - 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: 49.24 Conformation dependent library (CDL) restraints added in 5.0 seconds 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 13 through 41 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 158 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'B' and resid 13 through 41 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 158 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'C' and resid 13 through 41 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 158 Processing helix chain 'C' and resid 162 through 174 Processing helix chain 'D' and resid 13 through 41 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 158 Processing helix chain 'D' and resid 162 through 174 Processing helix chain 'E' and resid 13 through 41 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 158 Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'F' and resid 13 through 41 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 158 Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'G' and resid 13 through 41 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 158 Processing helix chain 'G' and resid 162 through 174 Processing helix chain 'H' and resid 13 through 41 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 158 Processing helix chain 'H' and resid 162 through 174 Processing helix chain 'I' and resid 13 through 41 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 158 Processing helix chain 'I' and resid 162 through 174 Processing helix chain 'J' and resid 13 through 41 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 158 Processing helix chain 'J' and resid 162 through 174 Processing helix chain 'K' and resid 13 through 41 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 158 Processing helix chain 'K' and resid 162 through 174 Processing helix chain 'L' and resid 13 through 41 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 158 Processing helix chain 'L' and resid 162 through 174 Processing helix chain 'M' and resid 13 through 41 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 158 Processing helix chain 'M' and resid 162 through 174 Processing helix chain 'N' and resid 13 through 41 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 158 Processing helix chain 'N' and resid 162 through 174 Processing helix chain 'O' and resid 13 through 41 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 158 Processing helix chain 'O' and resid 162 through 174 Processing helix chain 'P' and resid 13 through 41 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 158 Processing helix chain 'P' and resid 162 through 174 Processing helix chain 'Q' and resid 13 through 41 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 158 Processing helix chain 'Q' and resid 162 through 174 Processing helix chain 'R' and resid 13 through 41 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 158 Processing helix chain 'R' and resid 162 through 174 Processing helix chain 'S' and resid 13 through 41 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 158 Processing helix chain 'S' and resid 162 through 174 Processing helix chain 'T' and resid 13 through 41 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 158 Processing helix chain 'T' and resid 162 through 174 Processing helix chain 'U' and resid 13 through 41 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 158 Processing helix chain 'U' and resid 162 through 174 Processing helix chain 'V' and resid 13 through 41 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 158 Processing helix chain 'V' and resid 162 through 174 Processing helix chain 'W' and resid 13 through 41 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 158 Processing helix chain 'W' and resid 162 through 174 Processing helix chain 'X' and resid 13 through 41 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 158 Processing helix chain 'X' and resid 162 through 174 2664 hydrogen bonds defined for protein. 7992 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: 24.66 Time building geometry restraints manager: 51.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.77 - 0.98: 32608 0.98 - 1.19: 32 1.19 - 1.39: 14222 1.39 - 1.60: 19450 1.60 - 1.80: 216 Bond restraints: 66528 Sorted by residual: bond pdb=" CB SER F 5 " pdb=" HB2 SER F 5 " ideal model delta sigma weight residual 0.970 1.036 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" OG SER F 5 " pdb=" HG SER F 5 " ideal model delta sigma weight residual 0.840 0.774 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CB SER B 5 " pdb=" HB2 SER B 5 " ideal model delta sigma weight residual 0.970 1.035 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" OG SER B 5 " pdb=" HG SER B 5 " ideal model delta sigma weight residual 0.840 0.775 0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" CB SER F 5 " pdb=" HB3 SER F 5 " ideal model delta sigma weight residual 0.970 1.022 -0.052 2.00e-02 2.50e+03 6.64e+00 ... (remaining 66523 not shown) Histogram of bond angle deviations from ideal: 79.52 - 90.43: 4 90.43 - 101.33: 99 101.33 - 112.23: 75143 112.23 - 123.13: 38473 123.13 - 134.03: 6257 Bond angle restraints: 119976 Sorted by residual: angle pdb=" OG SER B 5 " pdb=" CB SER B 5 " pdb=" HB3 SER B 5 " ideal model delta sigma weight residual 109.00 79.52 29.48 3.00e+00 1.11e-01 9.65e+01 angle pdb=" OG SER F 5 " pdb=" CB SER F 5 " pdb=" HB3 SER F 5 " ideal model delta sigma weight residual 109.00 79.62 29.38 3.00e+00 1.11e-01 9.59e+01 angle pdb=" HB2 SER F 5 " pdb=" CB SER F 5 " pdb=" HB3 SER F 5 " ideal model delta sigma weight residual 110.00 89.28 20.72 3.00e+00 1.11e-01 4.77e+01 angle pdb=" HB2 SER B 5 " pdb=" CB SER B 5 " pdb=" HB3 SER B 5 " ideal model delta sigma weight residual 110.00 89.30 20.70 3.00e+00 1.11e-01 4.76e+01 angle pdb=" OG SER B 5 " pdb=" CB SER B 5 " pdb=" HB2 SER B 5 " ideal model delta sigma weight residual 109.00 126.01 -17.01 3.00e+00 1.11e-01 3.22e+01 ... (remaining 119971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 24508 17.48 - 34.97: 1653 34.97 - 52.45: 312 52.45 - 69.93: 95 69.93 - 87.41: 96 Dihedral angle restraints: 26664 sinusoidal: 12504 harmonic: 14160 Sorted by residual: dihedral pdb=" CA VAL J 46 " pdb=" C VAL J 46 " pdb=" N ALA J 47 " pdb=" CA ALA J 47 " ideal model delta harmonic sigma weight residual 180.00 163.85 16.15 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA VAL Q 46 " pdb=" C VAL Q 46 " pdb=" N ALA Q 47 " pdb=" CA ALA Q 47 " ideal model delta harmonic sigma weight residual 180.00 163.87 16.13 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA VAL U 46 " pdb=" C VAL U 46 " pdb=" N ALA U 47 " pdb=" CA ALA U 47 " ideal model delta harmonic sigma weight residual 180.00 163.87 16.13 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 26661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2974 0.028 - 0.057: 1221 0.057 - 0.085: 509 0.085 - 0.114: 98 0.114 - 0.142: 70 Chirality restraints: 4872 Sorted by residual: chirality pdb=" CA PRO O 127 " pdb=" N PRO O 127 " pdb=" C PRO O 127 " pdb=" CB PRO O 127 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA PRO E 127 " pdb=" N PRO E 127 " pdb=" C PRO E 127 " pdb=" CB PRO E 127 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA PRO X 127 " pdb=" N PRO X 127 " pdb=" C PRO X 127 " pdb=" CB PRO X 127 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 4869 not shown) Planarity restraints: 9984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 66 " 0.015 2.00e-02 2.50e+03 9.09e-03 2.48e+00 pdb=" CG TYR F 66 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR F 66 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR F 66 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 66 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 66 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR F 66 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 66 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR F 66 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR F 66 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR F 66 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR F 66 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 66 " 0.015 2.00e-02 2.50e+03 9.08e-03 2.48e+00 pdb=" CG TYR I 66 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR I 66 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR I 66 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR I 66 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR I 66 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR I 66 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR I 66 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR I 66 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR I 66 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR I 66 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR I 66 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 66 " 0.015 2.00e-02 2.50e+03 9.08e-03 2.47e+00 pdb=" CG TYR V 66 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR V 66 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR V 66 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR V 66 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR V 66 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR V 66 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR V 66 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR V 66 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR V 66 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR V 66 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR V 66 " 0.001 2.00e-02 2.50e+03 ... (remaining 9981 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 18395 2.33 - 2.97: 173273 2.97 - 3.61: 247562 3.61 - 4.24: 341689 4.24 - 4.88: 536445 Nonbonded interactions: 1317364 Sorted by model distance: nonbonded pdb=" HE ARG J 68 " pdb=" O HOH J 203 " model vdw 1.694 1.850 nonbonded pdb=" HH TYR D 168 " pdb=" OG1 THR T 174 " model vdw 1.732 1.850 nonbonded pdb=" HH TYR F 168 " pdb=" OG1 THR N 174 " model vdw 1.736 1.850 nonbonded pdb=" OG1 THR H 174 " pdb=" HH TYR P 168 " model vdw 1.739 1.850 nonbonded pdb=" HH TYR K 168 " pdb=" OG1 THR U 174 " model vdw 1.740 1.850 ... (remaining 1317359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 33240 68332 True True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 S 120 5.16 5 C 21000 2.51 5 N 5808 2.21 5 O 8732 1.98 5 H 32664 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.290 Set model interpretation parameters: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 10.690 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.240 Process input model: 199.570 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:10.630 Internal consistency checks: 0.000 Total: 223.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.044 33864 Angle : 0.690 6.123 45552 Chirality : 0.038 0.142 4872 Planarity : 0.003 0.025 5976 Dihedral : 14.942 87.413 12768 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.12), residues: 4080 helix: 1.54 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : -0.95 (0.18), residues: 768 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 720 time to evaluate : 4.604 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 720 average time/residue: 4.1339 time to fit residues: 2983.6580 Evaluate side-chains 532 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 532 time to evaluate : 4.608 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 6.9990 chunk 309 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 319 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 238 optimal weight: 7.9990 chunk 370 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 29 GLN A 75 GLN B 25 ASN B 29 GLN B 75 GLN B 83 GLN C 25 ASN C 29 GLN C 75 GLN C 83 GLN D 25 ASN D 29 GLN D 75 GLN D 83 GLN E 25 ASN E 29 GLN E 75 GLN E 83 GLN F 25 ASN F 29 GLN F 75 GLN G 25 ASN G 29 GLN G 75 GLN G 83 GLN H 25 ASN H 29 GLN H 75 GLN H 83 GLN I 25 ASN I 29 GLN I 75 GLN I 83 GLN J 25 ASN J 29 GLN J 75 GLN J 83 GLN K 25 ASN K 29 GLN K 75 GLN K 83 GLN L 25 ASN L 29 GLN L 75 GLN L 83 GLN M 25 ASN M 29 GLN M 75 GLN M 83 GLN N 25 ASN N 29 GLN N 75 GLN N 83 GLN O 25 ASN O 29 GLN O 75 GLN O 83 GLN P 25 ASN P 29 GLN P 75 GLN P 83 GLN Q 25 ASN Q 29 GLN Q 75 GLN Q 83 GLN R 25 ASN R 29 GLN R 75 GLN R 83 GLN S 25 ASN S 29 GLN S 75 GLN S 83 GLN T 25 ASN T 29 GLN T 75 GLN T 83 GLN U 25 ASN U 29 GLN U 75 GLN U 83 GLN V 25 ASN V 29 GLN V 75 GLN V 83 GLN W 25 ASN W 29 GLN W 75 GLN W 83 GLN X 25 ASN X 29 GLN X 75 GLN X 83 GLN Total number of N/Q/H flips: 94 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.021 33864 Angle : 0.552 5.066 45552 Chirality : 0.034 0.130 4872 Planarity : 0.004 0.026 5976 Dihedral : 4.348 17.593 4536 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.25 (0.13), residues: 4080 helix: 3.36 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.07 (0.22), residues: 768 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 48 poor density : 574 time to evaluate : 4.840 Fit side-chains outliers start: 48 outliers final: 0 residues processed: 598 average time/residue: 3.7205 time to fit residues: 2232.3435 Evaluate side-chains 588 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 588 time to evaluate : 4.535 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 308 optimal weight: 6.9990 chunk 252 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 371 optimal weight: 5.9990 chunk 400 optimal weight: 6.9990 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 297 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN B 29 GLN B 75 GLN C 29 GLN C 75 GLN D 29 GLN D 75 GLN E 29 GLN E 75 GLN F 29 GLN F 75 GLN G 29 GLN G 75 GLN H 29 GLN H 75 GLN I 29 GLN I 75 GLN J 29 GLN J 75 GLN K 29 GLN K 75 GLN L 29 GLN L 75 GLN M 29 GLN M 75 GLN N 29 GLN N 75 GLN O 29 GLN O 75 GLN P 29 GLN P 75 GLN Q 29 GLN Q 75 GLN R 29 GLN R 75 GLN S 29 GLN S 75 GLN T 29 GLN T 75 GLN U 29 GLN U 75 GLN V 29 GLN V 75 GLN W 29 GLN W 75 GLN X 29 GLN X 75 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.029 33864 Angle : 0.594 5.412 45552 Chirality : 0.037 0.147 4872 Planarity : 0.005 0.039 5976 Dihedral : 4.504 18.329 4536 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.40 (0.13), residues: 4080 helix: 3.43 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.31 (0.23), residues: 768 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 514 time to evaluate : 5.223 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 514 average time/residue: 3.5985 time to fit residues: 1857.7145 Evaluate side-chains 512 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 512 time to evaluate : 4.549 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 3.9990 chunk 279 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 chunk 372 optimal weight: 5.9990 chunk 394 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 353 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN A 83 GLN B 29 GLN B 75 GLN C 29 GLN C 75 GLN D 29 GLN D 75 GLN E 29 GLN E 75 GLN F 29 GLN F 75 GLN F 83 GLN G 29 GLN G 75 GLN H 29 GLN H 75 GLN I 29 GLN I 75 GLN J 29 GLN J 75 GLN K 29 GLN K 75 GLN L 29 GLN L 75 GLN M 29 GLN M 75 GLN N 29 GLN N 75 GLN O 29 GLN O 75 GLN P 29 GLN P 75 GLN Q 29 GLN Q 75 GLN R 29 GLN R 75 GLN S 29 GLN S 75 GLN T 29 GLN T 75 GLN U 29 GLN U 75 GLN V 29 GLN V 75 GLN W 29 GLN W 75 GLN X 29 GLN X 75 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.023 33864 Angle : 0.548 5.417 45552 Chirality : 0.036 0.144 4872 Planarity : 0.004 0.033 5976 Dihedral : 4.407 17.667 4536 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.59 (0.13), residues: 4080 helix: 3.59 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.26 (0.23), residues: 768 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 533 time to evaluate : 4.702 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 533 average time/residue: 3.5068 time to fit residues: 1876.7914 Evaluate side-chains 532 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 532 time to evaluate : 4.524 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 293 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 336 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 353 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN A 83 GLN B 29 GLN B 75 GLN C 29 GLN C 75 GLN D 29 GLN D 75 GLN E 29 GLN E 75 GLN F 29 GLN F 75 GLN F 83 GLN G 29 GLN G 75 GLN H 29 GLN H 75 GLN I 29 GLN I 75 GLN J 29 GLN J 75 GLN K 29 GLN K 75 GLN L 29 GLN L 75 GLN M 29 GLN M 75 GLN N 29 GLN N 75 GLN O 29 GLN O 75 GLN P 29 GLN P 75 GLN P 83 GLN Q 29 GLN Q 75 GLN R 29 GLN R 75 GLN S 29 GLN S 75 GLN S 83 GLN T 29 GLN T 75 GLN U 29 GLN U 75 GLN U 83 GLN V 29 GLN V 75 GLN W 29 GLN W 75 GLN X 29 GLN X 75 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.025 33864 Angle : 0.581 5.485 45552 Chirality : 0.037 0.149 4872 Planarity : 0.005 0.039 5976 Dihedral : 4.494 18.311 4536 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.37 (0.13), residues: 4080 helix: 3.44 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.17 (0.23), residues: 768 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 525 time to evaluate : 4.664 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 525 average time/residue: 3.5203 time to fit residues: 1855.3949 Evaluate side-chains 522 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 522 time to evaluate : 4.504 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 8.9990 chunk 355 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 394 optimal weight: 6.9990 chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN A 83 GLN B 29 GLN B 75 GLN C 29 GLN C 75 GLN D 29 GLN D 75 GLN E 29 GLN E 75 GLN F 29 GLN F 75 GLN F 83 GLN G 29 GLN G 75 GLN H 29 GLN H 75 GLN I 29 GLN I 75 GLN J 29 GLN J 75 GLN K 29 GLN K 75 GLN L 29 GLN L 75 GLN M 29 GLN M 75 GLN N 29 GLN N 75 GLN O 29 GLN O 75 GLN P 29 GLN P 75 GLN P 83 GLN Q 29 GLN Q 75 GLN R 29 GLN R 75 GLN S 29 GLN S 75 GLN S 83 GLN T 29 GLN T 75 GLN U 29 GLN U 75 GLN U 83 GLN V 29 GLN V 75 GLN W 29 GLN W 75 GLN X 29 GLN X 75 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.026 33864 Angle : 0.583 5.527 45552 Chirality : 0.037 0.152 4872 Planarity : 0.005 0.039 5976 Dihedral : 4.506 18.300 4536 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.36 (0.13), residues: 4080 helix: 3.44 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.17 (0.23), residues: 768 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 528 time to evaluate : 4.567 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 528 average time/residue: 3.4682 time to fit residues: 1838.4387 Evaluate side-chains 524 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 524 time to evaluate : 4.570 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 393 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN A 83 GLN B 29 GLN B 75 GLN C 29 GLN C 75 GLN D 29 GLN D 75 GLN E 29 GLN E 75 GLN F 29 GLN F 75 GLN G 29 GLN G 75 GLN G 83 GLN H 29 GLN H 75 GLN I 29 GLN I 75 GLN J 29 GLN J 75 GLN K 29 GLN K 75 GLN L 29 GLN L 75 GLN M 29 GLN M 75 GLN N 29 GLN N 75 GLN O 29 GLN O 75 GLN P 29 GLN P 75 GLN P 83 GLN Q 29 GLN Q 75 GLN R 29 GLN R 75 GLN S 29 GLN S 75 GLN S 83 GLN T 29 GLN T 75 GLN U 29 GLN U 75 GLN U 83 GLN V 29 GLN V 75 GLN W 29 GLN W 75 GLN X 29 GLN X 75 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.017 33864 Angle : 0.499 5.313 45552 Chirality : 0.034 0.134 4872 Planarity : 0.004 0.025 5976 Dihedral : 4.234 16.419 4536 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.98 (0.13), residues: 4080 helix: 3.87 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.35 (0.23), residues: 768 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 567 time to evaluate : 4.619 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 567 average time/residue: 3.4636 time to fit residues: 1971.5044 Evaluate side-chains 552 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 552 time to evaluate : 4.563 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 234 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 309 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN A 83 GLN B 29 GLN B 75 GLN C 29 GLN C 75 GLN C 83 GLN D 29 GLN D 75 GLN D 83 GLN E 29 GLN E 75 GLN F 29 GLN F 75 GLN G 29 GLN G 75 GLN G 83 GLN H 29 GLN H 75 GLN H 83 GLN I 29 GLN I 75 GLN I 83 GLN J 29 GLN J 75 GLN K 29 GLN K 75 GLN K 83 GLN L 29 GLN L 75 GLN L 83 GLN M 29 GLN M 75 GLN N 29 GLN N 75 GLN N 83 GLN O 29 GLN O 75 GLN O 83 GLN P 29 GLN P 75 GLN P 83 GLN Q 29 GLN Q 75 GLN Q 83 GLN R 29 GLN R 75 GLN R 83 GLN S 29 GLN S 75 GLN S 83 GLN T 29 GLN T 75 GLN T 83 GLN U 29 GLN U 75 GLN U 83 GLN V 29 GLN V 75 GLN V 83 GLN W 29 GLN W 75 GLN X 29 GLN X 75 GLN X 83 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.023 33864 Angle : 0.552 5.406 45552 Chirality : 0.036 0.142 4872 Planarity : 0.005 0.038 5976 Dihedral : 4.399 17.924 4536 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.63 (0.13), residues: 4080 helix: 3.60 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.34 (0.23), residues: 768 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 556 time to evaluate : 4.835 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 556 average time/residue: 3.4218 time to fit residues: 1910.3632 Evaluate side-chains 520 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 520 time to evaluate : 4.559 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 8.9990 chunk 376 optimal weight: 5.9990 chunk 343 optimal weight: 6.9990 chunk 366 optimal weight: 0.9990 chunk 220 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 287 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 331 optimal weight: 3.9990 chunk 346 optimal weight: 6.9990 chunk 365 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN A 83 GLN B 29 GLN B 75 GLN B 83 GLN C 29 GLN C 75 GLN C 83 GLN D 29 GLN D 75 GLN D 83 GLN E 29 GLN E 75 GLN E 83 GLN F 29 GLN F 75 GLN G 29 GLN G 75 GLN G 83 GLN H 29 GLN H 75 GLN H 83 GLN I 29 GLN I 75 GLN I 83 GLN J 29 GLN J 75 GLN K 29 GLN K 75 GLN K 83 GLN L 29 GLN L 75 GLN L 83 GLN M 29 GLN M 75 GLN N 29 GLN N 75 GLN N 83 GLN O 29 GLN O 75 GLN O 83 GLN P 29 GLN P 75 GLN P 83 GLN Q 29 GLN Q 75 GLN Q 83 GLN R 29 GLN R 75 GLN R 83 GLN S 29 GLN S 75 GLN S 83 GLN T 29 GLN T 75 GLN T 83 GLN U 29 GLN U 75 GLN U 83 GLN V 29 GLN V 75 GLN V 83 GLN W 29 GLN W 75 GLN W 83 GLN X 29 GLN X 75 GLN X 83 GLN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.018 33864 Angle : 0.511 5.365 45552 Chirality : 0.034 0.138 4872 Planarity : 0.004 0.030 5976 Dihedral : 4.297 16.949 4536 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.87 (0.13), residues: 4080 helix: 3.78 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.40 (0.23), residues: 768 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 538 time to evaluate : 4.698 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 538 average time/residue: 3.5156 time to fit residues: 1898.8442 Evaluate side-chains 517 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 517 time to evaluate : 4.618 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 6.9990 chunk 387 optimal weight: 0.8980 chunk 236 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 269 optimal weight: 8.9990 chunk 406 optimal weight: 7.9990 chunk 374 optimal weight: 8.9990 chunk 323 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 250 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN A 83 GLN B 29 GLN B 75 GLN B 83 GLN C 29 GLN C 75 GLN C 83 GLN D 29 GLN D 75 GLN D 83 GLN E 29 GLN E 75 GLN E 83 GLN F 29 GLN F 75 GLN F 83 GLN G 29 GLN G 75 GLN G 83 GLN H 29 GLN H 75 GLN H 83 GLN I 29 GLN I 75 GLN I 83 GLN J 29 GLN J 75 GLN J 83 GLN K 29 GLN K 75 GLN K 83 GLN L 29 GLN L 75 GLN L 83 GLN M 29 GLN M 75 GLN M 83 GLN N 29 GLN N 75 GLN N 83 GLN O 29 GLN O 75 GLN O 83 GLN P 29 GLN P 75 GLN P 83 GLN Q 29 GLN Q 75 GLN Q 83 GLN R 29 GLN R 75 GLN R 83 GLN S 29 GLN S 75 GLN S 83 GLN T 29 GLN T 75 GLN T 83 GLN U 29 GLN U 75 GLN U 83 GLN V 29 GLN V 75 GLN V 83 GLN W 29 GLN W 75 GLN W 83 GLN X 29 GLN X 75 GLN X 83 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.026 33864 Angle : 0.588 5.498 45552 Chirality : 0.037 0.148 4872 Planarity : 0.005 0.040 5976 Dihedral : 4.496 18.506 4536 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.39 (0.13), residues: 4080 helix: 3.45 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.22 (0.23), residues: 768 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield and 0 Emsley and 4080 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 538 time to evaluate : 4.773 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 538 average time/residue: 3.5580 time to fit residues: 1922.6882 Evaluate side-chains 517 residues out of total 3480 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 517 time to evaluate : 4.539 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 6.9990 chunk 344 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 298 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 332 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN A 83 GLN B 29 GLN B 75 GLN B 83 GLN C 29 GLN C 75 GLN C 83 GLN D 29 GLN D 75 GLN D 83 GLN E 29 GLN E 75 GLN E 83 GLN F 29 GLN F 75 GLN F 83 GLN G 29 GLN G 75 GLN G 83 GLN H 29 GLN H 75 GLN H 83 GLN I 29 GLN I 75 GLN I 83 GLN J 29 GLN J 75 GLN J 83 GLN K 29 GLN K 75 GLN K 83 GLN L 29 GLN L 75 GLN L 83 GLN M 29 GLN M 75 GLN M 83 GLN N 29 GLN N 75 GLN N 83 GLN O 29 GLN O 75 GLN O 83 GLN P 29 GLN P 75 GLN P 83 GLN Q 29 GLN Q 75 GLN Q 83 GLN R 29 GLN R 75 GLN R 83 GLN S 29 GLN S 75 GLN S 83 GLN T 29 GLN T 75 GLN T 83 GLN U 29 GLN U 75 GLN U 83 GLN V 29 GLN V 75 GLN V 83 GLN W 29 GLN W 75 GLN W 83 GLN X 29 GLN X 75 GLN X 83 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.112497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.102476 restraints weight = 81223.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.105630 restraints weight = 42579.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.107662 restraints weight = 25615.456| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.004 0.021 33864 ANGLE : 0.535 5.488 45552 CHIRALITY : 0.035 0.145 4872 PLANARITY : 0.004 0.035 5976 DIHEDRAL : 4.399 17.561 4536 MIN NONBONDED DISTANCE : 2.000 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 2.44 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 1.18 % FAVORED : 98.82 % ROTAMER OUTLIERS : 0.69 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: 4.65 (0.13), RESIDUES: 4080 HELIX: 3.61 (0.08), RESIDUES: 3312 SHEET: NONE (NONE), RESIDUES: 0 LOOP : 0.38 (0.23), RESIDUES: 768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.021 33864 Angle : 0.535 5.488 45552 Chirality : 0.035 0.145 4872 Planarity : 0.004 0.035 5976 Dihedral : 4.399 17.561 4536 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.65 (0.13), residues: 4080 helix: 3.61 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.38 (0.23), residues: 768 =============================================================================== Job complete usr+sys time: 25040.18 seconds wall clock time: 430 minutes 25.55 seconds (25825.55 seconds total)