Starting phenix.real_space_refine on Fri Sep 27 17:48:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/09_2024/6wx6_21951.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/09_2024/6wx6_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_21951/09_2024/6wx6_21951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/09_2024/6wx6_21951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/09_2024/6wx6_21951.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/09_2024/6wx6_21951.cif" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.431 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: 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. Process input model Symmetric amino acids flipped. Time to flip 456 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 26.19, per 1000 atoms: 0.38 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 - 3.00 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: 13.53 Conformation dependent library (CDL) restraints added in 4.0 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. 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: 3.76 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: 23.85 Time building geometry restraints manager: 16.60 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: 0.00 - 5.90: 119930 5.90 - 11.79: 38 11.79 - 17.69: 4 17.69 - 23.58: 2 23.58 - 29.48: 2 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: 28180 17.48 - 34.97: 1773 34.97 - 52.45: 672 52.45 - 69.93: 263 69.93 - 87.41: 96 Dihedral angle restraints: 30984 sinusoidal: 16824 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 30981 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 - 2.28: 9681 2.28 - 2.86: 155771 2.86 - 3.44: 200894 3.44 - 4.02: 281067 4.02 - 4.60: 411336 Nonbonded interactions: 1058749 Sorted by model distance: nonbonded pdb=" HE ARG J 68 " pdb=" O HOH J 203 " model vdw 1.694 2.450 nonbonded pdb=" HH TYR D 168 " pdb=" OG1 THR T 174 " model vdw 1.732 2.450 nonbonded pdb=" HH TYR F 168 " pdb=" OG1 THR N 174 " model vdw 1.736 2.450 nonbonded pdb=" OG1 THR H 174 " pdb=" HH TYR P 168 " model vdw 1.739 2.450 nonbonded pdb=" HH TYR K 168 " pdb=" OG1 THR U 174 " model vdw 1.740 2.450 ... (remaining 1058744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 1.210 Extract box with map and model: 1.920 Check model and map are aligned: 0.440 Set scattering table: 0.480 Process input model: 113.330 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.460 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: 0.020 Load rotamer database and sin/cos tables:10.830 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 33864 Z= 0.404 Angle : 0.690 6.123 45552 Z= 0.363 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 % Allowed : 1.38 % Favored : 98.62 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 93 HIS 0.003 0.001 HIS O 118 PHE 0.013 0.003 PHE L 41 TYR 0.024 0.002 TYR F 66 ARG 0.004 0.001 ARG L 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 720 time to evaluate : 4.296 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 720 average time/residue: 4.4525 time to fit residues: 3604.1563 Evaluate side-chains 532 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 4.175 ------------------------------------------------------------------------------- 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: 2.9990 chunk 105 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 319 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 238 optimal weight: 6.9990 chunk 370 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 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 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: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33864 Z= 0.212 Angle : 0.543 4.976 45552 Z= 0.301 Chirality : 0.034 0.129 4872 Planarity : 0.004 0.026 5976 Dihedral : 4.309 17.351 4536 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.69 % Allowed : 4.83 % Favored : 94.48 % 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: 4.29 (0.13), residues: 4080 helix: 3.40 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.02 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 93 HIS 0.003 0.001 HIS V 128 PHE 0.019 0.003 PHE E 41 TYR 0.026 0.002 TYR N 66 ARG 0.002 0.001 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 565 time to evaluate : 4.234 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 565 average time/residue: 4.1588 time to fit residues: 2670.7200 Evaluate side-chains 532 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 4.204 ------------------------------------------------------------------------------- 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: 6.9990 chunk 308 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 371 optimal weight: 7.9990 chunk 400 optimal weight: 6.9990 chunk 330 optimal weight: 10.0000 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 297 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 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 M 25 ASN M 29 GLN M 75 GLN N 25 ASN N 29 GLN N 75 GLN O 25 ASN O 29 GLN O 75 GLN O 83 GLN P 25 ASN P 29 GLN P 75 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 T 25 ASN T 29 GLN T 75 GLN T 83 GLN U 25 ASN U 29 GLN U 75 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: 87 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 33864 Z= 0.313 Angle : 0.621 5.577 45552 Z= 0.349 Chirality : 0.038 0.146 4872 Planarity : 0.005 0.032 5976 Dihedral : 4.558 18.378 4536 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.07 % Allowed : 6.15 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.32 (0.13), residues: 4080 helix: 3.40 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : 0.18 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP T 93 HIS 0.005 0.002 HIS J 136 PHE 0.021 0.004 PHE N 41 TYR 0.024 0.003 TYR V 66 ARG 0.004 0.001 ARG W 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 574 time to evaluate : 4.196 Fit side-chains outliers start: 72 outliers final: 0 residues processed: 598 average time/residue: 3.7680 time to fit residues: 2582.9866 Evaluate side-chains 544 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 544 time to evaluate : 4.183 ------------------------------------------------------------------------------- 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: 4.9990 chunk 279 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 chunk 394 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 353 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 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 G 112 GLN H 29 GLN H 75 GLN H 83 GLN I 29 GLN I 75 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 M 29 GLN M 75 GLN N 29 GLN N 75 GLN O 29 GLN O 75 GLN O 83 GLN P 29 GLN P 75 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 T 29 GLN T 75 GLN T 83 GLN U 29 GLN U 75 GLN V 29 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: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 33864 Z= 0.172 Angle : 0.496 5.247 45552 Z= 0.277 Chirality : 0.033 0.128 4872 Planarity : 0.003 0.019 5976 Dihedral : 4.199 16.735 4536 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.69 % Allowed : 6.26 % Favored : 93.05 % 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: 4.95 (0.13), residues: 4080 helix: 3.86 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : 0.26 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 93 HIS 0.003 0.001 HIS M 128 PHE 0.015 0.002 PHE G 41 TYR 0.023 0.002 TYR R 66 ARG 0.002 0.000 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 592 time to evaluate : 4.278 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 592 average time/residue: 3.8417 time to fit residues: 2596.6876 Evaluate side-chains 563 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 563 time to evaluate : 4.172 ------------------------------------------------------------------------------- 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: 6.9990 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 336 optimal weight: 6.9990 chunk 272 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 4.9990 chunk 353 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 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 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 Q 29 GLN Q 75 GLN Q 83 GLN R 29 GLN R 75 GLN S 29 GLN S 75 GLN T 29 GLN T 75 GLN T 83 GLN U 29 GLN U 75 GLN V 29 GLN W 29 GLN W 75 GLN X 29 GLN X 75 GLN X 83 GLN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 33864 Z= 0.293 Angle : 0.586 5.477 45552 Z= 0.331 Chirality : 0.037 0.148 4872 Planarity : 0.005 0.031 5976 Dihedral : 4.499 18.057 4536 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.69 % Allowed : 6.35 % Favored : 92.96 % 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: 4.44 (0.13), residues: 4080 helix: 3.49 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.19 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 93 HIS 0.004 0.002 HIS Q 136 PHE 0.020 0.004 PHE S 41 TYR 0.021 0.002 TYR M 66 ARG 0.005 0.001 ARG W 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 580 time to evaluate : 4.210 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 580 average time/residue: 3.8754 time to fit residues: 2571.1397 Evaluate side-chains 562 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 562 time to evaluate : 4.180 ------------------------------------------------------------------------------- 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: 7.9990 chunk 355 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 394 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 207 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 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 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 J 29 GLN J 75 GLN K 29 GLN K 75 GLN K 83 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 O 83 GLN P 29 GLN P 75 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 T 29 GLN T 75 GLN T 83 GLN U 29 GLN U 75 GLN V 29 GLN V 75 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: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 33864 Z= 0.301 Angle : 0.587 5.498 45552 Z= 0.332 Chirality : 0.037 0.150 4872 Planarity : 0.005 0.030 5976 Dihedral : 4.526 18.164 4536 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.69 % Allowed : 6.35 % Favored : 92.96 % 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: 3.43 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.19 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 93 HIS 0.004 0.002 HIS N 136 PHE 0.020 0.003 PHE G 41 TYR 0.021 0.002 TYR E 66 ARG 0.005 0.001 ARG M 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 572 time to evaluate : 4.273 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 572 average time/residue: 3.8806 time to fit residues: 2538.8064 Evaluate side-chains 560 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 560 time to evaluate : 4.204 ------------------------------------------------------------------------------- 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: 7.9990 chunk 224 optimal weight: 4.9990 chunk 288 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 332 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 393 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 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 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 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 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 Q 29 GLN Q 75 GLN Q 83 GLN R 29 GLN R 75 GLN R 83 GLN S 29 GLN S 75 GLN T 29 GLN T 75 GLN T 83 GLN U 29 GLN U 75 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: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 33864 Z= 0.231 Angle : 0.538 5.436 45552 Z= 0.304 Chirality : 0.035 0.141 4872 Planarity : 0.004 0.025 5976 Dihedral : 4.426 17.651 4536 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.69 % Allowed : 6.35 % Favored : 92.96 % 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: 4.64 (0.13), residues: 4080 helix: 3.63 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : 0.26 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 93 HIS 0.003 0.001 HIS U 128 PHE 0.018 0.003 PHE A 41 TYR 0.022 0.002 TYR J 66 ARG 0.003 0.000 ARG V 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 582 time to evaluate : 4.182 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 582 average time/residue: 3.8269 time to fit residues: 2548.8342 Evaluate side-chains 571 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 571 time to evaluate : 4.152 ------------------------------------------------------------------------------- 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: 5.9990 chunk 157 optimal weight: 0.9990 chunk 234 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 250 optimal weight: 8.9990 chunk 267 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 309 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 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 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 J 29 GLN J 75 GLN J 83 GLN K 29 GLN K 75 GLN K 83 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 O 83 GLN P 29 GLN P 75 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 T 29 GLN T 75 GLN T 83 GLN U 29 GLN U 75 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: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33864 Z= 0.214 Angle : 0.525 5.370 45552 Z= 0.296 Chirality : 0.034 0.136 4872 Planarity : 0.004 0.024 5976 Dihedral : 4.383 17.242 4536 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.69 % Allowed : 6.44 % Favored : 92.87 % 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: 4.71 (0.13), residues: 4080 helix: 3.67 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : 0.30 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 93 HIS 0.004 0.001 HIS U 128 PHE 0.017 0.003 PHE G 41 TYR 0.022 0.002 TYR S 66 ARG 0.002 0.000 ARG W 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 586 time to evaluate : 4.165 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 586 average time/residue: 3.8223 time to fit residues: 2565.4831 Evaluate side-chains 574 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 574 time to evaluate : 4.199 ------------------------------------------------------------------------------- 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: 5.9990 chunk 366 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 287 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 331 optimal weight: 4.9990 chunk 346 optimal weight: 3.9990 chunk 365 optimal weight: 4.9990 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 29 GLN A 75 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 J 29 GLN J 75 GLN J 83 GLN K 29 GLN K 75 GLN K 83 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 O 83 GLN P 29 GLN P 75 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 V 29 GLN V 75 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: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 33864 Z= 0.231 Angle : 0.536 5.434 45552 Z= 0.303 Chirality : 0.035 0.138 4872 Planarity : 0.004 0.024 5976 Dihedral : 4.400 17.498 4536 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.69 % Allowed : 6.55 % Favored : 92.76 % 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: 4.64 (0.13), residues: 4080 helix: 3.62 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : 0.27 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP G 93 HIS 0.004 0.001 HIS K 128 PHE 0.018 0.003 PHE B 41 TYR 0.021 0.002 TYR S 66 ARG 0.003 0.000 ARG W 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 589 time to evaluate : 4.184 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 589 average time/residue: 3.8902 time to fit residues: 2626.0450 Evaluate side-chains 574 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 574 time to evaluate : 4.207 ------------------------------------------------------------------------------- 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: 6.9990 chunk 236 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 269 optimal weight: 8.9990 chunk 406 optimal weight: 10.0000 chunk 374 optimal weight: 7.9990 chunk 323 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 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 J 29 GLN J 75 GLN J 83 GLN K 29 GLN K 75 GLN K 83 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 O 83 GLN P 29 GLN P 75 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 V 29 GLN V 75 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: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 33864 Z= 0.305 Angle : 0.589 5.535 45552 Z= 0.335 Chirality : 0.037 0.148 4872 Planarity : 0.005 0.028 5976 Dihedral : 4.531 18.196 4536 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.69 % Allowed : 6.55 % Favored : 92.76 % 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: 4.34 (0.13), residues: 4080 helix: 3.41 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.19 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP G 93 HIS 0.005 0.002 HIS K 128 PHE 0.020 0.004 PHE P 41 TYR 0.020 0.003 TYR J 66 ARG 0.005 0.001 ARG N 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 575 time to evaluate : 4.297 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 575 average time/residue: 3.8479 time to fit residues: 2539.2771 Evaluate side-chains 562 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 562 time to evaluate : 4.204 ------------------------------------------------------------------------------- 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: 5.9990 chunk 344 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 298 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 324 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 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 G 112 GLN H 29 GLN H 75 GLN H 83 GLN I 29 GLN I 75 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 M 29 GLN M 75 GLN N 29 GLN N 75 GLN O 29 GLN O 75 GLN O 83 GLN P 29 GLN P 75 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 V 29 GLN V 75 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: 64 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.113621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.103766 restraints weight = 80294.626| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 0.74 r_work: 0.3008 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 1.62 restraints_weight: 0.2500 r_work: 0.2653 rms_B_bonded: 4.28 restraints_weight: 0.1250 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 33864 Z= 0.178 Angle : 0.497 5.268 45552 Z= 0.280 Chirality : 0.034 0.131 4872 Planarity : 0.004 0.024 5976 Dihedral : 4.272 16.800 4536 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.69 % Allowed : 6.55 % Favored : 92.76 % 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: 4.93 (0.13), residues: 4080 helix: 3.84 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : 0.30 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 93 HIS 0.004 0.001 HIS V 128 PHE 0.015 0.002 PHE G 41 TYR 0.023 0.002 TYR Q 66 ARG 0.001 0.000 ARG I 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34340.69 seconds wall clock time: 579 minutes 1.66 seconds (34741.66 seconds total)