Starting phenix.real_space_refine (version: dev) on Wed Apr 6 08:39:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/04_2022/6wx6_21951.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/04_2022/6wx6_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_21951/04_2022/6wx6_21951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/04_2022/6wx6_21951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/04_2022/6wx6_21951.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/04_2022/6wx6_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 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 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-dev-4553/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: 24.08, per 1000 atoms: 0.35 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 Amino 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: 48.40 Conformation dependent library (CDL) restraints added in 4.1 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: 0.72 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: 21.33 Time building geometry restraints manager: 50.42 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 - 2.28: 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 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 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 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 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 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: 1.400 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: 1.000 Extract box with map and model: 9.990 Check model and map are aligned: 0.780 Convert atoms to be neutral: 0.450 Process input model: 163.920 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:9.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 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 % 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, 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 : 4.492 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 720 average time/residue: 3.8254 time to fit residues: 3129.8624 Evaluate side-chains 532 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 4.475 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4273 ------------------------------------------------------------------------------- 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 29 GLN A 75 GLN 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 29 GLN F 75 GLN G 25 ASN G 29 GLN G 75 GLN G 83 GLN 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 29 GLN O 75 GLN O 83 GLN P 29 GLN P 75 GLN Q 25 ASN Q 29 GLN Q 75 GLN Q 83 GLN 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 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: 85 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 33864 Z= 0.231 Angle : 0.557 4.915 45552 Z= 0.310 Chirality : 0.035 0.133 4872 Planarity : 0.004 0.028 5976 Dihedral : 4.355 17.311 4536 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 1.02 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: 4.25 (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, 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 588 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 564 time to evaluate : 5.173 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 564 average time/residue: 3.5857 time to fit residues: 2334.4515 Evaluate side-chains 516 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 4.510 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5027 ------------------------------------------------------------------------------- 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: 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: 6.9990 chunk 297 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 C 29 GLN C 75 GLN D 29 GLN D 75 GLN E 29 GLN E 75 GLN F 25 ASN F 29 GLN F 75 GLN G 29 GLN G 75 GLN H 25 ASN 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 25 ASN O 29 GLN O 75 GLN P 25 ASN P 29 GLN P 75 GLN P 83 GLN Q 29 GLN Q 75 GLN R 25 ASN R 29 GLN R 75 GLN S 29 GLN S 75 GLN T 29 GLN U 29 GLN U 75 GLN V 25 ASN 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: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 33864 Z= 0.338 Angle : 0.637 5.538 45552 Z= 0.359 Chirality : 0.038 0.153 4872 Planarity : 0.005 0.043 5976 Dihedral : 4.591 18.722 4536 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 2.07 % 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: 4.13 (0.13), residues: 4080 helix: 3.28 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.09 (0.22), residues: 768 *********************** 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 599 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 527 time to evaluate : 4.494 Fit side-chains outliers start: 72 outliers final: 0 residues processed: 551 average time/residue: 3.3618 time to fit residues: 2142.9806 Evaluate side-chains 530 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 4.446 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4088 ------------------------------------------------------------------------------- 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: 6.9990 chunk 279 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 372 optimal weight: 5.9990 chunk 394 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 353 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 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 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 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: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.029 33864 Z= 0.318 Angle : 0.603 5.388 45552 Z= 0.342 Chirality : 0.038 0.153 4872 Planarity : 0.005 0.039 5976 Dihedral : 4.581 18.404 4536 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.93 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: 4.20 (0.13), residues: 4080 helix: 3.33 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : 0.07 (0.22), residues: 768 *********************** 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 572 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 548 time to evaluate : 5.500 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 548 average time/residue: 3.3899 time to fit residues: 2146.7264 Evaluate side-chains 538 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 4.448 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3953 ------------------------------------------------------------------------------- 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: 5.9990 chunk 223 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 293 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 336 optimal weight: 7.9990 chunk 272 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 353 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 C 29 GLN C 75 GLN D 29 GLN D 75 GLN E 29 GLN E 75 GLN F 29 GLN G 29 GLN G 75 GLN H 29 GLN H 75 GLN I 29 GLN I 75 GLN J 29 GLN K 29 GLN K 75 GLN L 29 GLN M 29 GLN N 29 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 T 29 GLN T 75 GLN U 29 GLN U 75 GLN V 29 GLN W 29 GLN W 75 GLN X 29 GLN X 75 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2396 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= 0.209 Angle : 0.520 5.366 45552 Z= 0.295 Chirality : 0.034 0.135 4872 Planarity : 0.004 0.028 5976 Dihedral : 4.341 16.796 4536 Min Nonbonded Distance : 2.037 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: 4.70 (0.13), residues: 4080 helix: 3.67 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : 0.30 (0.23), residues: 768 *********************** 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 576 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 552 time to evaluate : 4.795 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 552 average time/residue: 3.3680 time to fit residues: 2151.0465 Evaluate side-chains 535 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 535 time to evaluate : 4.463 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4270 ------------------------------------------------------------------------------- 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: 7.9990 chunk 97 optimal weight: 4.9990 chunk 394 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 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 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 K 29 GLN K 75 GLN L 29 GLN L 83 GLN M 29 GLN N 29 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 83 GLN T 29 GLN T 83 GLN U 29 GLN U 75 GLN U 83 GLN V 29 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: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2468 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= 0.276 Angle : 0.573 5.436 45552 Z= 0.325 Chirality : 0.036 0.145 4872 Planarity : 0.005 0.039 5976 Dihedral : 4.472 18.210 4536 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.95 % 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: 4.45 (0.13), residues: 4080 helix: 3.48 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.27 (0.23), residues: 768 *********************** 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 584 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 551 time to evaluate : 4.664 Fit side-chains outliers start: 33 outliers final: 0 residues processed: 551 average time/residue: 3.4215 time to fit residues: 2189.6057 Evaluate side-chains 551 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 551 time to evaluate : 3.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8144 ------------------------------------------------------------------------------- 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: 6.9990 chunk 44 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 288 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 181 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 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 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 K 29 GLN K 75 GLN L 29 GLN L 83 GLN M 29 GLN N 29 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 83 GLN T 29 GLN T 83 GLN U 29 GLN U 75 GLN U 83 GLN V 29 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: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.020 33864 Z= 0.234 Angle : 0.533 5.515 45552 Z= 0.304 Chirality : 0.035 0.141 4872 Planarity : 0.004 0.034 5976 Dihedral : 4.391 17.411 4536 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.88 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: 4.66 (0.13), residues: 4080 helix: 3.63 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.37 (0.23), residues: 768 *********************** 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 576 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 552 time to evaluate : 4.559 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 552 average time/residue: 3.3760 time to fit residues: 2154.4171 Evaluate side-chains 548 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 548 time to evaluate : 4.431 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4019 ------------------------------------------------------------------------------- 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: 4.9990 chunk 157 optimal weight: 8.9990 chunk 234 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 250 optimal weight: 7.9990 chunk 267 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 309 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 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 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 83 GLN K 29 GLN K 75 GLN K 83 GLN L 29 GLN L 83 GLN M 29 GLN M 83 GLN N 29 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 83 GLN T 29 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: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.022 33864 Z= 0.262 Angle : 0.558 5.446 45552 Z= 0.318 Chirality : 0.036 0.144 4872 Planarity : 0.005 0.035 5976 Dihedral : 4.422 17.813 4536 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.87 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: 4.57 (0.13), residues: 4080 helix: 3.56 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.31 (0.23), residues: 768 *********************** 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 577 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 553 time to evaluate : 4.540 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 553 average time/residue: 3.3750 time to fit residues: 2161.4108 Evaluate side-chains 551 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 551 time to evaluate : 4.409 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4348 ------------------------------------------------------------------------------- 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: 4.9990 chunk 366 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 287 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 331 optimal weight: 4.9990 chunk 346 optimal weight: 7.9990 chunk 365 optimal weight: 0.4980 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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 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 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 83 GLN K 29 GLN K 75 GLN K 83 GLN L 29 GLN L 83 GLN M 29 GLN M 83 GLN N 29 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 83 GLN T 29 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: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 33864 Z= 0.195 Angle : 0.509 5.388 45552 Z= 0.290 Chirality : 0.034 0.135 4872 Planarity : 0.004 0.028 5976 Dihedral : 4.290 16.736 4536 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.94 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: 4.90 (0.13), residues: 4080 helix: 3.78 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.47 (0.24), residues: 768 *********************** 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 577 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 553 time to evaluate : 4.836 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 553 average time/residue: 3.4236 time to fit residues: 2190.6202 Evaluate side-chains 552 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 552 time to evaluate : 4.485 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4738 ------------------------------------------------------------------------------- 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: 9.9990 chunk 236 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 269 optimal weight: 6.9990 chunk 406 optimal weight: 0.9990 chunk 374 optimal weight: 8.9990 chunk 323 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 250 optimal weight: 1.9990 chunk 198 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 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 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 83 GLN K 29 GLN K 75 GLN K 83 GLN L 29 GLN L 83 GLN M 29 GLN M 83 GLN N 29 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 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: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 33864 Z= 0.252 Angle : 0.553 5.426 45552 Z= 0.314 Chirality : 0.035 0.141 4872 Planarity : 0.004 0.033 5976 Dihedral : 4.384 17.543 4536 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.19 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: 4.62 (0.13), residues: 4080 helix: 3.60 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.36 (0.23), residues: 768 ********************** 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 566 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 542 time to evaluate : 4.488 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 542 average time/residue: 3.3780 time to fit residues: 2128.5394 Evaluate side-chains 541 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 541 time to evaluate : 4.479 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5380 ------------------------------------------------------------------------------- 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: 7.9990 chunk 298 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 324 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 332 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 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 83 GLN K 29 GLN K 75 GLN K 83 GLN L 29 GLN L 83 GLN M 29 GLN M 83 GLN N 29 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 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: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.111245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.101440 restraints weight = 81157.678| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 0.74 r_work: 0.3011 rms_B_bonded: 0.71 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 0.89 restraints_weight: 0.2500 r_work: 0.2937 rms_B_bonded: 1.28 restraints_weight: 0.1250 r_work: 0.2863 rms_B_bonded: 2.03 restraints_weight: 0.0625 r_work: 0.2746 rms_B_bonded: 3.46 restraints_weight: 0.0312 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 33864 Z= 0.248 Angle : 0.545 5.441 45552 Z= 0.311 Chirality : 0.035 0.142 4872 Planarity : 0.004 0.034 5976 Dihedral : 4.390 17.445 4536 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.40 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: 4.62 (0.13), residues: 4080 helix: 3.59 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.40 (0.23), residues: 768 =============================================================================== Job complete usr+sys time: 27152.84 seconds wall clock time: 478 minutes 51.31 seconds (28731.31 seconds total)