Starting phenix.real_space_refine on Sun Aug 24 21:44:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vdz_43157/08_2025/8vdz_43157.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vdz_43157/08_2025/8vdz_43157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vdz_43157/08_2025/8vdz_43157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vdz_43157/08_2025/8vdz_43157.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vdz_43157/08_2025/8vdz_43157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vdz_43157/08_2025/8vdz_43157.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 15021 2.51 5 N 4050 2.21 5 O 4533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23700 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1096 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Chain: "B" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1090 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain breaks: 1 Chain: "C" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1082 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Chain: "D" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1099 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 138} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "H" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 880 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "I" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1096 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Chain: "J" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1090 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain breaks: 1 Chain: "K" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1082 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Chain: "L" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1099 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 138} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "N" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "O" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "P" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 880 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "Q" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1096 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Chain: "R" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1084 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "S" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1082 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Chain: "T" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1099 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 138} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "U" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "V" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "W" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "X" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 880 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Time building chain proxies: 5.73, per 1000 atoms: 0.24 Number of scatterers: 23700 At special positions: 0 Unit cell: (131.655, 134.603, 129.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 4533 8.00 N 4050 7.00 C 15021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 985.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5670 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 24 sheets defined 59.1% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 24 through 45 Processing helix chain 'A' and resid 49 through 72 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.930A pdb=" N ILE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 137 Processing helix chain 'A' and resid 139 through 163 Processing helix chain 'B' and resid 24 through 45 Processing helix chain 'B' and resid 49 through 72 Processing helix chain 'B' and resid 80 through 96 removed outlier: 3.899A pdb=" N ILE B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 137 Processing helix chain 'B' and resid 139 through 163 Processing helix chain 'C' and resid 24 through 45 Processing helix chain 'C' and resid 49 through 72 Processing helix chain 'C' and resid 80 through 96 removed outlier: 3.942A pdb=" N ILE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 137 Processing helix chain 'C' and resid 139 through 163 Processing helix chain 'D' and resid 24 through 45 Processing helix chain 'D' and resid 49 through 72 Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.927A pdb=" N ILE D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 137 Processing helix chain 'D' and resid 139 through 163 Processing helix chain 'E' and resid 17 through 31 Processing helix chain 'E' and resid 73 through 91 Processing helix chain 'F' and resid 17 through 31 Processing helix chain 'F' and resid 73 through 91 Processing helix chain 'G' and resid 17 through 31 Processing helix chain 'G' and resid 73 through 91 Processing helix chain 'H' and resid 17 through 31 Processing helix chain 'H' and resid 73 through 91 Processing helix chain 'I' and resid 24 through 45 Processing helix chain 'I' and resid 49 through 72 Processing helix chain 'I' and resid 80 through 96 removed outlier: 3.938A pdb=" N ILE I 84 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 137 Processing helix chain 'I' and resid 139 through 163 Processing helix chain 'J' and resid 24 through 45 Processing helix chain 'J' and resid 49 through 72 Processing helix chain 'J' and resid 80 through 96 removed outlier: 3.900A pdb=" N ILE J 84 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 137 Processing helix chain 'J' and resid 139 through 163 Processing helix chain 'K' and resid 24 through 45 Processing helix chain 'K' and resid 49 through 72 Processing helix chain 'K' and resid 80 through 96 removed outlier: 3.917A pdb=" N ILE K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 137 Processing helix chain 'K' and resid 139 through 163 Processing helix chain 'L' and resid 24 through 45 Processing helix chain 'L' and resid 49 through 72 Processing helix chain 'L' and resid 80 through 96 removed outlier: 3.946A pdb=" N ILE L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 137 Processing helix chain 'L' and resid 139 through 163 Processing helix chain 'M' and resid 17 through 31 Processing helix chain 'M' and resid 73 through 91 Processing helix chain 'N' and resid 17 through 31 Processing helix chain 'N' and resid 36 through 39 Processing helix chain 'N' and resid 73 through 91 Processing helix chain 'O' and resid 17 through 31 Processing helix chain 'O' and resid 73 through 91 Processing helix chain 'P' and resid 17 through 31 Processing helix chain 'P' and resid 36 through 39 Processing helix chain 'P' and resid 73 through 91 Processing helix chain 'Q' and resid 24 through 45 Processing helix chain 'Q' and resid 49 through 72 Processing helix chain 'Q' and resid 80 through 96 removed outlier: 3.904A pdb=" N ILE Q 84 " --> pdb=" O SER Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 137 Processing helix chain 'Q' and resid 139 through 163 Processing helix chain 'R' and resid 24 through 45 Processing helix chain 'R' and resid 49 through 72 Processing helix chain 'R' and resid 80 through 96 removed outlier: 3.912A pdb=" N ILE R 84 " --> pdb=" O SER R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 137 Processing helix chain 'R' and resid 139 through 163 Processing helix chain 'S' and resid 24 through 45 Processing helix chain 'S' and resid 49 through 72 Processing helix chain 'S' and resid 80 through 96 removed outlier: 3.944A pdb=" N ILE S 84 " --> pdb=" O SER S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 137 Processing helix chain 'S' and resid 139 through 163 Processing helix chain 'T' and resid 24 through 45 Processing helix chain 'T' and resid 49 through 72 Processing helix chain 'T' and resid 80 through 96 removed outlier: 3.905A pdb=" N ILE T 84 " --> pdb=" O SER T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 137 Processing helix chain 'T' and resid 139 through 163 Processing helix chain 'U' and resid 17 through 31 Processing helix chain 'U' and resid 36 through 39 Processing helix chain 'U' and resid 73 through 91 Processing helix chain 'V' and resid 17 through 31 Processing helix chain 'V' and resid 73 through 91 Processing helix chain 'W' and resid 17 through 31 Processing helix chain 'W' and resid 73 through 90 Processing helix chain 'X' and resid 17 through 32 removed outlier: 3.645A pdb=" N SER X 32 " --> pdb=" O ALA X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 91 Processing sheet with id=AA1, first strand: chain 'M' and resid 49 through 52 removed outlier: 4.291A pdb=" N ALA M 49 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 4 " --> pdb=" O ARG E 43 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL E 45 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE E 6 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU E 47 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA E 8 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR E 61 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU E 62 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLU E 105 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA E 64 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ARG E 107 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU E 66 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET E 109 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE E 68 " --> pdb=" O MET E 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AA3, first strand: chain 'E' and resid 49 through 52 removed outlier: 4.296A pdb=" N ALA E 49 " --> pdb=" O PHE U 44 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU U 4 " --> pdb=" O ARG U 43 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL U 45 " --> pdb=" O LEU U 4 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE U 6 " --> pdb=" O VAL U 45 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU U 47 " --> pdb=" O ILE U 6 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA U 8 " --> pdb=" O LEU U 47 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR U 61 " --> pdb=" O THR U 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 115 through 119 removed outlier: 6.526A pdb=" N LEU M 62 " --> pdb=" O SER M 103 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N GLU M 105 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA M 64 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ARG M 107 " --> pdb=" O ALA M 64 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU M 66 " --> pdb=" O ARG M 107 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N MET M 109 " --> pdb=" O LEU M 66 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE M 68 " --> pdb=" O MET M 109 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR M 61 " --> pdb=" O THR M 9 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU M 4 " --> pdb=" O ARG M 43 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL M 45 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE M 6 " --> pdb=" O VAL M 45 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU M 47 " --> pdb=" O ILE M 6 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA M 8 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA U 49 " --> pdb=" O PHE M 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 49 through 52 removed outlier: 4.345A pdb=" N ALA G 49 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU F 4 " --> pdb=" O ARG F 43 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL F 45 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE F 6 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU F 47 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA F 8 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR F 61 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU F 62 " --> pdb=" O SER F 103 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLU F 105 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA F 64 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ARG F 107 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU F 66 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N MET F 109 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE F 68 " --> pdb=" O MET F 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 12 through 14 Processing sheet with id=AA7, first strand: chain 'F' and resid 49 through 52 removed outlier: 4.317A pdb=" N ALA F 49 " --> pdb=" O PHE P 44 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU P 4 " --> pdb=" O ARG P 43 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL P 45 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE P 6 " --> pdb=" O VAL P 45 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU P 47 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA P 8 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR P 9 " --> pdb=" O TYR P 61 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR P 61 " --> pdb=" O THR P 9 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU P 62 " --> pdb=" O SER P 103 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N GLU P 105 " --> pdb=" O LEU P 62 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA P 64 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ARG P 107 " --> pdb=" O ALA P 64 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU P 66 " --> pdb=" O ARG P 107 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N MET P 109 " --> pdb=" O LEU P 66 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE P 68 " --> pdb=" O MET P 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 115 through 119 removed outlier: 6.420A pdb=" N LEU G 62 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N GLU G 105 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA G 64 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ARG G 107 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU G 66 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N MET G 109 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE G 68 " --> pdb=" O MET G 109 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR G 61 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR G 9 " --> pdb=" O TYR G 61 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU G 4 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL G 45 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE G 6 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU G 47 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA G 8 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA P 49 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 13 through 14 Processing sheet with id=AB1, first strand: chain 'V' and resid 49 through 52 removed outlier: 4.352A pdb=" N ALA V 49 " --> pdb=" O PHE H 44 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU H 4 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL H 45 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE H 6 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU H 47 " --> pdb=" O ILE H 6 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA H 8 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR H 61 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU H 62 " --> pdb=" O SER H 103 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU H 105 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA H 64 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ARG H 107 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU H 66 " --> pdb=" O ARG H 107 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N MET H 109 " --> pdb=" O LEU H 66 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE H 68 " --> pdb=" O MET H 109 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 14 Processing sheet with id=AB3, first strand: chain 'H' and resid 49 through 52 removed outlier: 4.317A pdb=" N ALA H 49 " --> pdb=" O PHE W 44 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU W 4 " --> pdb=" O ARG W 43 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL W 45 " --> pdb=" O LEU W 4 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE W 6 " --> pdb=" O VAL W 45 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU W 47 " --> pdb=" O ILE W 6 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA W 8 " --> pdb=" O LEU W 47 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR W 61 " --> pdb=" O THR W 9 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU W 62 " --> pdb=" O SER W 103 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLU W 105 " --> pdb=" O LEU W 62 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA W 64 " --> pdb=" O GLU W 105 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ARG W 107 " --> pdb=" O ALA W 64 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU W 66 " --> pdb=" O ARG W 107 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N MET W 109 " --> pdb=" O LEU W 66 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE W 68 " --> pdb=" O MET W 109 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 115 through 119 removed outlier: 6.464A pdb=" N LEU V 62 " --> pdb=" O SER V 103 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLU V 105 " --> pdb=" O LEU V 62 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA V 64 " --> pdb=" O GLU V 105 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ARG V 107 " --> pdb=" O ALA V 64 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU V 66 " --> pdb=" O ARG V 107 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET V 109 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE V 68 " --> pdb=" O MET V 109 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR V 61 " --> pdb=" O THR V 9 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR V 9 " --> pdb=" O TYR V 61 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU V 4 " --> pdb=" O ARG V 43 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL V 45 " --> pdb=" O LEU V 4 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE V 6 " --> pdb=" O VAL V 45 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU V 47 " --> pdb=" O ILE V 6 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA V 8 " --> pdb=" O LEU V 47 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA W 49 " --> pdb=" O PHE V 44 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 13 through 14 Processing sheet with id=AB6, first strand: chain 'O' and resid 49 through 52 removed outlier: 4.350A pdb=" N ALA O 49 " --> pdb=" O PHE N 44 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU N 4 " --> pdb=" O ARG N 43 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL N 45 " --> pdb=" O LEU N 4 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE N 6 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU N 47 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA N 8 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR N 61 " --> pdb=" O THR N 9 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU N 62 " --> pdb=" O SER N 103 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLU N 105 " --> pdb=" O LEU N 62 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA N 64 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG N 107 " --> pdb=" O ALA N 64 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU N 66 " --> pdb=" O ARG N 107 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET N 109 " --> pdb=" O LEU N 66 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE N 68 " --> pdb=" O MET N 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 13 through 14 Processing sheet with id=AB8, first strand: chain 'N' and resid 49 through 52 removed outlier: 4.338A pdb=" N ALA N 49 " --> pdb=" O PHE X 44 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU X 4 " --> pdb=" O ARG X 43 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL X 45 " --> pdb=" O LEU X 4 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE X 6 " --> pdb=" O VAL X 45 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU X 47 " --> pdb=" O ILE X 6 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA X 8 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR X 61 " --> pdb=" O THR X 9 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU X 62 " --> pdb=" O SER X 103 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLU X 105 " --> pdb=" O LEU X 62 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA X 64 " --> pdb=" O GLU X 105 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ARG X 107 " --> pdb=" O ALA X 64 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU X 66 " --> pdb=" O ARG X 107 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET X 109 " --> pdb=" O LEU X 66 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE X 68 " --> pdb=" O MET X 109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 115 through 119 removed outlier: 6.511A pdb=" N LEU O 62 " --> pdb=" O SER O 103 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N GLU O 105 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA O 64 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ARG O 107 " --> pdb=" O ALA O 64 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU O 66 " --> pdb=" O ARG O 107 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET O 109 " --> pdb=" O LEU O 66 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE O 68 " --> pdb=" O MET O 109 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR O 61 " --> pdb=" O THR O 9 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU O 4 " --> pdb=" O ARG O 43 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL O 45 " --> pdb=" O LEU O 4 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE O 6 " --> pdb=" O VAL O 45 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU O 47 " --> pdb=" O ILE O 6 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA O 8 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA X 49 " --> pdb=" O PHE O 44 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 13 through 14 Processing sheet with id=AC2, first strand: chain 'P' and resid 13 through 14 Processing sheet with id=AC3, first strand: chain 'U' and resid 13 through 14 Processing sheet with id=AC4, first strand: chain 'V' and resid 13 through 14 Processing sheet with id=AC5, first strand: chain 'W' and resid 13 through 14 Processing sheet with id=AC6, first strand: chain 'X' and resid 12 through 14 1687 hydrogen bonds defined for protein. 4914 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: 4.16 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7997 1.34 - 1.46: 3480 1.46 - 1.58: 12303 1.58 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 23936 Sorted by residual: bond pdb=" CD GLU R 135 " pdb=" OE1 GLU R 135 " ideal model delta sigma weight residual 1.249 1.229 0.020 1.90e-02 2.77e+03 1.09e+00 bond pdb=" CG1 ILE Q 121 " pdb=" CD1 ILE Q 121 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 8.24e-01 bond pdb=" N GLU R 135 " pdb=" CA GLU R 135 " ideal model delta sigma weight residual 1.458 1.470 -0.011 1.26e-02 6.30e+03 8.10e-01 bond pdb=" CG1 ILE K 121 " pdb=" CD1 ILE K 121 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 7.86e-01 bond pdb=" C GLY W 94 " pdb=" N GLY W 95 " ideal model delta sigma weight residual 1.331 1.318 0.013 1.46e-02 4.69e+03 7.75e-01 ... (remaining 23931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 31150 1.08 - 2.16: 867 2.16 - 3.23: 170 3.23 - 4.31: 23 4.31 - 5.39: 13 Bond angle restraints: 32223 Sorted by residual: angle pdb=" C ARG R 134 " pdb=" N GLU R 135 " pdb=" CA GLU R 135 " ideal model delta sigma weight residual 120.58 115.79 4.79 1.71e+00 3.42e-01 7.86e+00 angle pdb=" N GLU R 135 " pdb=" CA GLU R 135 " pdb=" CB GLU R 135 " ideal model delta sigma weight residual 110.20 114.22 -4.02 1.49e+00 4.50e-01 7.28e+00 angle pdb=" C ASP C 24 " pdb=" N SER C 25 " pdb=" CA SER C 25 " ideal model delta sigma weight residual 120.26 123.68 -3.42 1.34e+00 5.57e-01 6.50e+00 angle pdb=" C ASP D 24 " pdb=" N SER D 25 " pdb=" CA SER D 25 " ideal model delta sigma weight residual 120.26 123.62 -3.36 1.34e+00 5.57e-01 6.27e+00 angle pdb=" C ASP B 24 " pdb=" N SER B 25 " pdb=" CA SER B 25 " ideal model delta sigma weight residual 120.26 123.37 -3.11 1.34e+00 5.57e-01 5.40e+00 ... (remaining 32218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13741 17.94 - 35.89: 724 35.89 - 53.83: 124 53.83 - 71.77: 29 71.77 - 89.71: 11 Dihedral angle restraints: 14629 sinusoidal: 5824 harmonic: 8805 Sorted by residual: dihedral pdb=" CA ARG M 107 " pdb=" C ARG M 107 " pdb=" N GLU M 108 " pdb=" CA GLU M 108 " ideal model delta harmonic sigma weight residual -180.00 -163.70 -16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB GLU S 50 " pdb=" CG GLU S 50 " pdb=" CD GLU S 50 " pdb=" OE1 GLU S 50 " ideal model delta sinusoidal sigma weight residual 0.00 -89.71 89.71 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU I 58 " pdb=" CG GLU I 58 " pdb=" CD GLU I 58 " pdb=" OE1 GLU I 58 " ideal model delta sinusoidal sigma weight residual 0.00 88.61 -88.61 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 14626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2951 0.040 - 0.080: 631 0.080 - 0.120: 267 0.120 - 0.160: 2 0.160 - 0.200: 1 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA GLU R 135 " pdb=" N GLU R 135 " pdb=" C GLU R 135 " pdb=" CB GLU R 135 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA SER S 25 " pdb=" N SER S 25 " pdb=" C SER S 25 " pdb=" CB SER S 25 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA VAL E 5 " pdb=" N VAL E 5 " pdb=" C VAL E 5 " pdb=" CB VAL E 5 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 3849 not shown) Planarity restraints: 4091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 64 " -0.016 2.00e-02 2.50e+03 1.02e-02 2.08e+00 pdb=" CG TYR R 64 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR R 64 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR R 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR R 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 64 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR R 64 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 64 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER P 17 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO P 18 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO P 18 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO P 18 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 17 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO G 18 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO G 18 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 18 " 0.017 5.00e-02 4.00e+02 ... (remaining 4088 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 163 2.63 - 3.19: 20735 3.19 - 3.76: 37809 3.76 - 4.33: 53173 4.33 - 4.90: 88474 Nonbonded interactions: 200354 Sorted by model distance: nonbonded pdb=" OG SER G 17 " pdb=" OE1 GLU G 20 " model vdw 2.056 3.040 nonbonded pdb=" OG SER P 17 " pdb=" OE1 GLU P 20 " model vdw 2.064 3.040 nonbonded pdb=" OG SER W 17 " pdb=" OE1 GLU W 20 " model vdw 2.068 3.040 nonbonded pdb=" OG SER N 17 " pdb=" OE1 GLU N 20 " model vdw 2.070 3.040 nonbonded pdb=" OG SER X 17 " pdb=" OE1 GLU X 20 " model vdw 2.072 3.040 ... (remaining 200349 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 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'B' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'C' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'D' and (resid 23 through 99 or resid 103 through 163)) selection = (chain 'I' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'J' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'K' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'L' and (resid 23 through 99 or resid 103 through 163)) selection = (chain 'Q' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'R' and (resid 23 through 99 or resid 103 through 163)) selection = (chain 'S' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'T' and (resid 23 through 99 or resid 103 through 163)) } ncs_group { reference = (chain 'E' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'F' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'G' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'H' selection = (chain 'M' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'N' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'O' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'P' selection = (chain 'U' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'V' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'W' and (resid 2 through 55 or resid 57 through 119)) 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: 1.650 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.830 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 : 0.003 0.035 23936 Z= 0.130 Angle : 0.462 5.390 32223 Z= 0.261 Chirality : 0.038 0.200 3852 Planarity : 0.003 0.031 4091 Dihedral : 11.964 89.713 8959 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.43 (0.14), residues: 3015 helix: 3.17 (0.11), residues: 1773 sheet: 2.47 (0.23), residues: 396 loop : 0.11 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 59 TYR 0.023 0.002 TYR R 64 PHE 0.004 0.001 PHE R 40 TRP 0.012 0.002 TRP A 86 HIS 0.002 0.000 HIS O 3 Details of bonding type rmsd covalent geometry : bond 0.00274 (23936) covalent geometry : angle 0.46154 (32223) hydrogen bonds : bond 0.10435 ( 1687) hydrogen bonds : angle 4.40574 ( 4914) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 607 time to evaluate : 0.972 Fit side-chains REVERT: E 13 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7801 (mtm-85) REVERT: I 77 GLU cc_start: 0.7196 (tp30) cc_final: 0.6976 (tp30) REVERT: K 77 GLU cc_start: 0.7515 (tp30) cc_final: 0.7190 (tp30) REVERT: K 95 MET cc_start: 0.8047 (mtp) cc_final: 0.7722 (ttm) REVERT: K 116 ASP cc_start: 0.8439 (m-30) cc_final: 0.8047 (m-30) REVERT: O 48 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7316 (tp30) REVERT: P 39 ASP cc_start: 0.7889 (m-30) cc_final: 0.7538 (m-30) REVERT: R 95 MET cc_start: 0.8095 (mtt) cc_final: 0.7761 (mtp) REVERT: R 116 ASP cc_start: 0.8324 (m-30) cc_final: 0.7989 (m-30) REVERT: S 97 MET cc_start: 0.7647 (mtp) cc_final: 0.7363 (mtm) REVERT: V 13 ARG cc_start: 0.8133 (mtp180) cc_final: 0.7931 (mtp180) outliers start: 0 outliers final: 0 residues processed: 607 average time/residue: 0.8604 time to fit residues: 573.5135 Evaluate side-chains 479 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.134631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.106632 restraints weight = 23852.144| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.48 r_work: 0.2850 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23936 Z= 0.152 Angle : 0.454 5.778 32223 Z= 0.246 Chirality : 0.040 0.139 3852 Planarity : 0.004 0.035 4091 Dihedral : 3.551 14.004 3339 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.74 % Allowed : 8.33 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.26 (0.14), residues: 3015 helix: 3.05 (0.11), residues: 1770 sheet: 2.33 (0.22), residues: 396 loop : 0.06 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 43 TYR 0.014 0.002 TYR X 61 PHE 0.005 0.001 PHE C 154 TRP 0.010 0.002 TRP L 86 HIS 0.002 0.001 HIS P 3 Details of bonding type rmsd covalent geometry : bond 0.00351 (23936) covalent geometry : angle 0.45434 (32223) hydrogen bonds : bond 0.05267 ( 1687) hydrogen bonds : angle 3.91582 ( 4914) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 495 time to evaluate : 0.973 Fit side-chains REVERT: A 29 GLU cc_start: 0.8464 (tt0) cc_final: 0.8015 (mt-10) REVERT: B 43 GLU cc_start: 0.7991 (tt0) cc_final: 0.7726 (tp30) REVERT: B 114 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8312 (mmtp) REVERT: B 135 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: C 43 GLU cc_start: 0.8203 (tt0) cc_final: 0.7836 (tm-30) REVERT: C 50 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7315 (tp30) REVERT: C 69 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8295 (tm-30) REVERT: E 105 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8706 (tt0) REVERT: F 20 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7627 (mp0) REVERT: G 51 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8373 (mpt180) REVERT: H 20 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7521 (mp0) REVERT: I 36 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: I 77 GLU cc_start: 0.7713 (tp30) cc_final: 0.7385 (tp30) REVERT: J 82 GLU cc_start: 0.7658 (pm20) cc_final: 0.7367 (pp20) REVERT: K 95 MET cc_start: 0.8137 (mtp) cc_final: 0.7841 (ttm) REVERT: K 116 ASP cc_start: 0.8860 (m-30) cc_final: 0.8582 (m-30) REVERT: L 47 TYR cc_start: 0.8817 (m-80) cc_final: 0.8492 (m-80) REVERT: L 50 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7221 (mm-30) REVERT: L 65 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7874 (mmtm) REVERT: L 73 LYS cc_start: 0.8575 (ttpt) cc_final: 0.8166 (tttt) REVERT: M 15 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7307 (mm-30) REVERT: O 48 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8035 (tp30) REVERT: P 39 ASP cc_start: 0.8403 (m-30) cc_final: 0.8117 (m-30) REVERT: R 29 GLU cc_start: 0.8431 (tt0) cc_final: 0.7929 (mm-30) REVERT: R 116 ASP cc_start: 0.8815 (m-30) cc_final: 0.8550 (m-30) REVERT: S 97 MET cc_start: 0.7898 (mtp) cc_final: 0.7577 (mtm) REVERT: S 114 LYS cc_start: 0.8408 (mmtt) cc_final: 0.8185 (mmtp) REVERT: U 20 GLU cc_start: 0.7985 (mp0) cc_final: 0.7768 (mp0) REVERT: W 23 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7414 (mm-30) REVERT: X 20 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: X 98 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7479 (mt-10) outliers start: 43 outliers final: 5 residues processed: 510 average time/residue: 0.9711 time to fit residues: 544.5109 Evaluate side-chains 492 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 479 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain M residue 15 GLU Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain X residue 20 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 178 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 170 optimal weight: 0.7980 chunk 103 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 24 GLN P 24 GLN W 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.135880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.108139 restraints weight = 23818.269| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.45 r_work: 0.2930 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23936 Z= 0.110 Angle : 0.395 5.832 32223 Z= 0.216 Chirality : 0.038 0.130 3852 Planarity : 0.003 0.030 4091 Dihedral : 3.302 13.076 3339 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.66 % Allowed : 10.23 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.45 (0.14), residues: 3015 helix: 3.25 (0.11), residues: 1776 sheet: 2.29 (0.21), residues: 396 loop : 0.06 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 43 TYR 0.013 0.002 TYR X 61 PHE 0.004 0.001 PHE C 154 TRP 0.012 0.002 TRP L 86 HIS 0.001 0.000 HIS N 63 Details of bonding type rmsd covalent geometry : bond 0.00235 (23936) covalent geometry : angle 0.39538 (32223) hydrogen bonds : bond 0.04443 ( 1687) hydrogen bonds : angle 3.63840 ( 4914) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 496 time to evaluate : 1.008 Fit side-chains REVERT: A 29 GLU cc_start: 0.8403 (tt0) cc_final: 0.7969 (mt-10) REVERT: A 77 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6870 (tp30) REVERT: B 43 GLU cc_start: 0.8058 (tt0) cc_final: 0.7761 (tp30) REVERT: C 43 GLU cc_start: 0.8131 (tt0) cc_final: 0.7911 (tm-30) REVERT: D 114 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7976 (mmtp) REVERT: D 135 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7967 (mt-10) REVERT: F 20 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7641 (mp0) REVERT: G 51 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8310 (mpt180) REVERT: G 58 GLU cc_start: 0.7495 (tt0) cc_final: 0.7270 (tt0) REVERT: G 59 ARG cc_start: 0.8848 (mtt180) cc_final: 0.8575 (mtt180) REVERT: H 20 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7622 (mp0) REVERT: H 23 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6355 (tp30) REVERT: I 29 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8057 (mm-30) REVERT: I 36 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: I 73 LYS cc_start: 0.8694 (tttm) cc_final: 0.8467 (tttm) REVERT: I 75 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8058 (mptt) REVERT: I 77 GLU cc_start: 0.7592 (tp30) cc_final: 0.7356 (tp30) REVERT: J 82 GLU cc_start: 0.7546 (pm20) cc_final: 0.7287 (pp20) REVERT: K 95 MET cc_start: 0.8083 (mtp) cc_final: 0.7802 (ttm) REVERT: K 116 ASP cc_start: 0.8876 (m-30) cc_final: 0.8544 (m-30) REVERT: L 47 TYR cc_start: 0.8789 (m-80) cc_final: 0.8387 (m-80) REVERT: L 50 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7171 (mm-30) REVERT: L 73 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8132 (tttt) REVERT: M 15 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7247 (mm-30) REVERT: O 48 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7996 (tp30) REVERT: P 39 ASP cc_start: 0.8334 (m-30) cc_final: 0.8052 (m-30) REVERT: R 29 GLU cc_start: 0.8316 (tt0) cc_final: 0.7819 (mm-30) REVERT: S 97 MET cc_start: 0.7794 (mtp) cc_final: 0.7478 (mtm) REVERT: U 23 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6479 (tp30) REVERT: W 23 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7360 (mm-30) REVERT: X 20 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: X 50 TYR cc_start: 0.9116 (p90) cc_final: 0.8905 (p90) REVERT: X 98 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7429 (mt-10) outliers start: 41 outliers final: 3 residues processed: 508 average time/residue: 0.9788 time to fit residues: 546.9147 Evaluate side-chains 478 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 466 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 15 GLU Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain X residue 20 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 285 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 24 GLN P 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.131128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.103218 restraints weight = 23940.612| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.44 r_work: 0.2862 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23936 Z= 0.201 Angle : 0.493 5.844 32223 Z= 0.262 Chirality : 0.041 0.146 3852 Planarity : 0.004 0.056 4091 Dihedral : 3.678 13.407 3339 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.83 % Allowed : 10.83 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.08 (0.14), residues: 3015 helix: 2.98 (0.11), residues: 1752 sheet: 2.23 (0.22), residues: 396 loop : -0.11 (0.19), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 43 TYR 0.015 0.002 TYR O 50 PHE 0.006 0.001 PHE C 154 TRP 0.007 0.001 TRP T 86 HIS 0.003 0.001 HIS N 63 Details of bonding type rmsd covalent geometry : bond 0.00484 (23936) covalent geometry : angle 0.49318 (32223) hydrogen bonds : bond 0.05896 ( 1687) hydrogen bonds : angle 3.97317 ( 4914) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 502 time to evaluate : 0.897 Fit side-chains REVERT: A 77 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7050 (tp30) REVERT: B 43 GLU cc_start: 0.8138 (tt0) cc_final: 0.7845 (tp30) REVERT: C 43 GLU cc_start: 0.8270 (tt0) cc_final: 0.7845 (tm-30) REVERT: C 50 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7379 (tp30) REVERT: D 25 SER cc_start: 0.8298 (m) cc_final: 0.8045 (p) REVERT: D 69 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: D 76 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8354 (mt) REVERT: E 23 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6597 (tp30) REVERT: E 105 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8846 (tt0) REVERT: F 20 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7750 (mp0) REVERT: G 51 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8335 (mpt180) REVERT: G 58 GLU cc_start: 0.7562 (tt0) cc_final: 0.7293 (tt0) REVERT: G 59 ARG cc_start: 0.9022 (mtt180) cc_final: 0.8766 (mtt180) REVERT: H 20 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7770 (mp0) REVERT: H 23 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6512 (tp30) REVERT: I 73 LYS cc_start: 0.8856 (tttm) cc_final: 0.8650 (tttm) REVERT: I 75 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7791 (mtmt) REVERT: I 77 GLU cc_start: 0.7814 (tp30) cc_final: 0.7486 (tm-30) REVERT: J 82 GLU cc_start: 0.7786 (pm20) cc_final: 0.7488 (pp20) REVERT: K 29 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8242 (mt-10) REVERT: K 95 MET cc_start: 0.8132 (mtp) cc_final: 0.7817 (ttm) REVERT: K 116 ASP cc_start: 0.8944 (m-30) cc_final: 0.8705 (m-30) REVERT: L 47 TYR cc_start: 0.8916 (m-80) cc_final: 0.8495 (m-80) REVERT: L 50 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7221 (mm-30) REVERT: L 65 LYS cc_start: 0.8541 (mtpt) cc_final: 0.7963 (mmtm) REVERT: L 73 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8254 (tttt) REVERT: L 96 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7403 (mt-10) REVERT: M 15 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: M 23 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6635 (tp30) REVERT: M 51 ARG cc_start: 0.8671 (mpt180) cc_final: 0.8454 (mpt180) REVERT: O 24 GLN cc_start: 0.8293 (mt0) cc_final: 0.8058 (mt0) REVERT: P 39 ASP cc_start: 0.8436 (m-30) cc_final: 0.8151 (m-30) REVERT: P 105 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8764 (tm-30) REVERT: R 29 GLU cc_start: 0.8440 (tt0) cc_final: 0.7975 (mm-30) REVERT: R 116 ASP cc_start: 0.8904 (m-30) cc_final: 0.8652 (m-30) REVERT: S 97 MET cc_start: 0.8062 (mtp) cc_final: 0.7695 (mtm) REVERT: S 114 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8314 (mmtp) REVERT: T 114 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8550 (mmtt) REVERT: V 20 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7948 (mp0) REVERT: W 51 ARG cc_start: 0.8460 (mpt180) cc_final: 0.8213 (mpt180) REVERT: W 58 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7174 (tp30) REVERT: X 20 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: X 58 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7388 (tt0) REVERT: X 98 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7582 (mt-10) outliers start: 70 outliers final: 15 residues processed: 525 average time/residue: 0.9652 time to fit residues: 557.6937 Evaluate side-chains 518 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 488 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 7 GLU Chi-restraints excluded: chain M residue 15 GLU Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain W residue 58 GLU Chi-restraints excluded: chain X residue 20 GLU Chi-restraints excluded: chain X residue 58 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 117 optimal weight: 0.0270 chunk 210 optimal weight: 4.9990 chunk 233 optimal weight: 0.5980 chunk 221 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 285 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 GLN M 24 GLN W 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.135340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.107511 restraints weight = 23671.909| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.45 r_work: 0.2920 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23936 Z= 0.104 Angle : 0.391 5.826 32223 Z= 0.214 Chirality : 0.038 0.131 3852 Planarity : 0.003 0.032 4091 Dihedral : 3.274 13.111 3339 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Rotamer: Outliers : 2.30 % Allowed : 12.45 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.37 (0.14), residues: 3015 helix: 3.22 (0.11), residues: 1776 sheet: 2.25 (0.21), residues: 396 loop : -0.05 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 43 TYR 0.013 0.002 TYR E 61 PHE 0.004 0.001 PHE R 154 TRP 0.013 0.003 TRP C 86 HIS 0.002 0.000 HIS X 63 Details of bonding type rmsd covalent geometry : bond 0.00219 (23936) covalent geometry : angle 0.39088 (32223) hydrogen bonds : bond 0.04277 ( 1687) hydrogen bonds : angle 3.57451 ( 4914) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 476 time to evaluate : 1.000 Fit side-chains REVERT: A 65 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7723 (tptp) REVERT: A 77 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6894 (tp30) REVERT: B 43 GLU cc_start: 0.8065 (tt0) cc_final: 0.7841 (tp30) REVERT: C 43 GLU cc_start: 0.8124 (tt0) cc_final: 0.7920 (tm-30) REVERT: D 114 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7952 (mmtp) REVERT: E 23 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6474 (tp30) REVERT: F 20 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7605 (mp0) REVERT: G 51 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8186 (mpt180) REVERT: H 20 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7584 (mp0) REVERT: H 23 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6289 (tp30) REVERT: I 73 LYS cc_start: 0.8744 (tttm) cc_final: 0.8521 (tttm) REVERT: I 75 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8104 (mptt) REVERT: I 77 GLU cc_start: 0.7448 (tp30) cc_final: 0.7169 (tp30) REVERT: J 29 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7917 (mm-30) REVERT: J 82 GLU cc_start: 0.7707 (pm20) cc_final: 0.7342 (pp20) REVERT: J 95 MET cc_start: 0.8014 (mtp) cc_final: 0.7605 (mtt) REVERT: K 95 MET cc_start: 0.8118 (mtp) cc_final: 0.7841 (ttm) REVERT: K 116 ASP cc_start: 0.8785 (m-30) cc_final: 0.8442 (m-30) REVERT: L 47 TYR cc_start: 0.8820 (m-80) cc_final: 0.8360 (m-80) REVERT: L 50 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7138 (mm-30) REVERT: L 69 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: L 73 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8171 (tttt) REVERT: M 15 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: M 23 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6445 (tp30) REVERT: M 51 ARG cc_start: 0.8558 (mpt180) cc_final: 0.8336 (mpt180) REVERT: P 39 ASP cc_start: 0.8404 (m-30) cc_final: 0.8124 (m-30) REVERT: P 51 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8355 (mpt180) REVERT: R 29 GLU cc_start: 0.8287 (tt0) cc_final: 0.7734 (mm-30) REVERT: S 97 MET cc_start: 0.7818 (mtp) cc_final: 0.7422 (mtm) REVERT: V 117 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7961 (mtt90) REVERT: X 15 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7308 (mt-10) REVERT: X 20 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: X 50 TYR cc_start: 0.9117 (p90) cc_final: 0.8871 (p90) REVERT: X 51 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8270 (mpt180) REVERT: X 98 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7429 (mt-10) outliers start: 57 outliers final: 10 residues processed: 494 average time/residue: 0.9851 time to fit residues: 535.3257 Evaluate side-chains 485 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 460 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 15 GLU Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain R residue 64 TYR Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 117 ARG Chi-restraints excluded: chain X residue 20 GLU Chi-restraints excluded: chain X residue 51 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 208 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 24 GLN P 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.132471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.104476 restraints weight = 23865.058| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.44 r_work: 0.2885 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23936 Z= 0.146 Angle : 0.442 5.806 32223 Z= 0.238 Chirality : 0.039 0.136 3852 Planarity : 0.003 0.037 4091 Dihedral : 3.432 12.803 3339 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.02 % Allowed : 12.65 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.26 (0.14), residues: 3015 helix: 3.15 (0.11), residues: 1764 sheet: 2.29 (0.21), residues: 396 loop : -0.15 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 43 TYR 0.013 0.002 TYR O 61 PHE 0.005 0.001 PHE C 154 TRP 0.009 0.002 TRP C 86 HIS 0.002 0.001 HIS P 3 Details of bonding type rmsd covalent geometry : bond 0.00336 (23936) covalent geometry : angle 0.44245 (32223) hydrogen bonds : bond 0.05042 ( 1687) hydrogen bonds : angle 3.74991 ( 4914) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 488 time to evaluate : 0.985 Fit side-chains REVERT: A 77 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6931 (tp30) REVERT: B 43 GLU cc_start: 0.8192 (tt0) cc_final: 0.7908 (tp30) REVERT: B 114 LYS cc_start: 0.8553 (mttm) cc_final: 0.8253 (mmtp) REVERT: C 43 GLU cc_start: 0.8178 (tt0) cc_final: 0.7961 (tm-30) REVERT: C 50 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7268 (tp30) REVERT: D 69 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: D 76 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8255 (mt) REVERT: D 114 LYS cc_start: 0.8309 (mmtt) cc_final: 0.8059 (mmtp) REVERT: E 23 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6515 (tp30) REVERT: F 20 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7638 (mp0) REVERT: G 51 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8275 (mpt180) REVERT: H 20 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7656 (mp0) REVERT: H 23 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6299 (tp30) REVERT: I 73 LYS cc_start: 0.8730 (tttm) cc_final: 0.8510 (tttm) REVERT: I 75 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8030 (mptt) REVERT: I 77 GLU cc_start: 0.7593 (tp30) cc_final: 0.7245 (tm-30) REVERT: J 29 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7895 (mm-30) REVERT: J 82 GLU cc_start: 0.7718 (pm20) cc_final: 0.7344 (pp20) REVERT: J 95 MET cc_start: 0.8069 (mtp) cc_final: 0.7621 (mtt) REVERT: K 29 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8192 (mt-10) REVERT: K 95 MET cc_start: 0.8107 (mtp) cc_final: 0.7809 (ttm) REVERT: K 116 ASP cc_start: 0.8883 (m-30) cc_final: 0.8593 (m-30) REVERT: L 47 TYR cc_start: 0.8850 (m-80) cc_final: 0.8424 (m-80) REVERT: L 50 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7220 (mm-30) REVERT: L 65 LYS cc_start: 0.8436 (mtpt) cc_final: 0.7846 (mmtm) REVERT: L 69 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: L 73 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8201 (tttt) REVERT: M 15 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: M 51 ARG cc_start: 0.8595 (mpt180) cc_final: 0.8363 (mpt180) REVERT: O 24 GLN cc_start: 0.8285 (mt0) cc_final: 0.8017 (mt0) REVERT: O 58 GLU cc_start: 0.7718 (tt0) cc_final: 0.7499 (tt0) REVERT: P 39 ASP cc_start: 0.8404 (m-30) cc_final: 0.8121 (m-30) REVERT: P 105 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8816 (tm-30) REVERT: R 29 GLU cc_start: 0.8333 (tt0) cc_final: 0.7811 (mm-30) REVERT: S 97 MET cc_start: 0.7931 (mtp) cc_final: 0.7542 (mtm) REVERT: U 23 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6308 (tp30) REVERT: V 20 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7766 (mp0) REVERT: X 15 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7300 (mt-10) REVERT: X 20 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: X 50 TYR cc_start: 0.9209 (p90) cc_final: 0.8921 (p90) REVERT: X 51 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8297 (mpt180) REVERT: X 98 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7520 (mt-10) outliers start: 50 outliers final: 16 residues processed: 503 average time/residue: 0.9862 time to fit residues: 545.1564 Evaluate side-chains 509 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 478 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 15 GLU Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain U residue 7 GLU Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain X residue 20 GLU Chi-restraints excluded: chain X residue 51 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 176 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 291 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 24 GLN W 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.134927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.106848 restraints weight = 23701.533| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.46 r_work: 0.2893 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23936 Z= 0.116 Angle : 0.410 5.788 32223 Z= 0.223 Chirality : 0.038 0.132 3852 Planarity : 0.003 0.032 4091 Dihedral : 3.295 13.050 3339 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 1.78 % Allowed : 13.74 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.36 (0.14), residues: 3015 helix: 3.21 (0.11), residues: 1776 sheet: 2.30 (0.21), residues: 396 loop : -0.09 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 43 TYR 0.014 0.002 TYR O 50 PHE 0.004 0.001 PHE C 154 TRP 0.012 0.002 TRP C 86 HIS 0.001 0.000 HIS P 3 Details of bonding type rmsd covalent geometry : bond 0.00254 (23936) covalent geometry : angle 0.41049 (32223) hydrogen bonds : bond 0.04493 ( 1687) hydrogen bonds : angle 3.59625 ( 4914) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 476 time to evaluate : 1.082 Fit side-chains REVERT: A 77 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6841 (tp30) REVERT: B 43 GLU cc_start: 0.8114 (tt0) cc_final: 0.7890 (tp30) REVERT: C 43 GLU cc_start: 0.8103 (tt0) cc_final: 0.7895 (tm-30) REVERT: C 50 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7260 (tp30) REVERT: D 69 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: D 76 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8248 (mt) REVERT: E 23 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6430 (tp30) REVERT: F 20 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7639 (mp0) REVERT: F 23 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6478 (tp30) REVERT: G 20 GLU cc_start: 0.7948 (mp0) cc_final: 0.7625 (pm20) REVERT: G 51 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8266 (mpt180) REVERT: G 58 GLU cc_start: 0.7603 (tt0) cc_final: 0.7297 (pt0) REVERT: H 20 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7664 (mp0) REVERT: H 23 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6242 (tp30) REVERT: I 73 LYS cc_start: 0.8725 (tttm) cc_final: 0.8514 (tttm) REVERT: I 75 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7952 (mptt) REVERT: I 77 GLU cc_start: 0.7571 (tp30) cc_final: 0.7225 (tm-30) REVERT: J 82 GLU cc_start: 0.7674 (pm20) cc_final: 0.7285 (pp20) REVERT: J 95 MET cc_start: 0.7993 (mtp) cc_final: 0.7674 (ttp) REVERT: K 95 MET cc_start: 0.8103 (mtp) cc_final: 0.7836 (ttm) REVERT: K 116 ASP cc_start: 0.8822 (m-30) cc_final: 0.8505 (m-30) REVERT: L 36 GLU cc_start: 0.8521 (tt0) cc_final: 0.8291 (tt0) REVERT: L 47 TYR cc_start: 0.8832 (m-80) cc_final: 0.8366 (m-80) REVERT: L 50 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7125 (mm-30) REVERT: L 69 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: L 73 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8128 (tttt) REVERT: M 51 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8285 (mpt180) REVERT: N 7 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: O 20 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: O 24 GLN cc_start: 0.8241 (mt0) cc_final: 0.7959 (mt0) REVERT: P 39 ASP cc_start: 0.8355 (m-30) cc_final: 0.8061 (m-30) REVERT: R 29 GLU cc_start: 0.8318 (tt0) cc_final: 0.7803 (mm-30) REVERT: S 97 MET cc_start: 0.7919 (mtp) cc_final: 0.7517 (mtm) REVERT: U 23 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6264 (tp30) REVERT: V 20 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7717 (mp0) REVERT: W 58 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7140 (tp30) REVERT: X 15 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7203 (mt-10) REVERT: X 20 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: X 50 TYR cc_start: 0.9147 (p90) cc_final: 0.8802 (p90) REVERT: X 51 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8284 (mpt180) REVERT: X 98 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7482 (mt-10) outliers start: 44 outliers final: 15 residues processed: 487 average time/residue: 0.9416 time to fit residues: 504.6987 Evaluate side-chains 489 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 457 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 7 GLU Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain R residue 64 TYR Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain W residue 7 GLU Chi-restraints excluded: chain W residue 58 GLU Chi-restraints excluded: chain X residue 20 GLU Chi-restraints excluded: chain X residue 51 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 157 optimal weight: 0.9980 chunk 249 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 279 optimal weight: 5.9990 chunk 266 optimal weight: 0.6980 chunk 226 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 213 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.133643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.105484 restraints weight = 23754.364| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.45 r_work: 0.2863 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23936 Z= 0.131 Angle : 0.430 5.784 32223 Z= 0.232 Chirality : 0.039 0.135 3852 Planarity : 0.003 0.032 4091 Dihedral : 3.354 12.992 3339 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.86 % Allowed : 14.27 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.30 (0.14), residues: 3015 helix: 3.20 (0.11), residues: 1764 sheet: 2.30 (0.21), residues: 396 loop : -0.16 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 43 TYR 0.016 0.002 TYR O 50 PHE 0.004 0.001 PHE B 154 TRP 0.010 0.002 TRP C 86 HIS 0.002 0.001 HIS P 3 Details of bonding type rmsd covalent geometry : bond 0.00296 (23936) covalent geometry : angle 0.42950 (32223) hydrogen bonds : bond 0.04755 ( 1687) hydrogen bonds : angle 3.66431 ( 4914) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 481 time to evaluate : 0.945 Fit side-chains REVERT: A 77 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6860 (tp30) REVERT: B 43 GLU cc_start: 0.8151 (tt0) cc_final: 0.7938 (tp30) REVERT: C 43 GLU cc_start: 0.8168 (tt0) cc_final: 0.7958 (tm-30) REVERT: C 50 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7262 (tp30) REVERT: D 69 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: D 76 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8295 (mt) REVERT: E 23 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6440 (tp30) REVERT: F 20 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7664 (mp0) REVERT: F 23 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6492 (tp30) REVERT: G 51 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8273 (mpt180) REVERT: G 58 GLU cc_start: 0.7656 (tt0) cc_final: 0.7287 (pt0) REVERT: H 20 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7679 (mp0) REVERT: H 23 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6250 (tp30) REVERT: I 73 LYS cc_start: 0.8736 (tttm) cc_final: 0.8532 (tttm) REVERT: I 75 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8093 (mptt) REVERT: I 77 GLU cc_start: 0.7716 (tp30) cc_final: 0.7360 (tm-30) REVERT: J 82 GLU cc_start: 0.7702 (pm20) cc_final: 0.7336 (pp20) REVERT: J 95 MET cc_start: 0.8000 (mtp) cc_final: 0.7682 (ttp) REVERT: K 29 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8200 (mt-10) REVERT: K 95 MET cc_start: 0.8111 (mtp) cc_final: 0.7844 (ttm) REVERT: K 116 ASP cc_start: 0.8875 (m-30) cc_final: 0.8567 (m-30) REVERT: L 36 GLU cc_start: 0.8557 (tt0) cc_final: 0.8305 (tt0) REVERT: L 47 TYR cc_start: 0.8867 (m-80) cc_final: 0.8396 (m-80) REVERT: L 50 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7153 (mm-30) REVERT: L 65 LYS cc_start: 0.8333 (mtpt) cc_final: 0.7747 (mmtm) REVERT: L 69 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: L 73 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8192 (tttt) REVERT: M 51 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8290 (mpt180) REVERT: O 20 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: P 39 ASP cc_start: 0.8377 (m-30) cc_final: 0.8076 (m-30) REVERT: P 105 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8646 (tm-30) REVERT: R 29 GLU cc_start: 0.8349 (tt0) cc_final: 0.7852 (mm-30) REVERT: S 97 MET cc_start: 0.7971 (mtp) cc_final: 0.7575 (mtm) REVERT: U 23 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6305 (tp30) REVERT: V 20 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7738 (mp0) REVERT: W 58 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7133 (tp30) REVERT: X 15 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7211 (mt-10) REVERT: X 20 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: X 50 TYR cc_start: 0.9201 (p90) cc_final: 0.8862 (p90) REVERT: X 51 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8356 (mpt180) REVERT: X 98 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7503 (mt-10) outliers start: 46 outliers final: 17 residues processed: 491 average time/residue: 0.9844 time to fit residues: 531.7864 Evaluate side-chains 504 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 470 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 7 GLU Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain R residue 64 TYR Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain U residue 7 GLU Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain W residue 7 GLU Chi-restraints excluded: chain W residue 58 GLU Chi-restraints excluded: chain X residue 20 GLU Chi-restraints excluded: chain X residue 51 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 188 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 24 GLN P 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.134893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.106773 restraints weight = 23763.018| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.46 r_work: 0.2836 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23936 Z= 0.120 Angle : 0.421 5.778 32223 Z= 0.228 Chirality : 0.039 0.132 3852 Planarity : 0.003 0.032 4091 Dihedral : 3.300 13.136 3339 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.66 % Allowed : 14.43 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.35 (0.14), residues: 3015 helix: 3.21 (0.11), residues: 1773 sheet: 2.31 (0.20), residues: 396 loop : -0.10 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 43 TYR 0.016 0.002 TYR O 50 PHE 0.004 0.001 PHE C 154 TRP 0.011 0.002 TRP C 86 HIS 0.001 0.000 HIS P 3 Details of bonding type rmsd covalent geometry : bond 0.00266 (23936) covalent geometry : angle 0.42129 (32223) hydrogen bonds : bond 0.04535 ( 1687) hydrogen bonds : angle 3.59821 ( 4914) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 460 time to evaluate : 1.048 Fit side-chains REVERT: A 77 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6885 (tp30) REVERT: B 43 GLU cc_start: 0.8197 (tt0) cc_final: 0.7988 (tp30) REVERT: C 43 GLU cc_start: 0.8178 (tt0) cc_final: 0.7973 (tm-30) REVERT: D 69 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: D 76 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8289 (mt) REVERT: E 23 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6545 (tp30) REVERT: F 20 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7712 (mp0) REVERT: F 23 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6614 (tp30) REVERT: G 20 GLU cc_start: 0.7894 (mp0) cc_final: 0.7694 (pm20) REVERT: G 51 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8304 (mpt180) REVERT: G 58 GLU cc_start: 0.7648 (tt0) cc_final: 0.7324 (pt0) REVERT: H 20 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7746 (mp0) REVERT: H 23 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6375 (tp30) REVERT: I 29 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8149 (mm-30) REVERT: I 75 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8131 (mppt) REVERT: I 77 GLU cc_start: 0.7642 (tp30) cc_final: 0.7348 (tm-30) REVERT: J 82 GLU cc_start: 0.7747 (pm20) cc_final: 0.7350 (pp20) REVERT: J 95 MET cc_start: 0.8013 (mtp) cc_final: 0.7714 (ttp) REVERT: K 95 MET cc_start: 0.8126 (mtp) cc_final: 0.7867 (ttm) REVERT: K 116 ASP cc_start: 0.8867 (m-30) cc_final: 0.8563 (m-30) REVERT: L 47 TYR cc_start: 0.8839 (m-80) cc_final: 0.8363 (m-80) REVERT: L 50 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7155 (mm-30) REVERT: L 69 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: L 73 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8219 (tttt) REVERT: P 39 ASP cc_start: 0.8409 (m-30) cc_final: 0.8122 (m-30) REVERT: P 105 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8712 (tm-30) REVERT: R 29 GLU cc_start: 0.8452 (tt0) cc_final: 0.7954 (mm-30) REVERT: S 97 MET cc_start: 0.7929 (mtp) cc_final: 0.7529 (mtm) REVERT: U 23 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6442 (tp30) REVERT: V 20 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7786 (mp0) REVERT: W 58 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7164 (tp30) REVERT: X 15 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7235 (mt-10) REVERT: X 20 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: X 50 TYR cc_start: 0.9194 (p90) cc_final: 0.8843 (p90) REVERT: X 51 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8347 (mpt180) REVERT: X 98 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7532 (mt-10) outliers start: 41 outliers final: 19 residues processed: 474 average time/residue: 0.9766 time to fit residues: 509.2725 Evaluate side-chains 483 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 449 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 7 GLU Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain R residue 64 TYR Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain U residue 7 GLU Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain W residue 7 GLU Chi-restraints excluded: chain W residue 58 GLU Chi-restraints excluded: chain X residue 20 GLU Chi-restraints excluded: chain X residue 51 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 59 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.132194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.104112 restraints weight = 23787.532| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.46 r_work: 0.2841 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23936 Z= 0.177 Angle : 0.489 6.025 32223 Z= 0.261 Chirality : 0.041 0.136 3852 Planarity : 0.004 0.039 4091 Dihedral : 3.568 13.134 3339 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.46 % Allowed : 15.08 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.11 (0.14), residues: 3015 helix: 3.04 (0.11), residues: 1749 sheet: 2.29 (0.21), residues: 396 loop : -0.20 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 43 TYR 0.020 0.002 TYR O 50 PHE 0.005 0.001 PHE C 154 TRP 0.007 0.001 TRP T 86 HIS 0.002 0.001 HIS R 46 Details of bonding type rmsd covalent geometry : bond 0.00421 (23936) covalent geometry : angle 0.48944 (32223) hydrogen bonds : bond 0.05478 ( 1687) hydrogen bonds : angle 3.85042 ( 4914) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 483 time to evaluate : 1.026 Fit side-chains REVERT: A 77 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6905 (tp30) REVERT: B 29 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8210 (mt-10) REVERT: B 43 GLU cc_start: 0.8128 (tt0) cc_final: 0.7763 (tp30) REVERT: B 114 LYS cc_start: 0.8636 (mmtm) cc_final: 0.8398 (mmtp) REVERT: C 43 GLU cc_start: 0.8215 (tt0) cc_final: 0.7986 (tm-30) REVERT: C 50 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7297 (tp30) REVERT: D 25 SER cc_start: 0.8221 (m) cc_final: 0.7964 (p) REVERT: D 69 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: D 76 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8310 (mt) REVERT: D 114 LYS cc_start: 0.8338 (mmtt) cc_final: 0.8074 (mmtp) REVERT: E 23 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6619 (tp30) REVERT: F 20 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7712 (mp0) REVERT: F 23 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6529 (tp30) REVERT: G 20 GLU cc_start: 0.7925 (mp0) cc_final: 0.7702 (pm20) REVERT: G 51 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8290 (mpt180) REVERT: G 58 GLU cc_start: 0.7708 (tt0) cc_final: 0.7302 (pt0) REVERT: H 20 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7666 (mp0) REVERT: H 23 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6344 (tp30) REVERT: I 75 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7999 (mppt) REVERT: I 77 GLU cc_start: 0.7566 (tp30) cc_final: 0.7326 (tm-30) REVERT: I 97 MET cc_start: 0.7940 (mtp) cc_final: 0.7548 (mtm) REVERT: J 82 GLU cc_start: 0.7710 (pm20) cc_final: 0.7345 (pp20) REVERT: J 95 MET cc_start: 0.8037 (mtp) cc_final: 0.7578 (mtt) REVERT: K 29 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8170 (mt-10) REVERT: K 95 MET cc_start: 0.8061 (mtp) cc_final: 0.7771 (ttm) REVERT: K 116 ASP cc_start: 0.8918 (m-30) cc_final: 0.8649 (m-30) REVERT: L 47 TYR cc_start: 0.8920 (m-80) cc_final: 0.8531 (m-80) REVERT: L 50 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7178 (mm-30) REVERT: L 65 LYS cc_start: 0.8444 (mtpt) cc_final: 0.7750 (tptm) REVERT: L 69 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: L 73 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8237 (tttt) REVERT: L 96 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7331 (mt-10) REVERT: O 20 GLU cc_start: 0.7975 (mp0) cc_final: 0.7499 (pm20) REVERT: O 24 GLN cc_start: 0.8244 (mt0) cc_final: 0.8005 (mt0) REVERT: P 39 ASP cc_start: 0.8416 (m-30) cc_final: 0.8117 (m-30) REVERT: P 105 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8745 (tm-30) REVERT: R 29 GLU cc_start: 0.8382 (tt0) cc_final: 0.7860 (mm-30) REVERT: S 97 MET cc_start: 0.8068 (mtp) cc_final: 0.7672 (mtm) REVERT: U 23 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6317 (tp30) REVERT: V 20 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7809 (mp0) REVERT: W 58 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7129 (tp30) REVERT: X 7 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: X 15 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7219 (mt-10) REVERT: X 20 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: X 50 TYR cc_start: 0.9253 (p90) cc_final: 0.8972 (p90) REVERT: X 98 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7536 (mt-10) outliers start: 36 outliers final: 15 residues processed: 492 average time/residue: 0.9787 time to fit residues: 529.9564 Evaluate side-chains 510 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 480 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain W residue 58 GLU Chi-restraints excluded: chain X residue 7 GLU Chi-restraints excluded: chain X residue 20 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 55 optimal weight: 0.3980 chunk 228 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 260 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 24 GLN W 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.132494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.104217 restraints weight = 23677.214| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.46 r_work: 0.2877 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23936 Z= 0.156 Angle : 0.468 5.912 32223 Z= 0.251 Chirality : 0.040 0.134 3852 Planarity : 0.003 0.035 4091 Dihedral : 3.519 12.903 3339 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.41 % Allowed : 14.83 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.12 (0.14), residues: 3015 helix: 3.05 (0.11), residues: 1749 sheet: 2.29 (0.21), residues: 396 loop : -0.20 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 43 TYR 0.020 0.002 TYR O 50 PHE 0.004 0.001 PHE C 154 TRP 0.008 0.002 TRP C 86 HIS 0.002 0.001 HIS R 46 Details of bonding type rmsd covalent geometry : bond 0.00366 (23936) covalent geometry : angle 0.46771 (32223) hydrogen bonds : bond 0.05152 ( 1687) hydrogen bonds : angle 3.77967 ( 4914) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10821.78 seconds wall clock time: 185 minutes 3.68 seconds (11103.68 seconds total)