Starting phenix.real_space_refine on Fri Jun 20 01:38:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vdz_43157/06_2025/8vdz_43157.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vdz_43157/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vdz_43157/06_2025/8vdz_43157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vdz_43157/06_2025/8vdz_43157.map" model { file = "/net/cci-nas-00/data/ceres_data/8vdz_43157/06_2025/8vdz_43157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vdz_43157/06_2025/8vdz_43157.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.40, per 1000 atoms: 0.69 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: 5.91 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 2.52 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: 10.54 Time building geometry restraints manager: 6.49 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: 55.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 57.190 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:16.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.310 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.012 0.002 TRP A 86 HIS 0.002 0.000 HIS O 3 PHE 0.004 0.001 PHE R 40 TYR 0.023 0.002 TYR R 64 ARG 0.003 0.000 ARG E 59 Details of bonding type rmsd hydrogen bonds : bond 0.10435 ( 1687) hydrogen bonds : angle 4.40574 ( 4914) covalent geometry : bond 0.00274 (23936) covalent geometry : angle 0.46154 (32223) *********************** 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 : 3.049 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: 0.7723 (ttm) REVERT: K 116 ASP cc_start: 0.8439 (m-30) cc_final: 0.8043 (m-30) REVERT: O 48 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7315 (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: 0.7733 (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: 1.9360 time to fit residues: 1292.3915 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 : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 230 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 266 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.134796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.107115 restraints weight = 23854.688| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.44 r_work: 0.2877 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1040 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= 0.136 Angle : 0.435 5.662 32223 Z= 0.237 Chirality : 0.039 0.135 3852 Planarity : 0.003 0.031 4091 Dihedral : 3.476 13.553 3339 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.66 % Allowed : 8.08 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.14), residues: 3015 helix: 3.11 (0.11), residues: 1776 sheet: 2.35 (0.22), residues: 396 loop : 0.09 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 86 HIS 0.002 0.001 HIS F 63 PHE 0.004 0.001 PHE C 154 TYR 0.014 0.002 TYR X 61 ARG 0.003 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.04998 ( 1687) hydrogen bonds : angle 3.85103 ( 4914) covalent geometry : bond 0.00307 (23936) covalent geometry : angle 0.43530 (32223) *********************** 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 529 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 488 time to evaluate : 2.850 Fit side-chains REVERT: A 29 GLU cc_start: 0.8414 (tt0) cc_final: 0.7994 (mt-10) REVERT: B 43 GLU cc_start: 0.8006 (tt0) cc_final: 0.7756 (tp30) REVERT: B 135 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: C 43 GLU cc_start: 0.8178 (tt0) cc_final: 0.7939 (tm-30) REVERT: C 50 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7336 (tp30) REVERT: C 69 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8250 (tm-30) REVERT: D 65 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8397 (tttm) REVERT: E 105 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8663 (tt0) REVERT: F 20 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7661 (mp0) REVERT: G 20 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: H 20 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7434 (mp0) REVERT: I 36 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: I 77 GLU cc_start: 0.7658 (tp30) cc_final: 0.7366 (tp30) REVERT: J 82 GLU cc_start: 0.7620 (pm20) cc_final: 0.7318 (pp20) REVERT: K 95 MET cc_start: 0.8128 (mtp) cc_final: 0.7833 (ttm) REVERT: K 116 ASP cc_start: 0.8808 (m-30) cc_final: 0.8540 (m-30) REVERT: L 47 TYR cc_start: 0.8804 (m-80) cc_final: 0.8461 (m-80) REVERT: L 65 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7818 (mmtm) REVERT: L 73 LYS cc_start: 0.8526 (ttpt) cc_final: 0.8123 (tttt) REVERT: M 15 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7300 (mm-30) REVERT: O 48 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8010 (tp30) REVERT: P 39 ASP cc_start: 0.8334 (m-30) cc_final: 0.8062 (m-30) REVERT: R 116 ASP cc_start: 0.8770 (m-30) cc_final: 0.8457 (m-30) REVERT: S 97 MET cc_start: 0.7859 (mtp) cc_final: 0.7559 (mtm) REVERT: S 114 LYS cc_start: 0.8384 (mmtt) cc_final: 0.8164 (mmtp) REVERT: W 23 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7407 (mm-30) REVERT: X 20 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7790 (mt-10) REVERT: X 98 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7436 (mt-10) outliers start: 41 outliers final: 5 residues processed: 504 average time/residue: 1.9026 time to fit residues: 1056.5443 Evaluate side-chains 487 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 473 time to evaluate : 2.890 ------------------------------------------------------------------------------- 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 D residue 65 LYS Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 97 MET 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 141 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 281 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 259 optimal weight: 0.9990 chunk 264 optimal weight: 6.9990 chunk 282 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 X 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.133940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.105993 restraints weight = 23675.534| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.45 r_work: 0.2878 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1236 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= 0.133 Angle : 0.422 5.808 32223 Z= 0.229 Chirality : 0.039 0.133 3852 Planarity : 0.003 0.032 4091 Dihedral : 3.417 12.961 3339 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 1.82 % Allowed : 9.98 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.14), residues: 3015 helix: 3.13 (0.11), residues: 1776 sheet: 2.30 (0.22), residues: 396 loop : 0.06 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 86 HIS 0.002 0.001 HIS N 63 PHE 0.005 0.001 PHE C 154 TYR 0.013 0.002 TYR O 61 ARG 0.004 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.04893 ( 1687) hydrogen bonds : angle 3.75171 ( 4914) covalent geometry : bond 0.00299 (23936) covalent geometry : angle 0.42225 (32223) *********************** 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 544 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 499 time to evaluate : 2.460 Fit side-chains REVERT: A 29 GLU cc_start: 0.8481 (tt0) cc_final: 0.8273 (mt-10) REVERT: A 77 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6968 (tp30) REVERT: B 43 GLU cc_start: 0.8086 (tt0) cc_final: 0.7786 (tp30) REVERT: C 43 GLU cc_start: 0.8180 (tt0) cc_final: 0.7961 (tm-30) REVERT: C 50 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7269 (tp30) REVERT: C 69 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: D 114 LYS cc_start: 0.8275 (mmtt) cc_final: 0.8047 (mmtp) REVERT: D 135 GLU cc_start: 0.8238 (mt-10) cc_final: 0.8030 (mt-10) REVERT: E 105 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8714 (tt0) REVERT: F 20 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7640 (mp0) REVERT: G 58 GLU cc_start: 0.7569 (tt0) cc_final: 0.7327 (tt0) REVERT: G 59 ARG cc_start: 0.8901 (mtt180) cc_final: 0.8641 (mtt180) REVERT: H 20 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7617 (mp0) REVERT: H 23 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6390 (tp30) REVERT: I 29 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8073 (mm-30) REVERT: I 36 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: I 73 LYS cc_start: 0.8698 (tttm) cc_final: 0.8462 (tttm) REVERT: I 75 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8158 (mptt) REVERT: I 77 GLU cc_start: 0.7617 (tp30) cc_final: 0.7292 (tp30) REVERT: J 82 GLU cc_start: 0.7622 (pm20) cc_final: 0.7335 (pp20) REVERT: K 95 MET cc_start: 0.8057 (mtp) cc_final: 0.7755 (ttm) REVERT: K 116 ASP cc_start: 0.8867 (m-30) cc_final: 0.8587 (m-30) REVERT: L 47 TYR cc_start: 0.8819 (m-80) cc_final: 0.8531 (m-80) REVERT: L 50 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7167 (mm-30) REVERT: L 73 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8171 (tttt) REVERT: M 15 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7270 (mm-30) REVERT: O 48 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8006 (tp30) REVERT: P 39 ASP cc_start: 0.8370 (m-30) cc_final: 0.8089 (m-30) REVERT: R 116 ASP cc_start: 0.8827 (m-30) cc_final: 0.8476 (m-30) REVERT: S 97 MET cc_start: 0.7845 (mtp) cc_final: 0.7496 (mtm) REVERT: T 114 LYS cc_start: 0.8649 (mmtp) cc_final: 0.8373 (mmtt) REVERT: X 20 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: X 50 TYR cc_start: 0.9160 (p90) cc_final: 0.8908 (p90) REVERT: X 51 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8281 (mpt180) REVERT: X 98 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7449 (mt-10) outliers start: 45 outliers final: 8 residues processed: 510 average time/residue: 1.8878 time to fit residues: 1060.0881 Evaluate side-chains 488 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 470 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain B residue 69 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 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 29 GLU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain M residue 15 GLU Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain X residue 20 GLU Chi-restraints excluded: chain X residue 51 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 133 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 276 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 X 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.134087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.105921 restraints weight = 23881.468| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.48 r_work: 0.2831 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23936 Z= 0.134 Angle : 0.421 5.833 32223 Z= 0.227 Chirality : 0.039 0.138 3852 Planarity : 0.003 0.034 4091 Dihedral : 3.397 12.817 3339 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 2.26 % Allowed : 11.12 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.14), residues: 3015 helix: 3.14 (0.11), residues: 1770 sheet: 2.28 (0.21), residues: 396 loop : 0.00 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 86 HIS 0.002 0.001 HIS P 3 PHE 0.005 0.001 PHE C 154 TYR 0.013 0.002 TYR O 61 ARG 0.004 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 1687) hydrogen bonds : angle 3.73131 ( 4914) covalent geometry : bond 0.00305 (23936) covalent geometry : angle 0.42103 (32223) *********************** 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 540 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 484 time to evaluate : 2.884 Fit side-chains REVERT: A 29 GLU cc_start: 0.8494 (tt0) cc_final: 0.8289 (mt-10) REVERT: A 77 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6945 (tp30) REVERT: B 43 GLU cc_start: 0.8141 (tt0) cc_final: 0.7827 (tp30) REVERT: C 43 GLU cc_start: 0.8204 (tt0) cc_final: 0.7991 (tm-30) REVERT: C 50 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7275 (tp30) REVERT: D 69 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: D 76 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8295 (mt) REVERT: D 114 LYS cc_start: 0.8252 (mmtt) cc_final: 0.8027 (mmtp) REVERT: E 23 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6581 (tp30) REVERT: E 105 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8714 (tt0) REVERT: F 20 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7632 (mp0) REVERT: H 20 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7628 (mp0) REVERT: H 23 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6537 (tp30) REVERT: I 73 LYS cc_start: 0.8727 (tttm) cc_final: 0.8503 (tttm) REVERT: I 75 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8042 (mptt) REVERT: I 77 GLU cc_start: 0.7576 (tp30) cc_final: 0.7300 (tp30) REVERT: J 82 GLU cc_start: 0.7695 (pm20) cc_final: 0.7363 (pp20) REVERT: K 95 MET cc_start: 0.8046 (mtp) cc_final: 0.7748 (ttm) REVERT: K 116 ASP cc_start: 0.8871 (m-30) cc_final: 0.8591 (m-30) REVERT: K 135 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: L 47 TYR cc_start: 0.8826 (m-80) cc_final: 0.8375 (m-80) REVERT: L 50 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7203 (mm-30) REVERT: L 73 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8145 (tttt) REVERT: M 15 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7252 (mm-30) REVERT: M 23 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6484 (tp30) REVERT: M 51 ARG cc_start: 0.8613 (mpt180) cc_final: 0.8387 (mpt180) REVERT: M 58 GLU cc_start: 0.7692 (tt0) cc_final: 0.7480 (tt0) REVERT: O 24 GLN cc_start: 0.8293 (mt0) cc_final: 0.8040 (mt0) REVERT: O 48 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8026 (tp30) REVERT: P 39 ASP cc_start: 0.8400 (m-30) cc_final: 0.8118 (m-30) REVERT: R 29 GLU cc_start: 0.8429 (tt0) cc_final: 0.7935 (mm-30) REVERT: R 116 ASP cc_start: 0.8835 (m-30) cc_final: 0.8489 (m-30) REVERT: S 97 MET cc_start: 0.7889 (mtp) cc_final: 0.7537 (mtm) REVERT: T 77 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6836 (tp30) REVERT: T 114 LYS cc_start: 0.8639 (mmtp) cc_final: 0.8381 (mmtt) REVERT: U 23 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6466 (tp30) REVERT: V 20 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7744 (mp0) REVERT: W 23 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7367 (mm-30) REVERT: W 58 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7172 (tp30) REVERT: X 20 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: X 50 TYR cc_start: 0.9188 (p90) cc_final: 0.8881 (p90) REVERT: X 51 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8293 (mpt180) REVERT: X 98 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7508 (mt-10) outliers start: 56 outliers final: 13 residues processed: 496 average time/residue: 2.3348 time to fit residues: 1278.0827 Evaluate side-chains 499 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 470 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain B residue 69 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 H residue 7 GLU Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain K residue 135 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain M residue 15 GLU Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 77 GLU Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 54 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 266 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 X 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.132110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.103965 restraints weight = 23831.402| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.46 r_work: 0.2839 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1453 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= 0.166 Angle : 0.456 5.842 32223 Z= 0.244 Chirality : 0.040 0.137 3852 Planarity : 0.004 0.044 4091 Dihedral : 3.537 12.996 3339 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 3.03 % Allowed : 10.99 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.14), residues: 3015 helix: 3.10 (0.11), residues: 1752 sheet: 2.24 (0.21), residues: 396 loop : -0.10 (0.19), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP T 86 HIS 0.002 0.001 HIS R 46 PHE 0.005 0.001 PHE F 35 TYR 0.015 0.002 TYR O 50 ARG 0.006 0.000 ARG V 43 Details of bonding type rmsd hydrogen bonds : bond 0.05384 ( 1687) hydrogen bonds : angle 3.83953 ( 4914) covalent geometry : bond 0.00390 (23936) covalent geometry : angle 0.45586 (32223) *********************** 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 574 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 499 time to evaluate : 2.881 Fit side-chains REVERT: A 29 GLU cc_start: 0.8476 (tt0) cc_final: 0.8041 (mm-30) REVERT: A 77 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6998 (tp30) REVERT: B 43 GLU cc_start: 0.8132 (tt0) cc_final: 0.7755 (tp30) REVERT: B 114 LYS cc_start: 0.8556 (mttm) cc_final: 0.8345 (mmtm) REVERT: C 43 GLU cc_start: 0.8210 (tt0) cc_final: 0.7963 (tm-30) REVERT: C 50 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7288 (tp30) REVERT: D 25 SER cc_start: 0.8245 (m) cc_final: 0.7973 (p) REVERT: D 69 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7566 (tm-30) REVERT: D 76 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8319 (mt) REVERT: D 114 LYS cc_start: 0.8306 (mmtt) cc_final: 0.8071 (mmtp) REVERT: E 23 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6523 (tp30) REVERT: F 20 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7694 (mp0) REVERT: G 58 GLU cc_start: 0.7622 (tt0) cc_final: 0.7391 (tt0) REVERT: H 20 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7642 (mp0) REVERT: H 23 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6415 (tp30) REVERT: I 73 LYS cc_start: 0.8813 (tttm) cc_final: 0.8604 (tttm) REVERT: I 75 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8148 (mppt) REVERT: I 77 GLU cc_start: 0.7669 (tp30) cc_final: 0.7351 (tm-30) REVERT: J 82 GLU cc_start: 0.7737 (pm20) cc_final: 0.7387 (pp20) REVERT: J 114 LYS cc_start: 0.8540 (mmtt) cc_final: 0.8225 (mmtp) REVERT: K 29 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8156 (mt-10) REVERT: K 95 MET cc_start: 0.8062 (mtp) cc_final: 0.7750 (ttm) REVERT: K 116 ASP cc_start: 0.8926 (m-30) cc_final: 0.8663 (m-30) REVERT: K 135 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: L 47 TYR cc_start: 0.8902 (m-80) cc_final: 0.8527 (m-80) REVERT: L 69 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: L 73 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8220 (tttt) REVERT: M 15 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: M 51 ARG cc_start: 0.8607 (mpt180) cc_final: 0.8394 (mpt180) REVERT: O 20 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: O 24 GLN cc_start: 0.8277 (mt0) cc_final: 0.8024 (mt0) REVERT: P 39 ASP cc_start: 0.8426 (m-30) cc_final: 0.8134 (m-30) REVERT: P 105 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8689 (tm-30) REVERT: R 29 GLU cc_start: 0.8371 (tt0) cc_final: 0.7902 (mm-30) REVERT: R 116 ASP cc_start: 0.8867 (m-30) cc_final: 0.8569 (m-30) REVERT: S 97 MET cc_start: 0.7982 (mtp) cc_final: 0.7599 (mtm) REVERT: S 135 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7920 (mt-10) REVERT: T 114 LYS cc_start: 0.8709 (mmtp) cc_final: 0.8474 (mmtt) REVERT: U 23 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6301 (tp30) REVERT: V 20 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7801 (mp0) REVERT: V 51 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8122 (mpt180) REVERT: W 58 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7181 (tp30) REVERT: X 20 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: X 50 TYR cc_start: 0.9225 (p90) cc_final: 0.8936 (p90) REVERT: X 51 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8312 (mpt180) REVERT: X 58 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7266 (tt0) REVERT: X 98 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7563 (mt-10) outliers start: 75 outliers final: 17 residues processed: 522 average time/residue: 1.8925 time to fit residues: 1089.6330 Evaluate side-chains 528 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 493 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain B residue 69 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 F residue 54 THR 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 135 GLU Chi-restraints excluded: chain L residue 65 LYS 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 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 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 23 GLU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain V residue 51 ARG 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 51 ARG Chi-restraints excluded: chain X residue 58 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 103 optimal weight: 0.0070 chunk 157 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 240 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 X 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.134874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.106946 restraints weight = 23635.439| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.45 r_work: 0.2896 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23936 Z= 0.111 Angle : 0.401 5.857 32223 Z= 0.219 Chirality : 0.038 0.132 3852 Planarity : 0.003 0.031 4091 Dihedral : 3.289 13.148 3339 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.22 % Allowed : 11.96 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.14), residues: 3015 helix: 3.23 (0.11), residues: 1776 sheet: 2.30 (0.21), residues: 396 loop : -0.06 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 86 HIS 0.001 0.000 HIS P 3 PHE 0.004 0.001 PHE C 154 TYR 0.013 0.002 TYR E 61 ARG 0.003 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 1687) hydrogen bonds : angle 3.58071 ( 4914) covalent geometry : bond 0.00240 (23936) covalent geometry : angle 0.40104 (32223) *********************** 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 544 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 489 time to evaluate : 2.545 Fit side-chains REVERT: A 65 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7714 (tptp) REVERT: A 77 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6837 (tp30) REVERT: B 43 GLU cc_start: 0.8132 (tt0) cc_final: 0.7830 (tp30) REVERT: D 69 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: D 76 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8246 (mt) REVERT: D 114 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7987 (mmtp) REVERT: E 23 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6481 (tp30) REVERT: F 20 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7612 (mp0) REVERT: H 20 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7606 (mp0) REVERT: H 23 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6420 (tp30) REVERT: I 73 LYS cc_start: 0.8769 (tttm) cc_final: 0.8556 (tttm) REVERT: I 75 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8032 (mppt) REVERT: I 77 GLU cc_start: 0.7463 (tp30) cc_final: 0.7184 (tm-30) REVERT: J 29 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7910 (mm-30) REVERT: J 82 GLU cc_start: 0.7638 (pm20) cc_final: 0.7282 (pp20) REVERT: K 95 MET cc_start: 0.8116 (mtp) cc_final: 0.7836 (ttm) REVERT: K 116 ASP cc_start: 0.8825 (m-30) cc_final: 0.8504 (m-30) REVERT: L 47 TYR cc_start: 0.8786 (m-80) cc_final: 0.8382 (m-80) REVERT: L 50 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7183 (mm-30) REVERT: L 69 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: L 73 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8190 (tttt) REVERT: M 51 ARG cc_start: 0.8564 (mpt180) cc_final: 0.8344 (mpt180) REVERT: O 20 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: O 58 GLU cc_start: 0.7145 (tt0) cc_final: 0.6917 (tt0) REVERT: P 39 ASP cc_start: 0.8389 (m-30) cc_final: 0.8101 (m-30) REVERT: P 105 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8706 (tm-30) REVERT: R 29 GLU cc_start: 0.8376 (tt0) cc_final: 0.7886 (mm-30) REVERT: S 97 MET cc_start: 0.7851 (mtp) cc_final: 0.7448 (mtm) REVERT: T 77 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6796 (tp30) REVERT: U 23 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6371 (tp30) REVERT: V 20 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7693 (mp0) REVERT: W 58 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7184 (tp30) REVERT: X 15 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7317 (mt-10) REVERT: X 20 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: X 50 TYR cc_start: 0.9133 (p90) cc_final: 0.8798 (p90) REVERT: X 51 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8310 (mpt180) REVERT: X 98 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7456 (mt-10) outliers start: 55 outliers final: 10 residues processed: 503 average time/residue: 2.0361 time to fit residues: 1124.4148 Evaluate side-chains 478 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 451 time to evaluate : 2.583 ------------------------------------------------------------------------------- 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 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 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 O residue 20 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 77 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 187 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 77 optimal weight: 0.0050 chunk 60 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 24 GLN X 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 = 0.132268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.104259 restraints weight = 23981.556| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.47 r_work: 0.2851 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23936 Z= 0.178 Angle : 0.477 5.845 32223 Z= 0.254 Chirality : 0.040 0.138 3852 Planarity : 0.004 0.042 4091 Dihedral : 3.575 13.009 3339 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.14 % Allowed : 13.10 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.14), residues: 3015 helix: 3.02 (0.11), residues: 1758 sheet: 2.26 (0.21), residues: 396 loop : -0.21 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 86 HIS 0.003 0.001 HIS R 46 PHE 0.005 0.001 PHE C 154 TYR 0.016 0.002 TYR O 50 ARG 0.007 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.05540 ( 1687) hydrogen bonds : angle 3.87178 ( 4914) covalent geometry : bond 0.00424 (23936) covalent geometry : angle 0.47678 (32223) *********************** 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 545 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 492 time to evaluate : 2.717 Fit side-chains REVERT: A 77 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6962 (tp30) REVERT: B 43 GLU cc_start: 0.8289 (tt0) cc_final: 0.7911 (tp30) REVERT: B 114 LYS cc_start: 0.8589 (mttm) cc_final: 0.8368 (mmtm) REVERT: D 25 SER cc_start: 0.8284 (m) cc_final: 0.8040 (p) REVERT: D 69 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: D 76 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8361 (mt) REVERT: D 114 LYS cc_start: 0.8408 (mmtt) cc_final: 0.8178 (mmtp) REVERT: E 23 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6538 (tp30) REVERT: F 20 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7781 (mp0) REVERT: H 20 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7734 (mp0) REVERT: H 23 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6440 (tp30) REVERT: I 36 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: I 75 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8004 (mppt) REVERT: I 77 GLU cc_start: 0.7641 (tp30) cc_final: 0.7300 (tm-30) REVERT: J 29 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8045 (mm-30) REVERT: J 82 GLU cc_start: 0.7763 (pm20) cc_final: 0.7407 (pp20) REVERT: K 29 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8221 (mt-10) REVERT: K 95 MET cc_start: 0.8085 (mtp) cc_final: 0.7768 (ttm) REVERT: K 116 ASP cc_start: 0.8951 (m-30) cc_final: 0.8700 (m-30) REVERT: K 135 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: L 47 TYR cc_start: 0.8945 (m-80) cc_final: 0.8491 (m-80) REVERT: L 69 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: L 73 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8280 (tttt) REVERT: L 96 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7472 (mt-10) REVERT: M 51 ARG cc_start: 0.8609 (mpt180) cc_final: 0.8393 (mpt180) REVERT: O 20 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: O 24 GLN cc_start: 0.8322 (mt0) cc_final: 0.8038 (mt0) REVERT: P 39 ASP cc_start: 0.8477 (m-30) cc_final: 0.8189 (m-30) REVERT: P 105 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8684 (tm-30) REVERT: R 29 GLU cc_start: 0.8429 (tt0) cc_final: 0.7935 (mm-30) REVERT: S 97 MET cc_start: 0.8071 (mtp) cc_final: 0.7680 (mtm) REVERT: T 77 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6823 (tp30) REVERT: T 114 LYS cc_start: 0.8739 (mmtp) cc_final: 0.8518 (mmtt) REVERT: U 23 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6371 (tp30) REVERT: V 20 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7888 (mp0) REVERT: W 51 ARG cc_start: 0.8464 (mpt180) cc_final: 0.8251 (mpt180) REVERT: W 58 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7156 (tp30) REVERT: X 15 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7334 (mt-10) REVERT: X 20 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: X 50 TYR cc_start: 0.9255 (p90) cc_final: 0.8988 (p90) REVERT: X 51 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8329 (mpt180) outliers start: 53 outliers final: 15 residues processed: 506 average time/residue: 1.8979 time to fit residues: 1058.2888 Evaluate side-chains 511 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 478 time to evaluate : 2.658 ------------------------------------------------------------------------------- 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 F residue 54 THR 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 36 GLU 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 135 GLU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain O residue 20 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 T residue 77 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 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 227 optimal weight: 3.9990 chunk 249 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 chunk 153 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 193 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 X 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.135160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.107167 restraints weight = 23849.875| |-----------------------------------------------------------------------------| r_work (start): 0.3043 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: 3.79 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1548 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 : 0.413 5.805 32223 Z= 0.225 Chirality : 0.038 0.132 3852 Planarity : 0.003 0.031 4091 Dihedral : 3.327 13.126 3339 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 1.78 % Allowed : 13.82 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.14), residues: 3015 helix: 3.18 (0.11), residues: 1770 sheet: 2.28 (0.21), residues: 396 loop : -0.12 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 86 HIS 0.001 0.000 HIS P 3 PHE 0.004 0.001 PHE R 154 TYR 0.014 0.002 TYR O 50 ARG 0.003 0.000 ARG V 43 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 1687) hydrogen bonds : angle 3.60952 ( 4914) covalent geometry : bond 0.00255 (23936) covalent geometry : angle 0.41321 (32223) *********************** 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 514 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 470 time to evaluate : 2.719 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6850 (tp30) REVERT: B 43 GLU cc_start: 0.8176 (tt0) cc_final: 0.7827 (tp30) REVERT: B 114 LYS cc_start: 0.8442 (mttm) cc_final: 0.8239 (mttm) REVERT: D 69 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: D 76 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8249 (mt) REVERT: D 114 LYS cc_start: 0.8239 (mmtt) cc_final: 0.8021 (mmtp) REVERT: E 23 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6447 (tp30) REVERT: F 20 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7621 (mp0) REVERT: F 23 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6438 (tp30) REVERT: G 20 GLU cc_start: 0.7918 (mp0) cc_final: 0.7654 (pm20) REVERT: G 58 GLU cc_start: 0.7650 (tt0) cc_final: 0.7294 (pt0) REVERT: H 20 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7668 (mp0) REVERT: H 23 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6236 (tp30) REVERT: I 75 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7931 (mppt) REVERT: I 77 GLU cc_start: 0.7613 (tp30) cc_final: 0.7304 (tm-30) REVERT: J 82 GLU cc_start: 0.7658 (pm20) cc_final: 0.7282 (pp20) REVERT: K 29 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8107 (mt-10) REVERT: K 95 MET cc_start: 0.8088 (mtp) cc_final: 0.7823 (ttm) REVERT: K 116 ASP cc_start: 0.8830 (m-30) cc_final: 0.8525 (m-30) REVERT: L 47 TYR cc_start: 0.8861 (m-80) cc_final: 0.8416 (m-80) REVERT: L 65 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7779 (tptp) REVERT: L 69 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: L 73 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8192 (tttt) REVERT: M 15 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7182 (mm-30) REVERT: M 51 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8288 (mpt180) REVERT: N 90 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7142 (mm-30) REVERT: O 20 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: P 39 ASP cc_start: 0.8410 (m-30) cc_final: 0.8116 (m-30) REVERT: P 105 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8498 (tm-30) REVERT: R 29 GLU cc_start: 0.8374 (tt0) cc_final: 0.7827 (mm-30) REVERT: S 97 MET cc_start: 0.7910 (mtp) cc_final: 0.7502 (mtm) REVERT: T 77 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6763 (tp30) REVERT: U 23 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6331 (tp30) REVERT: V 20 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7709 (mp0) REVERT: W 58 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7123 (tp30) REVERT: X 15 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7207 (mt-10) REVERT: X 20 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7701 (mt-10) REVERT: X 50 TYR cc_start: 0.9126 (p90) cc_final: 0.8774 (p90) REVERT: X 51 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8335 (mpt180) REVERT: X 98 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7488 (mt-10) outliers start: 44 outliers final: 12 residues processed: 481 average time/residue: 2.0422 time to fit residues: 1080.4131 Evaluate side-chains 497 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 466 time to evaluate : 2.826 ------------------------------------------------------------------------------- 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 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 L residue 65 LYS 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 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 R residue 92 LEU Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 77 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 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 118 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 287 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 263 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 24 GLN X 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.134559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.106687 restraints weight = 23729.984| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.44 r_work: 0.2840 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 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 0.038 23936 Z= 0.124 Angle : 0.430 5.809 32223 Z= 0.233 Chirality : 0.039 0.133 3852 Planarity : 0.003 0.031 4091 Dihedral : 3.337 13.168 3339 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.54 % Allowed : 14.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.14), residues: 3015 helix: 3.19 (0.11), residues: 1770 sheet: 2.29 (0.21), residues: 396 loop : -0.14 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 86 HIS 0.001 0.001 HIS P 3 PHE 0.004 0.001 PHE R 154 TYR 0.014 0.002 TYR O 50 ARG 0.004 0.000 ARG V 43 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 1687) hydrogen bonds : angle 3.63452 ( 4914) covalent geometry : bond 0.00278 (23936) covalent geometry : angle 0.43018 (32223) *********************** 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 513 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 475 time to evaluate : 2.663 Fit side-chains REVERT: A 77 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6795 (tp30) REVERT: B 43 GLU cc_start: 0.8177 (tt0) cc_final: 0.7824 (tp30) REVERT: D 69 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: D 76 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8261 (mt) REVERT: D 114 LYS cc_start: 0.8242 (mmtt) cc_final: 0.8028 (mmtp) REVERT: E 23 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6496 (tp30) REVERT: F 20 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7621 (mp0) REVERT: G 20 GLU cc_start: 0.7971 (mp0) cc_final: 0.7642 (pm20) REVERT: G 58 GLU cc_start: 0.7622 (tt0) cc_final: 0.7256 (pt0) REVERT: H 20 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7707 (mp0) REVERT: H 23 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6330 (tp30) REVERT: I 36 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: I 75 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8013 (mptt) REVERT: I 77 GLU cc_start: 0.7722 (tp30) cc_final: 0.7339 (tm-30) REVERT: J 82 GLU cc_start: 0.7709 (pm20) cc_final: 0.7307 (pp20) REVERT: K 29 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8218 (mt-10) REVERT: K 95 MET cc_start: 0.8091 (mtp) cc_final: 0.7826 (ttm) REVERT: K 116 ASP cc_start: 0.8839 (m-30) cc_final: 0.8541 (m-30) REVERT: L 47 TYR cc_start: 0.8833 (m-80) cc_final: 0.8373 (m-80) REVERT: L 50 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7169 (mm-30) REVERT: L 65 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7802 (tptp) REVERT: L 69 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: L 73 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8184 (tttt) REVERT: M 51 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8316 (mpt180) REVERT: O 20 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: O 58 GLU cc_start: 0.7682 (tt0) cc_final: 0.7461 (tt0) REVERT: P 39 ASP cc_start: 0.8407 (m-30) cc_final: 0.8119 (m-30) REVERT: P 105 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8498 (tm-30) REVERT: R 29 GLU cc_start: 0.8389 (tt0) cc_final: 0.7859 (mm-30) REVERT: S 97 MET cc_start: 0.7909 (mtp) cc_final: 0.7510 (mtm) REVERT: T 77 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6781 (tp30) REVERT: U 23 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6374 (tp30) REVERT: V 20 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7718 (mp0) REVERT: W 58 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7136 (tp30) REVERT: X 15 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7181 (mt-10) REVERT: X 20 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: X 50 TYR cc_start: 0.9163 (p90) cc_final: 0.8815 (p90) REVERT: X 51 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8350 (mpt180) REVERT: X 98 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7527 (mt-10) outliers start: 38 outliers final: 14 residues processed: 487 average time/residue: 1.9821 time to fit residues: 1063.1993 Evaluate side-chains 494 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 462 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER 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 54 THR 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 36 GLU Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS 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 R residue 92 LEU Chi-restraints excluded: chain T residue 77 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 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 161 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 198 optimal weight: 0.5980 chunk 216 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 269 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 292 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 24 GLN X 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 = 0.131164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.103246 restraints weight = 24113.672| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.45 r_work: 0.2832 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23936 Z= 0.201 Angle : 0.510 5.992 32223 Z= 0.271 Chirality : 0.041 0.140 3852 Planarity : 0.004 0.044 4091 Dihedral : 3.667 13.137 3339 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.37 % Allowed : 14.79 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.14), residues: 3015 helix: 2.96 (0.11), residues: 1749 sheet: 2.24 (0.21), residues: 396 loop : -0.23 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 86 HIS 0.003 0.001 HIS R 46 PHE 0.005 0.001 PHE K 40 TYR 0.019 0.002 TYR O 50 ARG 0.007 0.001 ARG V 43 Details of bonding type rmsd hydrogen bonds : bond 0.05784 ( 1687) hydrogen bonds : angle 3.91789 ( 4914) covalent geometry : bond 0.00485 (23936) covalent geometry : angle 0.51028 (32223) ********************** 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 536 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 502 time to evaluate : 2.665 Fit side-chains REVERT: A 77 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6961 (tp30) REVERT: D 25 SER cc_start: 0.8268 (m) cc_final: 0.7985 (p) REVERT: D 69 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: D 76 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8327 (mt) REVERT: D 114 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8124 (mmtp) REVERT: E 23 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6442 (tp30) REVERT: F 20 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7660 (mp0) REVERT: G 58 GLU cc_start: 0.7720 (tt0) cc_final: 0.7313 (pt0) REVERT: H 20 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7725 (mp0) REVERT: H 23 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6396 (tp30) REVERT: I 75 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8030 (mppt) REVERT: I 77 GLU cc_start: 0.7739 (tp30) cc_final: 0.7365 (tm-30) REVERT: I 97 MET cc_start: 0.7949 (mtp) cc_final: 0.7548 (mtm) REVERT: J 38 THR cc_start: 0.8772 (m) cc_final: 0.8513 (p) REVERT: J 82 GLU cc_start: 0.7753 (pm20) cc_final: 0.7378 (pp20) REVERT: J 114 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8239 (mmtp) REVERT: K 29 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8127 (mt-10) REVERT: K 95 MET cc_start: 0.8063 (mtp) cc_final: 0.7747 (ttm) REVERT: K 116 ASP cc_start: 0.8923 (m-30) cc_final: 0.8688 (m-30) REVERT: L 47 TYR cc_start: 0.8951 (m-80) cc_final: 0.8585 (m-80) REVERT: L 69 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: L 73 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8231 (tttt) REVERT: L 96 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7376 (mt-10) REVERT: M 51 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8355 (mpt180) REVERT: N 54 THR cc_start: 0.8733 (p) cc_final: 0.8477 (p) REVERT: O 20 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: O 24 GLN cc_start: 0.8334 (mt0) cc_final: 0.8038 (mt0) REVERT: P 39 ASP cc_start: 0.8420 (m-30) cc_final: 0.8120 (m-30) REVERT: P 105 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8756 (tm-30) REVERT: R 29 GLU cc_start: 0.8371 (tt0) cc_final: 0.7881 (mm-30) REVERT: S 97 MET cc_start: 0.8089 (mtp) cc_final: 0.7716 (mtm) REVERT: T 77 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6865 (tp30) REVERT: U 23 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6324 (tp30) REVERT: V 20 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7843 (mp0) REVERT: W 58 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7126 (tp30) REVERT: X 20 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: X 50 TYR cc_start: 0.9245 (p90) cc_final: 0.9042 (p90) REVERT: X 51 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8268 (mpt180) outliers start: 34 outliers final: 13 residues processed: 514 average time/residue: 1.9117 time to fit residues: 1081.4865 Evaluate side-chains 524 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 495 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER 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 54 THR 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 K residue 82 GLU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS 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 92 LEU Chi-restraints excluded: chain T residue 77 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 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 241 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 268 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 X 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.133488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.105646 restraints weight = 23802.014| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.44 r_work: 0.2861 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1612 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= 0.136 Angle : 0.449 5.893 32223 Z= 0.242 Chirality : 0.039 0.134 3852 Planarity : 0.003 0.032 4091 Dihedral : 3.466 13.028 3339 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 1.46 % Allowed : 14.75 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.14), residues: 3015 helix: 3.10 (0.11), residues: 1755 sheet: 2.25 (0.21), residues: 396 loop : -0.18 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 86 HIS 0.002 0.001 HIS P 3 PHE 0.004 0.001 PHE C 154 TYR 0.018 0.002 TYR O 50 ARG 0.004 0.000 ARG V 43 Details of bonding type rmsd hydrogen bonds : bond 0.04862 ( 1687) hydrogen bonds : angle 3.71598 ( 4914) covalent geometry : bond 0.00312 (23936) covalent geometry : angle 0.44859 (32223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23190.12 seconds wall clock time: 400 minutes 52.12 seconds (24052.12 seconds total)