Starting phenix.real_space_refine on Sun Sep 29 18:31:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdz_43157/09_2024/8vdz_43157.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdz_43157/09_2024/8vdz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdz_43157/09_2024/8vdz_43157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdz_43157/09_2024/8vdz_43157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdz_43157/09_2024/8vdz_43157.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdz_43157/09_2024/8vdz_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 14.00, per 1000 atoms: 0.59 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: 5.97 Conformation dependent library (CDL) restraints added in 3.0 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: 2.39 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: 7.67 Time building geometry restraints manager: 6.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7997 1.34 - 1.46: 3480 1.46 - 1.58: 12303 1.58 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 23936 Sorted by residual: bond pdb=" CD GLU R 135 " pdb=" OE1 GLU R 135 " ideal model delta sigma weight residual 1.249 1.229 0.020 1.90e-02 2.77e+03 1.09e+00 bond pdb=" CG1 ILE Q 121 " pdb=" CD1 ILE Q 121 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 8.24e-01 bond pdb=" N GLU R 135 " pdb=" CA GLU R 135 " ideal model delta sigma weight residual 1.458 1.470 -0.011 1.26e-02 6.30e+03 8.10e-01 bond pdb=" CG1 ILE K 121 " pdb=" CD1 ILE K 121 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 7.86e-01 bond pdb=" C GLY W 94 " pdb=" N GLY W 95 " ideal model delta sigma weight residual 1.331 1.318 0.013 1.46e-02 4.69e+03 7.75e-01 ... (remaining 23931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 31150 1.08 - 2.16: 867 2.16 - 3.23: 170 3.23 - 4.31: 23 4.31 - 5.39: 13 Bond angle restraints: 32223 Sorted by residual: angle pdb=" C ARG R 134 " pdb=" N GLU R 135 " pdb=" CA GLU R 135 " ideal model delta sigma weight residual 120.58 115.79 4.79 1.71e+00 3.42e-01 7.86e+00 angle pdb=" N GLU R 135 " pdb=" CA GLU R 135 " pdb=" CB GLU R 135 " ideal model delta sigma weight residual 110.20 114.22 -4.02 1.49e+00 4.50e-01 7.28e+00 angle pdb=" C ASP C 24 " pdb=" N SER C 25 " pdb=" CA SER C 25 " ideal model delta sigma weight residual 120.26 123.68 -3.42 1.34e+00 5.57e-01 6.50e+00 angle pdb=" C ASP D 24 " pdb=" N SER D 25 " pdb=" CA SER D 25 " ideal model delta sigma weight residual 120.26 123.62 -3.36 1.34e+00 5.57e-01 6.27e+00 angle pdb=" C ASP B 24 " pdb=" N SER B 25 " pdb=" CA SER B 25 " ideal model delta sigma weight residual 120.26 123.37 -3.11 1.34e+00 5.57e-01 5.40e+00 ... (remaining 32218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13741 17.94 - 35.89: 724 35.89 - 53.83: 124 53.83 - 71.77: 29 71.77 - 89.71: 11 Dihedral angle restraints: 14629 sinusoidal: 5824 harmonic: 8805 Sorted by residual: dihedral pdb=" CA ARG M 107 " pdb=" C ARG M 107 " pdb=" N GLU M 108 " pdb=" CA GLU M 108 " ideal model delta harmonic sigma weight residual -180.00 -163.70 -16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB GLU S 50 " pdb=" CG GLU S 50 " pdb=" CD GLU S 50 " pdb=" OE1 GLU S 50 " ideal model delta sinusoidal sigma weight residual 0.00 -89.71 89.71 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU I 58 " pdb=" CG GLU I 58 " pdb=" CD GLU I 58 " pdb=" OE1 GLU I 58 " ideal model delta sinusoidal sigma weight residual 0.00 88.61 -88.61 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 14626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2951 0.040 - 0.080: 631 0.080 - 0.120: 267 0.120 - 0.160: 2 0.160 - 0.200: 1 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA GLU R 135 " pdb=" N GLU R 135 " pdb=" C GLU R 135 " pdb=" CB GLU R 135 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA SER S 25 " pdb=" N SER S 25 " pdb=" C SER S 25 " pdb=" CB SER S 25 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA VAL E 5 " pdb=" N VAL E 5 " pdb=" C VAL E 5 " pdb=" CB VAL E 5 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 3849 not shown) Planarity restraints: 4091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 64 " -0.016 2.00e-02 2.50e+03 1.02e-02 2.08e+00 pdb=" CG TYR R 64 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR R 64 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR R 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR R 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 64 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR R 64 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 64 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER P 17 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO P 18 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO P 18 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO P 18 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 17 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO G 18 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO G 18 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 18 " 0.017 5.00e-02 4.00e+02 ... (remaining 4088 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 163 2.63 - 3.19: 20735 3.19 - 3.76: 37809 3.76 - 4.33: 53173 4.33 - 4.90: 88474 Nonbonded interactions: 200354 Sorted by model distance: nonbonded pdb=" OG SER G 17 " pdb=" OE1 GLU G 20 " model vdw 2.056 3.040 nonbonded pdb=" OG SER P 17 " pdb=" OE1 GLU P 20 " model vdw 2.064 3.040 nonbonded pdb=" OG SER W 17 " pdb=" OE1 GLU W 20 " model vdw 2.068 3.040 nonbonded pdb=" OG SER N 17 " pdb=" OE1 GLU N 20 " model vdw 2.070 3.040 nonbonded pdb=" OG SER X 17 " pdb=" OE1 GLU X 20 " model vdw 2.072 3.040 ... (remaining 200349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'B' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'C' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'D' and (resid 23 through 99 or resid 103 through 163)) selection = (chain 'I' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'J' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'K' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'L' and (resid 23 through 99 or resid 103 through 163)) selection = (chain 'Q' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'R' and (resid 23 through 99 or resid 103 through 163)) selection = (chain 'S' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'T' and (resid 23 through 99 or resid 103 through 163)) } ncs_group { reference = (chain 'E' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'F' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'G' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'H' selection = (chain 'M' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'N' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'O' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'P' selection = (chain 'U' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'V' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'W' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 51.320 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 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:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.250 ------------------------------------------------------------------------------- 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= 0.176 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 607 time to evaluate : 2.599 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: 1.9621 time to fit residues: 1308.5450 Evaluate side-chains 479 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 2.712 ------------------------------------------------------------------------------- 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: 3.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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= 0.198 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 *********************** 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 fitting. rotamer outliers: 41 poor density : 488 time to evaluate : 2.783 Fit side-chains REVERT: B 114 LYS cc_start: 0.8460 (mmtt) cc_final: 0.8240 (mmtp) REVERT: B 135 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7194 (mt-10) REVERT: C 50 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7071 (tp30) REVERT: C 69 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: D 65 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8091 (tttm) REVERT: E 105 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8594 (tt0) REVERT: F 20 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7304 (mp0) REVERT: G 51 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7991 (mpt180) REVERT: H 20 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7133 (mp0) REVERT: I 36 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7208 (tt0) REVERT: K 95 MET cc_start: 0.7983 (mtp) cc_final: 0.7662 (ttm) REVERT: K 116 ASP cc_start: 0.8331 (m-30) cc_final: 0.7948 (m-30) REVERT: L 47 TYR cc_start: 0.8748 (m-80) cc_final: 0.8417 (m-80) REVERT: L 65 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7683 (mmtm) REVERT: L 73 LYS cc_start: 0.8533 (ttpt) cc_final: 0.8191 (tttt) REVERT: M 15 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7243 (mm-30) REVERT: O 48 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7315 (tp30) REVERT: P 39 ASP cc_start: 0.7777 (m-30) cc_final: 0.7541 (m-30) REVERT: R 116 ASP cc_start: 0.8304 (m-30) cc_final: 0.7864 (m-30) REVERT: S 97 MET cc_start: 0.7809 (mtp) cc_final: 0.7474 (mtm) REVERT: S 114 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8142 (mmtp) REVERT: X 20 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: X 98 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7128 (mt-10) outliers start: 41 outliers final: 5 residues processed: 504 average time/residue: 1.8383 time to fit residues: 1021.4590 Evaluate side-chains 495 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 481 time to evaluate : 2.552 ------------------------------------------------------------------------------- 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 51 ARG 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 148 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 222 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 267 optimal weight: 0.7980 chunk 288 optimal weight: 6.9990 chunk 238 optimal weight: 0.9980 chunk 265 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23936 Z= 0.160 Angle : 0.401 5.799 32223 Z= 0.218 Chirality : 0.038 0.130 3852 Planarity : 0.003 0.030 4091 Dihedral : 3.314 13.057 3339 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.54 % Allowed : 10.39 % Favored : 88.08 % 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: 3.46 (0.14), residues: 3015 helix: 3.24 (0.11), residues: 1776 sheet: 2.32 (0.21), residues: 396 loop : 0.08 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 86 HIS 0.002 0.000 HIS N 63 PHE 0.004 0.001 PHE C 154 TYR 0.013 0.002 TYR X 61 ARG 0.003 0.000 ARG E 43 *********************** 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 533 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 495 time to evaluate : 2.923 Fit side-chains REVERT: A 29 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7153 (mt-10) REVERT: A 77 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6746 (tp30) REVERT: B 69 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: B 114 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8264 (mmtp) REVERT: C 69 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: D 65 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8094 (tttm) REVERT: D 114 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7851 (mmtp) REVERT: F 20 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7327 (mp0) REVERT: G 51 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7735 (mpt180) REVERT: H 20 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7244 (mp0) REVERT: H 23 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.5952 (tp30) REVERT: I 36 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: I 73 LYS cc_start: 0.8697 (tttm) cc_final: 0.8464 (tttm) REVERT: I 75 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8019 (mptt) REVERT: K 95 MET cc_start: 0.7941 (mtp) cc_final: 0.7635 (ttm) REVERT: K 116 ASP cc_start: 0.8404 (m-30) cc_final: 0.7954 (m-30) REVERT: L 36 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7739 (mt-10) REVERT: L 47 TYR cc_start: 0.8770 (m-80) cc_final: 0.8395 (m-80) REVERT: L 73 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8191 (tttt) REVERT: M 15 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: O 48 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7305 (tp30) REVERT: P 39 ASP cc_start: 0.7742 (m-30) cc_final: 0.7486 (m-30) REVERT: S 97 MET cc_start: 0.7784 (mtp) cc_final: 0.7443 (mtm) REVERT: U 23 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6165 (tp30) REVERT: W 37 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7886 (tm-30) REVERT: X 20 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: X 50 TYR cc_start: 0.8929 (p90) cc_final: 0.8661 (p90) REVERT: X 51 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7729 (mpt180) REVERT: X 98 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7110 (mt-10) outliers start: 38 outliers final: 2 residues processed: 503 average time/residue: 1.8620 time to fit residues: 1033.1831 Evaluate side-chains 488 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 473 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 15 GLU Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain 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 264 optimal weight: 0.1980 chunk 201 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 179 optimal weight: 8.9990 chunk 268 optimal weight: 0.9990 chunk 284 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 254 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23936 Z= 0.228 Angle : 0.441 5.846 32223 Z= 0.237 Chirality : 0.039 0.143 3852 Planarity : 0.004 0.041 4091 Dihedral : 3.462 12.774 3339 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.22 % Allowed : 11.24 % Favored : 86.54 % 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: 3.29 (0.14), residues: 3015 helix: 3.12 (0.11), residues: 1764 sheet: 2.29 (0.21), residues: 396 loop : 0.01 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 86 HIS 0.002 0.001 HIS R 46 PHE 0.005 0.001 PHE C 154 TYR 0.013 0.002 TYR O 61 ARG 0.005 0.000 ARG E 43 *********************** 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 544 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 489 time to evaluate : 2.775 Fit side-chains REVERT: A 29 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7117 (mt-10) REVERT: A 77 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6841 (tp30) REVERT: B 114 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8321 (mmtp) REVERT: C 50 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7094 (tp30) REVERT: C 69 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: D 65 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8152 (tttm) REVERT: D 69 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: D 76 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8315 (mt) REVERT: D 114 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7956 (mmtp) REVERT: E 23 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6112 (tp30) REVERT: E 105 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: F 20 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7349 (mp0) REVERT: G 51 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7736 (mpt180) REVERT: H 20 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7240 (mp0) REVERT: H 23 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6039 (tp30) REVERT: I 73 LYS cc_start: 0.8762 (tttm) cc_final: 0.8536 (tttm) REVERT: I 75 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7802 (mtmt) REVERT: K 29 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7182 (mt-10) REVERT: K 95 MET cc_start: 0.7933 (mtp) cc_final: 0.7606 (ttm) REVERT: K 116 ASP cc_start: 0.8436 (m-30) cc_final: 0.8045 (m-30) REVERT: L 47 TYR cc_start: 0.8846 (m-80) cc_final: 0.8549 (m-80) REVERT: L 73 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8235 (tttt) REVERT: M 15 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: M 23 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6029 (tp30) REVERT: M 51 ARG cc_start: 0.8178 (mpt180) cc_final: 0.7954 (mpt180) REVERT: O 24 GLN cc_start: 0.7983 (mt0) cc_final: 0.7722 (mt0) REVERT: P 39 ASP cc_start: 0.7858 (m-30) cc_final: 0.7594 (m-30) REVERT: R 29 GLU cc_start: 0.7527 (tt0) cc_final: 0.7175 (mm-30) REVERT: S 97 MET cc_start: 0.7930 (mtp) cc_final: 0.7540 (mtm) REVERT: T 114 LYS cc_start: 0.8630 (mmtp) cc_final: 0.8389 (mmtt) REVERT: W 51 ARG cc_start: 0.7995 (mpt180) cc_final: 0.7729 (mpt180) REVERT: X 20 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: X 50 TYR cc_start: 0.9031 (p90) cc_final: 0.8736 (p90) REVERT: X 51 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7789 (mpt180) REVERT: X 98 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7189 (mt-10) outliers start: 55 outliers final: 10 residues processed: 504 average time/residue: 1.8615 time to fit residues: 1034.1836 Evaluate side-chains 496 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 471 time to evaluate : 2.646 ------------------------------------------------------------------------------- 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 D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 15 GLU Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain W residue 7 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 236 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 117 optimal weight: 0.0050 chunk 242 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23936 Z= 0.291 Angle : 0.479 5.859 32223 Z= 0.255 Chirality : 0.041 0.139 3852 Planarity : 0.004 0.050 4091 Dihedral : 3.629 13.275 3339 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.79 % Allowed : 11.68 % Favored : 85.53 % 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: 3.07 (0.14), residues: 3015 helix: 2.97 (0.11), residues: 1758 sheet: 2.23 (0.22), residues: 396 loop : -0.14 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP T 86 HIS 0.002 0.001 HIS N 63 PHE 0.005 0.001 PHE F 35 TYR 0.015 0.002 TYR O 50 ARG 0.007 0.000 ARG V 43 *********************** 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 571 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 502 time to evaluate : 2.763 Fit side-chains REVERT: A 29 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7140 (mt-10) REVERT: A 77 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6883 (tp30) REVERT: B 114 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8336 (mmtp) REVERT: C 50 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7099 (tp30) REVERT: D 65 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8169 (tttm) REVERT: D 69 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: D 76 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8307 (mt) REVERT: D 114 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7923 (mmtp) REVERT: E 23 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6119 (tp30) REVERT: E 105 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8664 (tt0) REVERT: F 20 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7261 (mp0) REVERT: G 51 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7742 (mpt180) REVERT: H 20 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7270 (mp0) REVERT: H 23 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6043 (tp30) REVERT: I 73 LYS cc_start: 0.8734 (tttm) cc_final: 0.8523 (tttm) REVERT: I 75 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7789 (mtmt) REVERT: J 114 LYS cc_start: 0.8452 (mmtt) cc_final: 0.8105 (mmtp) REVERT: K 29 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7204 (mt-10) REVERT: K 95 MET cc_start: 0.7929 (mtp) cc_final: 0.7596 (ttm) REVERT: K 116 ASP cc_start: 0.8459 (m-30) cc_final: 0.8088 (m-30) REVERT: L 47 TYR cc_start: 0.8897 (m-80) cc_final: 0.8580 (m-80) REVERT: L 69 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: L 73 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8290 (tttt) REVERT: L 96 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7216 (mt-10) REVERT: M 15 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7212 (mm-30) REVERT: M 23 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6168 (tp30) REVERT: M 51 ARG cc_start: 0.8193 (mpt180) cc_final: 0.7973 (mpt180) REVERT: O 24 GLN cc_start: 0.8008 (mt0) cc_final: 0.7754 (mt0) REVERT: P 39 ASP cc_start: 0.7882 (m-30) cc_final: 0.7616 (m-30) REVERT: P 105 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8593 (tm-30) REVERT: R 29 GLU cc_start: 0.7492 (tt0) cc_final: 0.7200 (mm-30) REVERT: S 97 MET cc_start: 0.8046 (mtp) cc_final: 0.7632 (mtm) REVERT: T 77 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6827 (tp30) REVERT: T 114 LYS cc_start: 0.8665 (mmtp) cc_final: 0.8447 (mmtt) REVERT: U 23 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.5967 (tp30) REVERT: X 20 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: X 51 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7815 (mpt180) REVERT: X 98 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7231 (mt-10) outliers start: 69 outliers final: 16 residues processed: 522 average time/residue: 1.8652 time to fit residues: 1072.6603 Evaluate side-chains 524 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 490 time to evaluate : 2.494 ------------------------------------------------------------------------------- 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 C residue 135 GLU Chi-restraints excluded: chain D residue 65 LYS 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 G residue 51 ARG Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 15 GLU Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 77 GLU Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain T residue 97 MET 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 X residue 20 GLU Chi-restraints excluded: chain X residue 51 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 284 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23936 Z= 0.266 Angle : 0.467 5.837 32223 Z= 0.250 Chirality : 0.040 0.142 3852 Planarity : 0.004 0.042 4091 Dihedral : 3.594 13.158 3339 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.71 % Allowed : 12.09 % Favored : 85.21 % 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: 3.03 (0.14), residues: 3015 helix: 2.95 (0.11), residues: 1758 sheet: 2.20 (0.21), residues: 396 loop : -0.18 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 86 HIS 0.002 0.001 HIS F 63 PHE 0.005 0.001 PHE C 154 TYR 0.016 0.002 TYR O 50 ARG 0.006 0.000 ARG V 43 *********************** 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 557 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 490 time to evaluate : 2.969 Fit side-chains REVERT: A 77 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6883 (tp30) REVERT: C 50 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7086 (tp30) REVERT: D 65 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8166 (tttm) REVERT: D 69 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7112 (tm-30) REVERT: D 76 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8315 (mt) REVERT: D 114 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7955 (mmtp) REVERT: E 23 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6072 (tp30) REVERT: E 105 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: F 20 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7269 (mp0) REVERT: F 23 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6046 (tp30) REVERT: G 51 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7732 (mpt180) REVERT: G 58 GLU cc_start: 0.7254 (tt0) cc_final: 0.6925 (pt0) REVERT: H 20 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7254 (mp0) REVERT: H 23 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6005 (tp30) REVERT: I 73 LYS cc_start: 0.8680 (tttm) cc_final: 0.8464 (tttm) REVERT: I 75 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8165 (mppt) REVERT: K 29 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7202 (mt-10) REVERT: K 95 MET cc_start: 0.7919 (mtp) cc_final: 0.7602 (ttm) REVERT: K 116 ASP cc_start: 0.8462 (m-30) cc_final: 0.8082 (m-30) REVERT: L 47 TYR cc_start: 0.8883 (m-80) cc_final: 0.8491 (m-80) REVERT: L 69 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7123 (tm-30) REVERT: L 73 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8280 (tttt) REVERT: M 15 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: M 51 ARG cc_start: 0.8177 (mpt180) cc_final: 0.7949 (mpt180) REVERT: O 24 GLN cc_start: 0.8007 (mt0) cc_final: 0.7694 (mt0) REVERT: P 39 ASP cc_start: 0.7905 (m-30) cc_final: 0.7637 (m-30) REVERT: P 105 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8599 (tm-30) REVERT: R 29 GLU cc_start: 0.7498 (tt0) cc_final: 0.7214 (mm-30) REVERT: S 97 MET cc_start: 0.8069 (mtp) cc_final: 0.7652 (mtm) REVERT: T 52 MET cc_start: 0.7937 (mtm) cc_final: 0.7726 (mtp) REVERT: T 77 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6810 (tp30) REVERT: T 114 LYS cc_start: 0.8637 (mmtp) cc_final: 0.8423 (mmtt) REVERT: U 23 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.5829 (tp30) REVERT: U 51 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7919 (ttm170) REVERT: V 51 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7723 (mpt180) REVERT: W 58 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6787 (tp30) REVERT: X 15 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7433 (mt-10) REVERT: X 20 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: X 51 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7794 (mpt180) outliers start: 67 outliers final: 19 residues processed: 505 average time/residue: 1.8410 time to fit residues: 1025.6757 Evaluate side-chains 517 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 477 time to evaluate : 2.790 ------------------------------------------------------------------------------- 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 C residue 135 GLU Chi-restraints excluded: chain D residue 65 LYS 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 23 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 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 7 GLU Chi-restraints excluded: chain M residue 15 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 T residue 82 GLU Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 51 ARG 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 7 GLU Chi-restraints excluded: chain W residue 58 GLU Chi-restraints excluded: chain X residue 20 GLU Chi-restraints excluded: chain X residue 51 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 0.9990 chunk 32 optimal weight: 0.0020 chunk 162 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 239 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 chunk 283 optimal weight: 0.6980 chunk 177 optimal weight: 0.7980 chunk 172 optimal weight: 7.9990 chunk 130 optimal weight: 0.0970 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23936 Z= 0.133 Angle : 0.394 5.878 32223 Z= 0.216 Chirality : 0.038 0.130 3852 Planarity : 0.003 0.031 4091 Dihedral : 3.241 13.369 3339 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 1.78 % Allowed : 13.62 % Favored : 84.60 % 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: 1794 sheet: 2.30 (0.21), residues: 396 loop : -0.00 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 86 HIS 0.002 0.000 HIS P 3 PHE 0.004 0.001 PHE R 154 TYR 0.014 0.002 TYR E 61 ARG 0.003 0.000 ARG V 43 *********************** 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 514 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 470 time to evaluate : 2.792 Fit side-chains REVERT: A 65 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7681 (tttp) REVERT: A 77 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6740 (tp30) REVERT: B 69 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: D 52 MET cc_start: 0.8149 (mtt) cc_final: 0.7877 (mtp) REVERT: D 65 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8037 (tttm) REVERT: D 69 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6987 (tm-30) REVERT: D 76 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8252 (mt) REVERT: D 114 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7886 (mmtp) REVERT: E 23 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6041 (tp30) REVERT: F 20 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7301 (mp0) REVERT: G 51 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7695 (mpt180) REVERT: G 58 GLU cc_start: 0.7128 (tt0) cc_final: 0.6898 (pt0) REVERT: H 20 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7236 (mp0) REVERT: H 23 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.5826 (tp30) REVERT: I 73 LYS cc_start: 0.8679 (tttm) cc_final: 0.8463 (tttm) REVERT: I 75 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7940 (mppt) REVERT: K 95 MET cc_start: 0.7958 (mtp) cc_final: 0.7667 (ttm) REVERT: K 116 ASP cc_start: 0.8316 (m-30) cc_final: 0.7826 (m-30) REVERT: L 47 TYR cc_start: 0.8783 (m-80) cc_final: 0.8395 (m-80) REVERT: L 65 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7583 (tptm) REVERT: L 69 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: L 73 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8235 (tttt) REVERT: M 51 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7890 (mpt180) REVERT: O 20 GLU cc_start: 0.7592 (mp0) cc_final: 0.7387 (mp0) REVERT: O 24 GLN cc_start: 0.8018 (mt0) cc_final: 0.7706 (mt0) REVERT: O 51 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7914 (mpt180) REVERT: P 39 ASP cc_start: 0.7840 (m-30) cc_final: 0.7563 (m-30) REVERT: P 105 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8600 (tm-30) REVERT: S 97 MET cc_start: 0.7899 (mtp) cc_final: 0.7487 (mtm) REVERT: T 29 GLU cc_start: 0.7455 (tt0) cc_final: 0.7251 (mt-10) REVERT: T 77 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6776 (tp30) REVERT: U 23 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6029 (tp30) REVERT: U 51 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7864 (ttm170) REVERT: X 20 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: X 50 TYR cc_start: 0.8807 (p90) cc_final: 0.8587 (p90) REVERT: X 51 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7757 (mpt180) outliers start: 44 outliers final: 8 residues processed: 483 average time/residue: 1.8419 time to fit residues: 981.1944 Evaluate side-chains 487 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 460 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 65 LYS 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 G residue 51 ARG Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain R residue 64 TYR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain T residue 77 GLU Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 51 ARG Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain W residue 7 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 175 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23936 Z= 0.294 Angle : 0.488 5.866 32223 Z= 0.260 Chirality : 0.041 0.140 3852 Planarity : 0.004 0.042 4091 Dihedral : 3.594 12.973 3339 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.22 % Allowed : 13.82 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.14), residues: 3015 helix: 2.98 (0.11), residues: 1758 sheet: 2.24 (0.21), residues: 396 loop : -0.23 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 86 HIS 0.003 0.001 HIS R 46 PHE 0.005 0.001 PHE C 154 TYR 0.017 0.002 TYR O 50 ARG 0.007 0.000 ARG V 43 *********************** 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 545 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 490 time to evaluate : 2.627 Fit side-chains REVERT: A 77 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6854 (tp30) REVERT: B 43 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7065 (tp30) REVERT: B 114 LYS cc_start: 0.8473 (mttm) cc_final: 0.8203 (mmtt) REVERT: C 50 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7074 (tp30) REVERT: D 65 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8179 (tttm) REVERT: D 69 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: D 76 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8325 (mt) REVERT: D 114 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7912 (mmtp) REVERT: E 23 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6069 (tp30) REVERT: F 23 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6057 (tp30) REVERT: G 51 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7766 (mpt180) REVERT: H 20 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7286 (mp0) REVERT: H 23 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.5981 (tp30) REVERT: I 36 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: I 73 LYS cc_start: 0.8693 (tttm) cc_final: 0.8475 (tttm) REVERT: I 75 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8075 (mppt) REVERT: J 114 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8119 (mmtp) REVERT: K 29 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7167 (mt-10) REVERT: K 95 MET cc_start: 0.7938 (mtp) cc_final: 0.7579 (ttm) REVERT: K 116 ASP cc_start: 0.8461 (m-30) cc_final: 0.8076 (m-30) REVERT: L 47 TYR cc_start: 0.8902 (m-80) cc_final: 0.8574 (m-80) REVERT: L 69 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: L 73 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8285 (tttt) REVERT: L 96 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7221 (mt-10) REVERT: M 51 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7933 (mpt180) REVERT: O 24 GLN cc_start: 0.8030 (mt0) cc_final: 0.7707 (mt0) REVERT: P 39 ASP cc_start: 0.7911 (m-30) cc_final: 0.7637 (m-30) REVERT: P 105 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8590 (tm-30) REVERT: S 97 MET cc_start: 0.8086 (mtp) cc_final: 0.7677 (mtm) REVERT: T 52 MET cc_start: 0.7951 (mtm) cc_final: 0.7740 (mtp) REVERT: T 77 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6777 (tp30) REVERT: T 114 LYS cc_start: 0.8657 (mmtp) cc_final: 0.8426 (mmtt) REVERT: U 23 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.5862 (tp30) REVERT: U 51 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7957 (ttm170) REVERT: W 51 ARG cc_start: 0.7970 (mpt180) cc_final: 0.7749 (mpt180) REVERT: W 58 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6763 (tp30) REVERT: X 7 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: X 15 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7422 (mt-10) REVERT: X 20 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: X 50 TYR cc_start: 0.9038 (p90) cc_final: 0.8808 (p90) REVERT: X 51 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7776 (mpt180) REVERT: X 98 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7203 (mt-10) outliers start: 55 outliers final: 19 residues processed: 505 average time/residue: 1.8580 time to fit residues: 1034.1036 Evaluate side-chains 509 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 468 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 65 LYS 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 D residue 159 VAL Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 73 LYS Chi-restraints excluded: chain L residue 31 ASN 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 P residue 105 GLU Chi-restraints excluded: chain R residue 64 TYR Chi-restraints excluded: chain R residue 82 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 51 ARG 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 7 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 257 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 81 optimal weight: 0.0030 chunk 238 optimal weight: 3.9990 chunk 249 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1621 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= 0.205 Angle : 0.445 5.810 32223 Z= 0.240 Chirality : 0.039 0.135 3852 Planarity : 0.003 0.033 4091 Dihedral : 3.462 13.009 3339 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 2.02 % Allowed : 14.63 % Favored : 83.35 % 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: 3.16 (0.14), residues: 3015 helix: 3.05 (0.11), residues: 1761 sheet: 2.24 (0.21), residues: 396 loop : -0.13 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 86 HIS 0.002 0.001 HIS P 3 PHE 0.005 0.001 PHE C 154 TYR 0.017 0.002 TYR O 50 ARG 0.004 0.000 ARG V 43 *********************** 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 fitting. rotamer outliers: 50 poor density : 463 time to evaluate : 2.971 Fit side-chains REVERT: A 77 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6852 (tp30) REVERT: C 50 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7066 (tp30) REVERT: D 65 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8135 (tttm) REVERT: D 69 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: D 76 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8294 (mt) REVERT: D 114 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7919 (mmtp) REVERT: E 23 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6043 (tp30) REVERT: F 23 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6051 (tp30) REVERT: G 51 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7738 (mpt180) REVERT: G 58 GLU cc_start: 0.7232 (tt0) cc_final: 0.6985 (pt0) REVERT: H 20 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7252 (mp0) REVERT: H 23 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.5936 (tp30) REVERT: I 36 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: I 73 LYS cc_start: 0.8690 (tttm) cc_final: 0.8482 (tttm) REVERT: I 75 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8026 (mppt) REVERT: I 97 MET cc_start: 0.7936 (mtp) cc_final: 0.7469 (mtm) REVERT: J 114 LYS cc_start: 0.8384 (mmtt) cc_final: 0.8083 (mmtp) REVERT: K 29 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7181 (mt-10) REVERT: K 95 MET cc_start: 0.7982 (mtp) cc_final: 0.7666 (ttm) REVERT: K 116 ASP cc_start: 0.8403 (m-30) cc_final: 0.8006 (m-30) REVERT: L 47 TYR cc_start: 0.8869 (m-80) cc_final: 0.8531 (m-80) REVERT: L 69 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: L 73 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8240 (tttt) REVERT: M 15 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7149 (mm-30) REVERT: M 51 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7866 (mpt180) REVERT: O 24 GLN cc_start: 0.7994 (mt0) cc_final: 0.7694 (mt0) REVERT: P 39 ASP cc_start: 0.7861 (m-30) cc_final: 0.7588 (m-30) REVERT: P 105 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8558 (tm-30) REVERT: S 97 MET cc_start: 0.8032 (mtp) cc_final: 0.7614 (mtm) REVERT: T 52 MET cc_start: 0.7905 (mtm) cc_final: 0.7683 (mtp) REVERT: T 77 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6802 (tp30) REVERT: U 23 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.5823 (tp30) REVERT: W 58 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6768 (tp30) REVERT: X 7 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: X 15 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7419 (mt-10) REVERT: X 20 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: X 50 TYR cc_start: 0.8991 (p90) cc_final: 0.8739 (p90) REVERT: X 51 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7790 (mpt180) REVERT: X 98 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7163 (mt-10) outliers start: 50 outliers final: 15 residues processed: 477 average time/residue: 1.9607 time to fit residues: 1037.4693 Evaluate side-chains 495 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 459 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 65 LYS 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 G residue 51 ARG Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 73 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 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 T residue 82 GLU Chi-restraints excluded: chain U residue 7 GLU Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain W residue 7 GLU Chi-restraints excluded: chain W residue 58 GLU Chi-restraints excluded: chain X residue 7 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 173 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 chunk 269 optimal weight: 4.9990 chunk 233 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23936 Z= 0.345 Angle : 0.527 5.889 32223 Z= 0.280 Chirality : 0.042 0.142 3852 Planarity : 0.004 0.048 4091 Dihedral : 3.762 13.892 3339 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.66 % Allowed : 14.71 % Favored : 83.63 % 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: 2.83 (0.14), residues: 3015 helix: 2.80 (0.11), residues: 1749 sheet: 2.18 (0.21), residues: 396 loop : -0.27 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.003 0.001 HIS F 63 PHE 0.005 0.001 PHE K 40 TYR 0.021 0.002 TYR O 50 ARG 0.008 0.001 ARG E 43 ********************** 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 537 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 496 time to evaluate : 2.821 Fit side-chains REVERT: A 77 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: B 114 LYS cc_start: 0.8534 (mttm) cc_final: 0.8207 (mmtp) REVERT: C 50 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7133 (tp30) REVERT: D 69 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: D 76 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8319 (mt) REVERT: D 114 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7972 (mmtp) REVERT: E 23 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6097 (tp30) REVERT: F 23 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6085 (tp30) REVERT: F 34 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8372 (mm-40) REVERT: G 51 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7741 (mpt180) REVERT: G 58 GLU cc_start: 0.7235 (tt0) cc_final: 0.6993 (pt0) REVERT: H 20 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7209 (mp0) REVERT: H 23 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.5989 (tp30) REVERT: I 36 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: I 73 LYS cc_start: 0.8720 (tttm) cc_final: 0.8514 (tttm) REVERT: I 75 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8012 (mppt) REVERT: I 97 MET cc_start: 0.8140 (mtp) cc_final: 0.7660 (mtm) REVERT: J 114 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8108 (mmtp) REVERT: K 29 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7178 (mt-10) REVERT: K 95 MET cc_start: 0.7920 (mtp) cc_final: 0.7553 (ttm) REVERT: K 116 ASP cc_start: 0.8470 (m-30) cc_final: 0.8123 (m-30) REVERT: L 47 TYR cc_start: 0.8917 (m-80) cc_final: 0.8586 (m-80) REVERT: L 69 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: L 73 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8261 (tttt) REVERT: L 97 MET cc_start: 0.8047 (mtp) cc_final: 0.7690 (mtm) REVERT: M 51 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7944 (mpt180) REVERT: N 54 THR cc_start: 0.8861 (p) cc_final: 0.8588 (p) REVERT: O 24 GLN cc_start: 0.8026 (mt0) cc_final: 0.7726 (mt0) REVERT: P 39 ASP cc_start: 0.7932 (m-30) cc_final: 0.7660 (m-30) REVERT: P 105 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8591 (tm-30) REVERT: S 97 MET cc_start: 0.8122 (mtp) cc_final: 0.7766 (mtm) REVERT: T 52 MET cc_start: 0.7983 (mtm) cc_final: 0.7755 (mtp) REVERT: U 23 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.5877 (tp30) REVERT: V 20 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: W 58 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6779 (tp30) REVERT: X 7 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: X 15 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7446 (mt-10) REVERT: X 20 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: X 51 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7783 (mpt180) outliers start: 41 outliers final: 13 residues processed: 507 average time/residue: 1.8025 time to fit residues: 1008.4994 Evaluate side-chains 520 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 488 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU 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 F residue 23 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 73 LYS 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 P residue 105 GLU Chi-restraints excluded: chain R residue 92 LEU 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 20 GLU Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain W residue 58 GLU Chi-restraints excluded: chain X residue 7 GLU Chi-restraints excluded: chain X residue 20 GLU 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 185 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 215 optimal weight: 0.0000 chunk 34 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 239 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.134593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.106675 restraints weight = 23915.801| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.45 r_work: 0.2926 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23936 Z= 0.165 Angle : 0.430 5.765 32223 Z= 0.235 Chirality : 0.039 0.133 3852 Planarity : 0.003 0.033 4091 Dihedral : 3.403 14.246 3339 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.41 % Allowed : 15.12 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.16 (0.14), residues: 3015 helix: 3.06 (0.11), residues: 1770 sheet: 2.22 (0.21), residues: 396 loop : -0.18 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 86 HIS 0.002 0.001 HIS F 63 PHE 0.004 0.001 PHE R 154 TYR 0.017 0.002 TYR O 50 ARG 0.003 0.000 ARG V 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13609.92 seconds wall clock time: 235 minutes 47.38 seconds (14147.38 seconds total)