Starting phenix.real_space_refine on Fri Sep 27 23:07:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/09_2024/3j9x_6310.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/09_2024/3j9x_6310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/09_2024/3j9x_6310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/09_2024/3j9x_6310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/09_2024/3j9x_6310.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/09_2024/3j9x_6310.cif" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 0.011 sd= 0.065 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: 5 Type Number sf(0) Gaussians P 696 5.49 5 S 58 5.16 5 C 42804 2.51 5 N 12354 2.21 5 O 14790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 261 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 70702 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "B" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "C" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "D" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "E" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "F" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "G" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "H" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "I" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "J" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "K" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "L" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "M" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "O" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "P" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "Q" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "R" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "S" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "T" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "U" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "V" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "W" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "X" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "Y" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "Z" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "a" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "b" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "c" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "d" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "e" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "f" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "g" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "h" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "i" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "j" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "k" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "l" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "m" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "n" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "o" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "p" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "q" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "r" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "s" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "t" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "u" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "v" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "w" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "x" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "y" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "z" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "1" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "2" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "3" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "4" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "5" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "6" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "7" Number of atoms: 7134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 7134 Classifications: {'DNA': 348} Link IDs: {'rna3p': 347} Chain: "8" Number of atoms: 7134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 7134 Classifications: {'DNA': 348} Link IDs: {'rna3p': 347} Time building chain proxies: 28.64, per 1000 atoms: 0.41 Number of scatterers: 70702 At special positions: 0 Unit cell: (199.5, 199.5, 139.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 696 15.00 O 14790 8.00 N 12354 7.00 C 42804 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: 13.72 Conformation dependent library (CDL) restraints added in 5.6 seconds 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13688 Finding SS restraints... Secondary structure from input PDB file: 348 helices and 0 sheets defined 89.1% alpha, 0.0% beta 348 base pairs and 405 stacking pairs defined. Time for finding SS restraints: 21.03 Creating SS restraints... Processing helix chain 'A' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 37 through 66 Proline residue: A 50 - end of helix removed outlier: 3.771A pdb=" N VAL A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 91 removed outlier: 3.668A pdb=" N ALA A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 111 Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'B' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 49 Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 111 Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'C' and resid 9 through 26 removed outlier: 3.647A pdb=" N ASN C 26 " --> pdb=" O ASN C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 37 through 66 Proline residue: C 50 - end of helix removed outlier: 3.771A pdb=" N VAL C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 111 Processing helix chain 'C' and resid 114 through 126 Processing helix chain 'D' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 49 Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 111 Processing helix chain 'D' and resid 114 through 126 Processing helix chain 'E' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN E 26 " --> pdb=" O ASN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 37 through 66 Proline residue: E 50 - end of helix removed outlier: 3.771A pdb=" N VAL E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA E 74 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 Processing helix chain 'E' and resid 114 through 126 Processing helix chain 'F' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN F 26 " --> pdb=" O ASN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 49 Proline residue: F 39 - end of helix Processing helix chain 'F' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL F 55 " --> pdb=" O LYS F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA F 74 " --> pdb=" O GLY F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 Processing helix chain 'F' and resid 114 through 126 Processing helix chain 'G' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 37 through 66 Proline residue: G 50 - end of helix removed outlier: 3.772A pdb=" N VAL G 55 " --> pdb=" O LYS G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 111 Processing helix chain 'G' and resid 114 through 126 Processing helix chain 'H' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN H 26 " --> pdb=" O ASN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 49 Proline residue: H 39 - end of helix Processing helix chain 'H' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL H 55 " --> pdb=" O LYS H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA H 74 " --> pdb=" O GLY H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 111 Processing helix chain 'H' and resid 114 through 126 Processing helix chain 'I' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN I 26 " --> pdb=" O ASN I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 37 Processing helix chain 'I' and resid 37 through 66 Proline residue: I 50 - end of helix removed outlier: 3.771A pdb=" N VAL I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 91 removed outlier: 3.668A pdb=" N ALA I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 111 Processing helix chain 'I' and resid 114 through 126 Processing helix chain 'J' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN J 26 " --> pdb=" O ASN J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 49 Proline residue: J 39 - end of helix Processing helix chain 'J' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL J 55 " --> pdb=" O LYS J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 111 Processing helix chain 'J' and resid 114 through 126 Processing helix chain 'K' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN K 26 " --> pdb=" O ASN K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 37 through 66 Proline residue: K 50 - end of helix removed outlier: 3.772A pdb=" N VAL K 55 " --> pdb=" O LYS K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA K 74 " --> pdb=" O GLY K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 111 Processing helix chain 'K' and resid 114 through 126 Processing helix chain 'L' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN L 26 " --> pdb=" O ASN L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 49 Proline residue: L 39 - end of helix Processing helix chain 'L' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL L 55 " --> pdb=" O LYS L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA L 74 " --> pdb=" O GLY L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 111 Processing helix chain 'L' and resid 114 through 126 Processing helix chain 'M' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN M 26 " --> pdb=" O ASN M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 37 through 66 Proline residue: M 50 - end of helix removed outlier: 3.771A pdb=" N VAL M 55 " --> pdb=" O LYS M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA M 74 " --> pdb=" O GLY M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 111 Processing helix chain 'M' and resid 114 through 126 Processing helix chain 'N' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN N 26 " --> pdb=" O ASN N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 49 Proline residue: N 39 - end of helix Processing helix chain 'N' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL N 55 " --> pdb=" O LYS N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA N 74 " --> pdb=" O GLY N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 111 Processing helix chain 'N' and resid 114 through 126 Processing helix chain 'O' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN O 26 " --> pdb=" O ASN O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 37 through 66 Proline residue: O 50 - end of helix removed outlier: 3.772A pdb=" N VAL O 55 " --> pdb=" O LYS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA O 74 " --> pdb=" O GLY O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 111 Processing helix chain 'O' and resid 114 through 126 Processing helix chain 'P' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN P 26 " --> pdb=" O ASN P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 49 Proline residue: P 39 - end of helix Processing helix chain 'P' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL P 55 " --> pdb=" O LYS P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA P 74 " --> pdb=" O GLY P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 111 Processing helix chain 'P' and resid 114 through 126 Processing helix chain 'Q' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN Q 26 " --> pdb=" O ASN Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 37 Processing helix chain 'Q' and resid 37 through 66 Proline residue: Q 50 - end of helix removed outlier: 3.771A pdb=" N VAL Q 55 " --> pdb=" O LYS Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA Q 74 " --> pdb=" O GLY Q 70 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 111 Processing helix chain 'Q' and resid 114 through 126 Processing helix chain 'R' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN R 26 " --> pdb=" O ASN R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 49 Proline residue: R 39 - end of helix Processing helix chain 'R' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL R 55 " --> pdb=" O LYS R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA R 74 " --> pdb=" O GLY R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 111 Processing helix chain 'R' and resid 114 through 126 Processing helix chain 'S' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN S 26 " --> pdb=" O ASN S 22 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 37 Processing helix chain 'S' and resid 37 through 66 Proline residue: S 50 - end of helix removed outlier: 3.772A pdb=" N VAL S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA S 74 " --> pdb=" O GLY S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 93 through 111 Processing helix chain 'S' and resid 114 through 126 Processing helix chain 'T' and resid 9 through 26 removed outlier: 3.592A pdb=" N ASN T 26 " --> pdb=" O ASN T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 49 Proline residue: T 39 - end of helix Processing helix chain 'T' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA T 74 " --> pdb=" O GLY T 70 " (cutoff:3.500A) Processing helix chain 'T' and resid 93 through 111 Processing helix chain 'T' and resid 114 through 126 Processing helix chain 'U' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN U 26 " --> pdb=" O ASN U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 37 Processing helix chain 'U' and resid 37 through 66 Proline residue: U 50 - end of helix removed outlier: 3.771A pdb=" N VAL U 55 " --> pdb=" O LYS U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA U 74 " --> pdb=" O GLY U 70 " (cutoff:3.500A) Processing helix chain 'U' and resid 93 through 111 Processing helix chain 'U' and resid 114 through 126 Processing helix chain 'V' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN V 26 " --> pdb=" O ASN V 22 " (cutoff:3.500A) Processing helix chain 'V' and resid 26 through 49 Proline residue: V 39 - end of helix Processing helix chain 'V' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL V 55 " --> pdb=" O LYS V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA V 74 " --> pdb=" O GLY V 70 " (cutoff:3.500A) Processing helix chain 'V' and resid 93 through 111 Processing helix chain 'V' and resid 114 through 126 Processing helix chain 'W' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN W 26 " --> pdb=" O ASN W 22 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 37 Processing helix chain 'W' and resid 37 through 66 Proline residue: W 50 - end of helix removed outlier: 3.771A pdb=" N VAL W 55 " --> pdb=" O LYS W 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA W 74 " --> pdb=" O GLY W 70 " (cutoff:3.500A) Processing helix chain 'W' and resid 93 through 111 Processing helix chain 'W' and resid 114 through 126 Processing helix chain 'X' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN X 26 " --> pdb=" O ASN X 22 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 49 Proline residue: X 39 - end of helix Processing helix chain 'X' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL X 55 " --> pdb=" O LYS X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA X 74 " --> pdb=" O GLY X 70 " (cutoff:3.500A) Processing helix chain 'X' and resid 93 through 111 Processing helix chain 'X' and resid 114 through 126 Processing helix chain 'Y' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN Y 26 " --> pdb=" O ASN Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 37 Processing helix chain 'Y' and resid 37 through 66 Proline residue: Y 50 - end of helix removed outlier: 3.772A pdb=" N VAL Y 55 " --> pdb=" O LYS Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA Y 74 " --> pdb=" O GLY Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 93 through 111 Processing helix chain 'Y' and resid 114 through 126 Processing helix chain 'Z' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN Z 26 " --> pdb=" O ASN Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 26 through 49 Proline residue: Z 39 - end of helix Processing helix chain 'Z' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL Z 55 " --> pdb=" O LYS Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA Z 74 " --> pdb=" O GLY Z 70 " (cutoff:3.500A) Processing helix chain 'Z' and resid 93 through 111 Processing helix chain 'Z' and resid 114 through 126 Processing helix chain 'a' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN a 26 " --> pdb=" O ASN a 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 26 through 37 Processing helix chain 'a' and resid 37 through 66 Proline residue: a 50 - end of helix removed outlier: 3.773A pdb=" N VAL a 55 " --> pdb=" O LYS a 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA a 74 " --> pdb=" O GLY a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 111 Processing helix chain 'a' and resid 114 through 126 Processing helix chain 'b' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN b 26 " --> pdb=" O ASN b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 49 Proline residue: b 39 - end of helix Processing helix chain 'b' and resid 49 through 66 removed outlier: 3.741A pdb=" N VAL b 55 " --> pdb=" O LYS b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA b 74 " --> pdb=" O GLY b 70 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 111 Processing helix chain 'b' and resid 114 through 126 Processing helix chain 'c' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN c 26 " --> pdb=" O ASN c 22 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 37 through 66 Proline residue: c 50 - end of helix removed outlier: 3.772A pdb=" N VAL c 55 " --> pdb=" O LYS c 51 " (cutoff:3.500A) Processing helix chain 'c' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA c 74 " --> pdb=" O GLY c 70 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 111 Processing helix chain 'c' and resid 114 through 126 Processing helix chain 'd' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN d 26 " --> pdb=" O ASN d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 49 Proline residue: d 39 - end of helix Processing helix chain 'd' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL d 55 " --> pdb=" O LYS d 51 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA d 74 " --> pdb=" O GLY d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 111 Processing helix chain 'd' and resid 114 through 126 Processing helix chain 'e' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN e 26 " --> pdb=" O ASN e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 26 through 37 Processing helix chain 'e' and resid 37 through 66 Proline residue: e 50 - end of helix removed outlier: 3.771A pdb=" N VAL e 55 " --> pdb=" O LYS e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA e 74 " --> pdb=" O GLY e 70 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 111 Processing helix chain 'e' and resid 114 through 126 Processing helix chain 'f' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN f 26 " --> pdb=" O ASN f 22 " (cutoff:3.500A) Processing helix chain 'f' and resid 26 through 49 Proline residue: f 39 - end of helix Processing helix chain 'f' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL f 55 " --> pdb=" O LYS f 51 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA f 74 " --> pdb=" O GLY f 70 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 111 Processing helix chain 'f' and resid 114 through 126 Processing helix chain 'g' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN g 26 " --> pdb=" O ASN g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 37 through 66 Proline residue: g 50 - end of helix removed outlier: 3.771A pdb=" N VAL g 55 " --> pdb=" O LYS g 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA g 74 " --> pdb=" O GLY g 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 93 through 111 Processing helix chain 'g' and resid 114 through 126 Processing helix chain 'h' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN h 26 " --> pdb=" O ASN h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 26 through 49 Proline residue: h 39 - end of helix Processing helix chain 'h' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL h 55 " --> pdb=" O LYS h 51 " (cutoff:3.500A) Processing helix chain 'h' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA h 74 " --> pdb=" O GLY h 70 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 111 Processing helix chain 'h' and resid 114 through 126 Processing helix chain 'i' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN i 26 " --> pdb=" O ASN i 22 " (cutoff:3.500A) Processing helix chain 'i' and resid 26 through 37 Processing helix chain 'i' and resid 37 through 66 Proline residue: i 50 - end of helix removed outlier: 3.771A pdb=" N VAL i 55 " --> pdb=" O LYS i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA i 74 " --> pdb=" O GLY i 70 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 111 Processing helix chain 'i' and resid 114 through 126 Processing helix chain 'j' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN j 26 " --> pdb=" O ASN j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 26 through 49 Proline residue: j 39 - end of helix Processing helix chain 'j' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL j 55 " --> pdb=" O LYS j 51 " (cutoff:3.500A) Processing helix chain 'j' and resid 70 through 91 removed outlier: 3.646A pdb=" N ALA j 74 " --> pdb=" O GLY j 70 " (cutoff:3.500A) Processing helix chain 'j' and resid 93 through 111 Processing helix chain 'j' and resid 114 through 126 Processing helix chain 'k' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN k 26 " --> pdb=" O ASN k 22 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 37 Processing helix chain 'k' and resid 37 through 66 Proline residue: k 50 - end of helix removed outlier: 3.771A pdb=" N VAL k 55 " --> pdb=" O LYS k 51 " (cutoff:3.500A) Processing helix chain 'k' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA k 74 " --> pdb=" O GLY k 70 " (cutoff:3.500A) Processing helix chain 'k' and resid 93 through 111 Processing helix chain 'k' and resid 114 through 126 Processing helix chain 'l' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN l 26 " --> pdb=" O ASN l 22 " (cutoff:3.500A) Processing helix chain 'l' and resid 26 through 49 Proline residue: l 39 - end of helix Processing helix chain 'l' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL l 55 " --> pdb=" O LYS l 51 " (cutoff:3.500A) Processing helix chain 'l' and resid 70 through 91 removed outlier: 3.646A pdb=" N ALA l 74 " --> pdb=" O GLY l 70 " (cutoff:3.500A) Processing helix chain 'l' and resid 93 through 111 Processing helix chain 'l' and resid 114 through 126 Processing helix chain 'm' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN m 26 " --> pdb=" O ASN m 22 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 37 Processing helix chain 'm' and resid 37 through 66 Proline residue: m 50 - end of helix removed outlier: 3.770A pdb=" N VAL m 55 " --> pdb=" O LYS m 51 " (cutoff:3.500A) Processing helix chain 'm' and resid 70 through 91 removed outlier: 3.668A pdb=" N ALA m 74 " --> pdb=" O GLY m 70 " (cutoff:3.500A) Processing helix chain 'm' and resid 93 through 111 Processing helix chain 'm' and resid 114 through 126 Processing helix chain 'n' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN n 26 " --> pdb=" O ASN n 22 " (cutoff:3.500A) Processing helix chain 'n' and resid 26 through 49 Proline residue: n 39 - end of helix Processing helix chain 'n' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL n 55 " --> pdb=" O LYS n 51 " (cutoff:3.500A) Processing helix chain 'n' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA n 74 " --> pdb=" O GLY n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 93 through 111 Processing helix chain 'n' and resid 114 through 126 Processing helix chain 'o' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN o 26 " --> pdb=" O ASN o 22 " (cutoff:3.500A) Processing helix chain 'o' and resid 26 through 37 Processing helix chain 'o' and resid 37 through 66 Proline residue: o 50 - end of helix removed outlier: 3.772A pdb=" N VAL o 55 " --> pdb=" O LYS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA o 74 " --> pdb=" O GLY o 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 93 through 111 Processing helix chain 'o' and resid 114 through 126 Processing helix chain 'p' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN p 26 " --> pdb=" O ASN p 22 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 49 Proline residue: p 39 - end of helix Processing helix chain 'p' and resid 49 through 66 removed outlier: 3.741A pdb=" N VAL p 55 " --> pdb=" O LYS p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA p 74 " --> pdb=" O GLY p 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 93 through 111 Processing helix chain 'p' and resid 114 through 126 Processing helix chain 'q' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN q 26 " --> pdb=" O ASN q 22 " (cutoff:3.500A) Processing helix chain 'q' and resid 26 through 37 Processing helix chain 'q' and resid 37 through 66 Proline residue: q 50 - end of helix removed outlier: 3.772A pdb=" N VAL q 55 " --> pdb=" O LYS q 51 " (cutoff:3.500A) Processing helix chain 'q' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA q 74 " --> pdb=" O GLY q 70 " (cutoff:3.500A) Processing helix chain 'q' and resid 93 through 111 Processing helix chain 'q' and resid 114 through 126 Processing helix chain 'r' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN r 26 " --> pdb=" O ASN r 22 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 49 Proline residue: r 39 - end of helix Processing helix chain 'r' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL r 55 " --> pdb=" O LYS r 51 " (cutoff:3.500A) Processing helix chain 'r' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA r 74 " --> pdb=" O GLY r 70 " (cutoff:3.500A) Processing helix chain 'r' and resid 93 through 111 Processing helix chain 'r' and resid 114 through 126 Processing helix chain 's' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN s 26 " --> pdb=" O ASN s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 26 through 37 Processing helix chain 's' and resid 37 through 66 Proline residue: s 50 - end of helix removed outlier: 3.772A pdb=" N VAL s 55 " --> pdb=" O LYS s 51 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA s 74 " --> pdb=" O GLY s 70 " (cutoff:3.500A) Processing helix chain 's' and resid 93 through 111 Processing helix chain 's' and resid 114 through 126 Processing helix chain 't' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN t 26 " --> pdb=" O ASN t 22 " (cutoff:3.500A) Processing helix chain 't' and resid 26 through 49 Proline residue: t 39 - end of helix Processing helix chain 't' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL t 55 " --> pdb=" O LYS t 51 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 91 removed outlier: 3.646A pdb=" N ALA t 74 " --> pdb=" O GLY t 70 " (cutoff:3.500A) Processing helix chain 't' and resid 93 through 111 Processing helix chain 't' and resid 114 through 126 Processing helix chain 'u' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN u 26 " --> pdb=" O ASN u 22 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 37 Processing helix chain 'u' and resid 37 through 66 Proline residue: u 50 - end of helix removed outlier: 3.771A pdb=" N VAL u 55 " --> pdb=" O LYS u 51 " (cutoff:3.500A) Processing helix chain 'u' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA u 74 " --> pdb=" O GLY u 70 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 111 Processing helix chain 'u' and resid 114 through 126 Processing helix chain 'v' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN v 26 " --> pdb=" O ASN v 22 " (cutoff:3.500A) Processing helix chain 'v' and resid 26 through 49 Proline residue: v 39 - end of helix Processing helix chain 'v' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL v 55 " --> pdb=" O LYS v 51 " (cutoff:3.500A) Processing helix chain 'v' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA v 74 " --> pdb=" O GLY v 70 " (cutoff:3.500A) Processing helix chain 'v' and resid 93 through 111 Processing helix chain 'v' and resid 114 through 126 Processing helix chain 'w' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN w 26 " --> pdb=" O ASN w 22 " (cutoff:3.500A) Processing helix chain 'w' and resid 26 through 37 Processing helix chain 'w' and resid 37 through 66 Proline residue: w 50 - end of helix removed outlier: 3.773A pdb=" N VAL w 55 " --> pdb=" O LYS w 51 " (cutoff:3.500A) Processing helix chain 'w' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA w 74 " --> pdb=" O GLY w 70 " (cutoff:3.500A) Processing helix chain 'w' and resid 93 through 111 Processing helix chain 'w' and resid 114 through 126 Processing helix chain 'x' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN x 26 " --> pdb=" O ASN x 22 " (cutoff:3.500A) Processing helix chain 'x' and resid 26 through 49 Proline residue: x 39 - end of helix Processing helix chain 'x' and resid 49 through 66 removed outlier: 3.741A pdb=" N VAL x 55 " --> pdb=" O LYS x 51 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA x 74 " --> pdb=" O GLY x 70 " (cutoff:3.500A) Processing helix chain 'x' and resid 93 through 111 Processing helix chain 'x' and resid 114 through 126 Processing helix chain 'y' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN y 26 " --> pdb=" O ASN y 22 " (cutoff:3.500A) Processing helix chain 'y' and resid 26 through 37 Processing helix chain 'y' and resid 37 through 66 Proline residue: y 50 - end of helix removed outlier: 3.771A pdb=" N VAL y 55 " --> pdb=" O LYS y 51 " (cutoff:3.500A) Processing helix chain 'y' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA y 74 " --> pdb=" O GLY y 70 " (cutoff:3.500A) Processing helix chain 'y' and resid 93 through 111 Processing helix chain 'y' and resid 114 through 126 Processing helix chain 'z' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN z 26 " --> pdb=" O ASN z 22 " (cutoff:3.500A) Processing helix chain 'z' and resid 26 through 49 Proline residue: z 39 - end of helix Processing helix chain 'z' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL z 55 " --> pdb=" O LYS z 51 " (cutoff:3.500A) Processing helix chain 'z' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA z 74 " --> pdb=" O GLY z 70 " (cutoff:3.500A) Processing helix chain 'z' and resid 93 through 111 Processing helix chain 'z' and resid 114 through 126 Processing helix chain '1' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN 1 26 " --> pdb=" O ASN 1 22 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 37 Processing helix chain '1' and resid 37 through 66 Proline residue: 1 50 - end of helix removed outlier: 3.771A pdb=" N VAL 1 55 " --> pdb=" O LYS 1 51 " (cutoff:3.500A) Processing helix chain '1' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA 1 74 " --> pdb=" O GLY 1 70 " (cutoff:3.500A) Processing helix chain '1' and resid 93 through 111 Processing helix chain '1' and resid 114 through 126 Processing helix chain '2' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN 2 26 " --> pdb=" O ASN 2 22 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 49 Proline residue: 2 39 - end of helix Processing helix chain '2' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL 2 55 " --> pdb=" O LYS 2 51 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA 2 74 " --> pdb=" O GLY 2 70 " (cutoff:3.500A) Processing helix chain '2' and resid 93 through 111 Processing helix chain '2' and resid 114 through 126 Processing helix chain '3' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN 3 26 " --> pdb=" O ASN 3 22 " (cutoff:3.500A) Processing helix chain '3' and resid 26 through 37 Processing helix chain '3' and resid 37 through 66 Proline residue: 3 50 - end of helix removed outlier: 3.772A pdb=" N VAL 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) Processing helix chain '3' and resid 70 through 91 removed outlier: 3.665A pdb=" N ALA 3 74 " --> pdb=" O GLY 3 70 " (cutoff:3.500A) Processing helix chain '3' and resid 93 through 111 Processing helix chain '3' and resid 114 through 126 Processing helix chain '4' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN 4 26 " --> pdb=" O ASN 4 22 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 49 Proline residue: 4 39 - end of helix Processing helix chain '4' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL 4 55 " --> pdb=" O LYS 4 51 " (cutoff:3.500A) Processing helix chain '4' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA 4 74 " --> pdb=" O GLY 4 70 " (cutoff:3.500A) Processing helix chain '4' and resid 93 through 111 Processing helix chain '4' and resid 114 through 126 Processing helix chain '5' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN 5 26 " --> pdb=" O ASN 5 22 " (cutoff:3.500A) Processing helix chain '5' and resid 26 through 37 Processing helix chain '5' and resid 37 through 66 Proline residue: 5 50 - end of helix removed outlier: 3.773A pdb=" N VAL 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) Processing helix chain '5' and resid 70 through 91 removed outlier: 3.665A pdb=" N ALA 5 74 " --> pdb=" O GLY 5 70 " (cutoff:3.500A) Processing helix chain '5' and resid 93 through 111 Processing helix chain '5' and resid 114 through 126 Processing helix chain '6' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN 6 26 " --> pdb=" O ASN 6 22 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 49 Proline residue: 6 39 - end of helix Processing helix chain '6' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL 6 55 " --> pdb=" O LYS 6 51 " (cutoff:3.500A) Processing helix chain '6' and resid 70 through 91 removed outlier: 3.646A pdb=" N ALA 6 74 " --> pdb=" O GLY 6 70 " (cutoff:3.500A) Processing helix chain '6' and resid 93 through 111 Processing helix chain '6' and resid 114 through 126 4872 hydrogen bonds defined for protein. 14616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 696 hydrogen bonds 1392 hydrogen bond angles 0 basepair planarities 348 basepair parallelities 405 stacking parallelities Total time for adding SS restraints: 26.82 Time building geometry restraints manager: 16.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 13087 1.32 - 1.44: 20992 1.44 - 1.56: 38073 1.56 - 1.67: 1390 1.67 - 1.79: 116 Bond restraints: 73658 Sorted by residual: bond pdb=" CA ILE E 124 " pdb=" CB ILE E 124 " ideal model delta sigma weight residual 1.545 1.496 0.049 1.05e-02 9.07e+03 2.20e+01 bond pdb=" CA ILE s 124 " pdb=" CB ILE s 124 " ideal model delta sigma weight residual 1.545 1.496 0.049 1.05e-02 9.07e+03 2.16e+01 bond pdb=" CA ILE e 124 " pdb=" CB ILE e 124 " ideal model delta sigma weight residual 1.545 1.497 0.048 1.05e-02 9.07e+03 2.12e+01 bond pdb=" CA ILE u 124 " pdb=" CB ILE u 124 " ideal model delta sigma weight residual 1.545 1.497 0.048 1.05e-02 9.07e+03 2.12e+01 bond pdb=" CA ILE w 124 " pdb=" CB ILE w 124 " ideal model delta sigma weight residual 1.545 1.497 0.048 1.05e-02 9.07e+03 2.11e+01 ... (remaining 73653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 94373 1.94 - 3.88: 7945 3.88 - 5.82: 363 5.82 - 7.76: 493 7.76 - 9.70: 174 Bond angle restraints: 103348 Sorted by residual: angle pdb=" C GLY W 70 " pdb=" N PRO W 71 " pdb=" CA PRO W 71 " ideal model delta sigma weight residual 119.56 127.77 -8.21 1.02e+00 9.61e-01 6.47e+01 angle pdb=" C GLY 3 70 " pdb=" N PRO 3 71 " pdb=" CA PRO 3 71 " ideal model delta sigma weight residual 119.56 127.73 -8.17 1.02e+00 9.61e-01 6.41e+01 angle pdb=" C GLY 5 70 " pdb=" N PRO 5 71 " pdb=" CA PRO 5 71 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.02e+00 9.61e-01 6.38e+01 angle pdb=" C GLY y 70 " pdb=" N PRO y 71 " pdb=" CA PRO y 71 " ideal model delta sigma weight residual 119.56 127.69 -8.13 1.02e+00 9.61e-01 6.35e+01 angle pdb=" C GLY G 70 " pdb=" N PRO G 71 " pdb=" CA PRO G 71 " ideal model delta sigma weight residual 119.56 127.68 -8.12 1.02e+00 9.61e-01 6.34e+01 ... (remaining 103343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.53: 36907 14.53 - 29.05: 3578 29.05 - 43.58: 1033 43.58 - 58.11: 816 58.11 - 72.63: 174 Dihedral angle restraints: 42508 sinusoidal: 21048 harmonic: 21460 Sorted by residual: dihedral pdb=" N TYR J 10 " pdb=" CA TYR J 10 " pdb=" CB TYR J 10 " pdb=" CG TYR J 10 " ideal model delta sinusoidal sigma weight residual 60.00 109.49 -49.49 3 1.50e+01 4.44e-03 8.78e+00 dihedral pdb=" N TYR z 10 " pdb=" CA TYR z 10 " pdb=" CB TYR z 10 " pdb=" CG TYR z 10 " ideal model delta sinusoidal sigma weight residual 60.00 109.45 -49.45 3 1.50e+01 4.44e-03 8.78e+00 dihedral pdb=" N TYR D 10 " pdb=" CA TYR D 10 " pdb=" CB TYR D 10 " pdb=" CG TYR D 10 " ideal model delta sinusoidal sigma weight residual 60.00 109.44 -49.44 3 1.50e+01 4.44e-03 8.78e+00 ... (remaining 42505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 5397 0.048 - 0.097: 3729 0.097 - 0.145: 1753 0.145 - 0.194: 634 0.194 - 0.242: 203 Chirality restraints: 11716 Sorted by residual: chirality pdb=" CA ASN H 48 " pdb=" N ASN H 48 " pdb=" C ASN H 48 " pdb=" CB ASN H 48 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ASN T 48 " pdb=" N ASN T 48 " pdb=" C ASN T 48 " pdb=" CB ASN T 48 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ASN R 48 " pdb=" N ASN R 48 " pdb=" C ASN R 48 " pdb=" CB ASN R 48 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 11713 not shown) Planarity restraints: 11020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER I 38 " -0.072 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO I 39 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO I 39 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO I 39 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER 3 38 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO 3 39 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO 3 39 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO 3 39 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER U 38 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO U 39 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO U 39 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO U 39 " 0.056 5.00e-02 4.00e+02 ... (remaining 11017 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 28852 2.87 - 3.38: 74518 3.38 - 3.89: 139080 3.89 - 4.39: 167330 4.39 - 4.90: 251685 Nonbonded interactions: 661465 Sorted by model distance: nonbonded pdb=" OG1 THR 1 126 " pdb=" O SER 1 128 " model vdw 2.369 3.040 nonbonded pdb=" OG1 THR i 126 " pdb=" O SER i 128 " model vdw 2.369 3.040 nonbonded pdb=" OG1 THR m 126 " pdb=" O SER m 128 " model vdw 2.369 3.040 nonbonded pdb=" OG1 THR w 126 " pdb=" O SER w 128 " model vdw 2.369 3.040 nonbonded pdb=" OG1 THR U 126 " pdb=" O SER U 128 " model vdw 2.369 3.040 ... (remaining 661460 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '7' selection = chain '8' } 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 group one per residue 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: 0.590 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: 0.060 Extract box with map and model: 2.030 Check model and map are aligned: 0.410 Set scattering table: 0.490 Process input model: 131.670 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.710 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:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5798 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 : 0.014 0.058 73658 Z= 0.908 Angle : 1.239 9.697 103348 Z= 0.844 Chirality : 0.080 0.242 11716 Planarity : 0.017 0.109 11020 Dihedral : 14.920 72.632 28820 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 1.59 % Allowed : 2.78 % Favored : 95.63 % Rotamer: Outliers : 0.48 % Allowed : 0.00 % Favored : 99.52 % 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: -0.65 (0.08), residues: 7308 helix: -0.23 (0.06), residues: 6206 sheet: None (None), residues: 0 loop : -0.69 (0.16), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP W 17 PHE 0.019 0.006 PHE I 21 TYR 0.036 0.008 TYR N 76 ARG 0.006 0.001 ARG L 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2087 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 2058 time to evaluate : 5.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.4523 (tttt) cc_final: 0.3576 (mmpt) REVERT: H 96 LEU cc_start: 0.5845 (tp) cc_final: 0.5400 (tp) REVERT: H 111 PHE cc_start: 0.4888 (m-80) cc_final: 0.4596 (m-10) REVERT: K 45 PHE cc_start: 0.6982 (t80) cc_final: 0.6560 (t80) REVERT: Q 126 THR cc_start: 0.6234 (p) cc_final: 0.5918 (m) REVERT: W 124 ILE cc_start: 0.6451 (mm) cc_final: 0.6162 (mm) REVERT: Z 42 GLN cc_start: 0.6340 (mt0) cc_final: 0.5969 (mt0) REVERT: c 126 THR cc_start: 0.6254 (p) cc_final: 0.5236 (m) REVERT: d 10 TYR cc_start: 0.5228 (OUTLIER) cc_final: 0.4661 (p90) REVERT: h 111 PHE cc_start: 0.5979 (m-80) cc_final: 0.5613 (m-80) REVERT: k 124 ILE cc_start: 0.7776 (mm) cc_final: 0.7557 (mm) REVERT: k 126 THR cc_start: 0.7270 (p) cc_final: 0.7017 (p) REVERT: m 126 THR cc_start: 0.7037 (p) cc_final: 0.6780 (p) REVERT: n 47 THR cc_start: 0.6603 (m) cc_final: 0.6356 (m) REVERT: p 108 ILE cc_start: 0.6607 (mt) cc_final: 0.6309 (mt) REVERT: u 117 VAL cc_start: 0.7183 (t) cc_final: 0.6794 (t) REVERT: v 129 PRO cc_start: 0.3267 (Cg_exo) cc_final: 0.2985 (Cg_endo) REVERT: y 29 VAL cc_start: 0.6090 (t) cc_final: 0.5771 (t) REVERT: z 126 THR cc_start: 0.6119 (p) cc_final: 0.5849 (m) REVERT: 1 25 SER cc_start: 0.7015 (p) cc_final: 0.6576 (t) REVERT: 3 115 PRO cc_start: 0.8368 (Cg_exo) cc_final: 0.8098 (Cg_endo) REVERT: 6 89 ARG cc_start: 0.3903 (mtt-85) cc_final: 0.3264 (ttt180) outliers start: 29 outliers final: 19 residues processed: 2075 average time/residue: 0.6935 time to fit residues: 2433.3639 Evaluate side-chains 1008 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 988 time to evaluate : 5.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain V residue 10 TYR Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain Z residue 10 TYR Chi-restraints excluded: chain b residue 10 TYR Chi-restraints excluded: chain d residue 10 TYR Chi-restraints excluded: chain f residue 10 TYR Chi-restraints excluded: chain h residue 10 TYR Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain p residue 10 TYR Chi-restraints excluded: chain r residue 10 TYR Chi-restraints excluded: chain t residue 10 TYR Chi-restraints excluded: chain v residue 10 TYR Chi-restraints excluded: chain x residue 10 TYR Chi-restraints excluded: chain z residue 10 TYR Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 4 residue 10 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 645 optimal weight: 5.9990 chunk 579 optimal weight: 30.0000 chunk 321 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 390 optimal weight: 20.0000 chunk 309 optimal weight: 5.9990 chunk 598 optimal weight: 0.2980 chunk 231 optimal weight: 8.9990 chunk 364 optimal weight: 7.9990 chunk 445 optimal weight: 6.9990 chunk 693 optimal weight: 30.0000 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN E 46 GLN G 22 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** K 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN M 18 GLN M 46 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN P 42 GLN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 18 GLN R 46 GLN ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 18 GLN S 114 ASN U 12 GLN U 46 GLN V 18 GLN V 65 GLN W 12 GLN X 77 GLN ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 ASN b 42 GLN c 46 GLN ** d 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 114 ASN e 112 ASN ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 GLN ** f 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 36 ASN h 43 GLN ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 42 GLN k 43 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 42 GLN m 77 GLN n 77 GLN o 42 GLN o 43 GLN o 114 ASN q 43 GLN ** q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 114 ASN t 77 GLN u 18 GLN v 46 GLN v 123 ASN w 12 GLN w 18 GLN x 18 GLN x 46 GLN x 77 GLN x 123 ASN ** y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 65 GLN ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 123 ASN ** 1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 42 GLN ** 1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 43 GLN 2 123 ASN 3 46 GLN 4 12 GLN ** 4 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 46 GLN 4 123 ASN 6 18 GLN 6 43 GLN 6 77 GLN 6 112 ASN 6 123 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 73658 Z= 0.291 Angle : 0.710 9.524 103348 Z= 0.411 Chirality : 0.045 0.421 11716 Planarity : 0.008 0.070 11020 Dihedral : 15.281 62.419 16506 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.35 % Allowed : 9.93 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.09), residues: 7308 helix: 1.06 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.14 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 17 PHE 0.026 0.002 PHE p 24 TYR 0.036 0.002 TYR D 10 ARG 0.013 0.001 ARG u 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1597 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1393 time to evaluate : 6.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 TYR cc_start: 0.5794 (t80) cc_final: 0.5515 (t80) REVERT: A 16 LYS cc_start: 0.4217 (tttt) cc_final: 0.3304 (mmpt) REVERT: A 75 ILE cc_start: 0.3991 (mt) cc_final: 0.3479 (mt) REVERT: A 103 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6275 (tt) REVERT: B 10 TYR cc_start: 0.4656 (OUTLIER) cc_final: 0.4087 (p90) REVERT: C 33 ILE cc_start: 0.7832 (tt) cc_final: 0.7556 (tt) REVERT: C 47 THR cc_start: 0.4446 (m) cc_final: 0.4051 (m) REVERT: C 96 LEU cc_start: 0.5750 (OUTLIER) cc_final: 0.5440 (tt) REVERT: G 14 TYR cc_start: 0.7292 (t80) cc_final: 0.6469 (t80) REVERT: H 45 PHE cc_start: 0.6104 (t80) cc_final: 0.5853 (t80) REVERT: K 14 TYR cc_start: 0.7022 (t80) cc_final: 0.6649 (t80) REVERT: L 46 GLN cc_start: 0.6745 (mm-40) cc_final: 0.6470 (mm110) REVERT: M 96 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6371 (tt) REVERT: S 18 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6732 (tp-100) REVERT: T 46 GLN cc_start: 0.4676 (mt0) cc_final: 0.4175 (tm-30) REVERT: U 14 TYR cc_start: 0.6205 (t80) cc_final: 0.5807 (t80) REVERT: V 43 GLN cc_start: 0.6785 (pt0) cc_final: 0.6499 (pt0) REVERT: W 24 PHE cc_start: 0.4968 (t80) cc_final: 0.4691 (t80) REVERT: Y 90 ILE cc_start: 0.5249 (pt) cc_final: 0.5045 (pt) REVERT: Y 126 THR cc_start: 0.5812 (p) cc_final: 0.5589 (m) REVERT: Z 25 SER cc_start: 0.6352 (p) cc_final: 0.6109 (t) REVERT: b 42 GLN cc_start: 0.6811 (mt0) cc_final: 0.6578 (mt0) REVERT: c 45 PHE cc_start: 0.7309 (t80) cc_final: 0.7084 (t80) REVERT: c 107 TYR cc_start: 0.6721 (OUTLIER) cc_final: 0.5897 (t80) REVERT: e 107 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.5979 (t80) REVERT: g 66 TYR cc_start: 0.7128 (m-10) cc_final: 0.6756 (m-80) REVERT: i 124 ILE cc_start: 0.8467 (mm) cc_final: 0.8256 (mm) REVERT: o 69 THR cc_start: 0.7053 (OUTLIER) cc_final: 0.6758 (p) REVERT: s 14 TYR cc_start: 0.7041 (t80) cc_final: 0.6636 (t80) REVERT: s 18 GLN cc_start: 0.7217 (tp40) cc_final: 0.6647 (tp-100) REVERT: u 115 PRO cc_start: 0.6703 (Cg_exo) cc_final: 0.6476 (Cg_endo) REVERT: v 75 ILE cc_start: 0.6795 (mt) cc_final: 0.6278 (mt) REVERT: z 12 GLN cc_start: 0.6850 (mm-40) cc_final: 0.6545 (mm-40) REVERT: z 126 THR cc_start: 0.6180 (p) cc_final: 0.5798 (m) REVERT: 3 18 GLN cc_start: 0.7913 (tp40) cc_final: 0.7640 (tp40) REVERT: 4 126 THR cc_start: 0.7186 (OUTLIER) cc_final: 0.6643 (m) REVERT: 6 100 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7854 (tt) outliers start: 204 outliers final: 91 residues processed: 1506 average time/residue: 0.6433 time to fit residues: 1710.3747 Evaluate side-chains 1129 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1028 time to evaluate : 5.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 107 TYR Chi-restraints excluded: chain P residue 123 ASN Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain S residue 18 GLN Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 92 SER Chi-restraints excluded: chain T residue 122 VAL Chi-restraints excluded: chain V residue 10 TYR Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Z residue 10 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain b residue 10 TYR Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 107 TYR Chi-restraints excluded: chain d residue 10 TYR Chi-restraints excluded: chain e residue 107 TYR Chi-restraints excluded: chain f residue 10 TYR Chi-restraints excluded: chain f residue 116 GLN Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain h residue 10 TYR Chi-restraints excluded: chain i residue 33 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain k residue 53 THR Chi-restraints excluded: chain l residue 117 VAL Chi-restraints excluded: chain m residue 35 SER Chi-restraints excluded: chain m residue 69 THR Chi-restraints excluded: chain m residue 77 GLN Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 117 VAL Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain o residue 125 ILE Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 117 VAL Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain s residue 7 SER Chi-restraints excluded: chain t residue 40 VAL Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain w residue 124 ILE Chi-restraints excluded: chain w residue 133 VAL Chi-restraints excluded: chain x residue 10 TYR Chi-restraints excluded: chain y residue 28 THR Chi-restraints excluded: chain y residue 69 THR Chi-restraints excluded: chain z residue 43 GLN Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain z residue 123 ASN Chi-restraints excluded: chain 1 residue 28 THR Chi-restraints excluded: chain 1 residue 126 THR Chi-restraints excluded: chain 2 residue 43 GLN Chi-restraints excluded: chain 2 residue 103 LEU Chi-restraints excluded: chain 2 residue 124 ILE Chi-restraints excluded: chain 3 residue 124 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 4 residue 126 THR Chi-restraints excluded: chain 5 residue 11 SER Chi-restraints excluded: chain 6 residue 100 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 385 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 577 optimal weight: 10.0000 chunk 472 optimal weight: 30.0000 chunk 191 optimal weight: 5.9990 chunk 695 optimal weight: 6.9990 chunk 750 optimal weight: 30.0000 chunk 619 optimal weight: 7.9990 chunk 689 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 557 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 114 ASN C 43 GLN D 88 ASN ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN G 18 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 GLN J 36 ASN K 12 GLN ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN P 114 ASN Q 12 GLN ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 GLN S 77 GLN T 42 GLN ** T 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN V 46 GLN ** V 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 43 GLN ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 GLN ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN g 26 ASN ** g 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 46 GLN j 43 GLN j 46 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 46 GLN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 77 GLN q 43 GLN ** q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 44 ASN s 101 ASN t 44 ASN t 123 ASN u 116 GLN v 42 GLN v 46 GLN ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 42 GLN x 43 GLN x 46 GLN y 12 GLN ** y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 43 GLN z 123 ASN ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 65 GLN 6 46 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 73658 Z= 0.293 Angle : 0.697 10.748 103348 Z= 0.399 Chirality : 0.043 0.359 11716 Planarity : 0.006 0.067 11020 Dihedral : 14.291 60.718 16492 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.42 % Allowed : 11.71 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.09), residues: 7308 helix: 1.32 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.19 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 17 PHE 0.022 0.002 PHE 4 79 TYR 0.053 0.002 TYR U 14 ARG 0.020 0.001 ARG Z 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1487 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1279 time to evaluate : 5.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.4192 (mt) cc_final: 0.3823 (mt) REVERT: B 10 TYR cc_start: 0.5210 (OUTLIER) cc_final: 0.4090 (p90) REVERT: D 69 THR cc_start: 0.6746 (p) cc_final: 0.6499 (p) REVERT: D 117 VAL cc_start: 0.6301 (t) cc_final: 0.6061 (t) REVERT: E 66 TYR cc_start: 0.6084 (m-10) cc_final: 0.5715 (m-80) REVERT: E 107 TYR cc_start: 0.6293 (OUTLIER) cc_final: 0.5765 (t80) REVERT: G 66 TYR cc_start: 0.6846 (m-10) cc_final: 0.6464 (m-80) REVERT: L 46 GLN cc_start: 0.6807 (mm-40) cc_final: 0.6239 (mm110) REVERT: L 107 TYR cc_start: 0.5259 (OUTLIER) cc_final: 0.4005 (t80) REVERT: S 14 TYR cc_start: 0.6776 (t80) cc_final: 0.6483 (t80) REVERT: T 46 GLN cc_start: 0.4875 (mt0) cc_final: 0.4510 (tm-30) REVERT: W 79 PHE cc_start: 0.7420 (t80) cc_final: 0.7202 (t80) REVERT: Y 126 THR cc_start: 0.6235 (p) cc_final: 0.5728 (m) REVERT: c 45 PHE cc_start: 0.7491 (t80) cc_final: 0.7263 (t80) REVERT: c 100 ILE cc_start: 0.7329 (mt) cc_final: 0.7035 (mt) REVERT: d 42 GLN cc_start: 0.6878 (mp10) cc_final: 0.6537 (mp10) REVERT: k 10 TYR cc_start: 0.6924 (t80) cc_final: 0.6679 (t80) REVERT: n 14 TYR cc_start: 0.7571 (t80) cc_final: 0.7333 (t80) REVERT: o 69 THR cc_start: 0.7497 (OUTLIER) cc_final: 0.7209 (p) REVERT: p 99 MET cc_start: 0.7092 (tmm) cc_final: 0.6880 (tmm) REVERT: r 53 THR cc_start: 0.6681 (m) cc_final: 0.6229 (t) REVERT: u 14 TYR cc_start: 0.7485 (t80) cc_final: 0.7107 (t80) REVERT: u 123 ASN cc_start: 0.4822 (t0) cc_final: 0.4617 (t0) REVERT: y 124 ILE cc_start: 0.6553 (tt) cc_final: 0.6221 (mm) REVERT: z 126 THR cc_start: 0.6643 (p) cc_final: 0.6043 (m) REVERT: 1 25 SER cc_start: 0.6884 (p) cc_final: 0.6569 (t) REVERT: 1 89 ARG cc_start: 0.4477 (mtt-85) cc_final: 0.3748 (mmm160) REVERT: 3 124 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7312 (mm) REVERT: 6 99 MET cc_start: 0.6977 (tmm) cc_final: 0.6770 (tmm) outliers start: 208 outliers final: 105 residues processed: 1382 average time/residue: 0.6409 time to fit residues: 1559.3044 Evaluate side-chains 1102 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 992 time to evaluate : 5.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 66 TYR Chi-restraints excluded: chain G residue 12 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 107 TYR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 119 ASP Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 107 TYR Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 77 GLN Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 122 VAL Chi-restraints excluded: chain V residue 10 TYR Chi-restraints excluded: chain V residue 124 ILE Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Z residue 10 TYR Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain d residue 43 GLN Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain f residue 116 GLN Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain j residue 42 GLN Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain l residue 107 TYR Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 97 VAL Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain s residue 43 GLN Chi-restraints excluded: chain s residue 87 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain u residue 117 VAL Chi-restraints excluded: chain u residue 133 VAL Chi-restraints excluded: chain w residue 99 MET Chi-restraints excluded: chain w residue 133 VAL Chi-restraints excluded: chain x residue 10 TYR Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 124 ILE Chi-restraints excluded: chain y residue 28 THR Chi-restraints excluded: chain y residue 69 THR Chi-restraints excluded: chain y residue 126 THR Chi-restraints excluded: chain z residue 43 GLN Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 92 SER Chi-restraints excluded: chain z residue 122 VAL Chi-restraints excluded: chain z residue 123 ASN Chi-restraints excluded: chain z residue 124 ILE Chi-restraints excluded: chain 1 residue 28 THR Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 124 ILE Chi-restraints excluded: chain 2 residue 126 THR Chi-restraints excluded: chain 3 residue 87 LEU Chi-restraints excluded: chain 3 residue 124 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 4 residue 92 SER Chi-restraints excluded: chain 5 residue 65 GLN Chi-restraints excluded: chain 6 residue 65 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 686 optimal weight: 8.9990 chunk 522 optimal weight: 40.0000 chunk 360 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 331 optimal weight: 50.0000 chunk 466 optimal weight: 5.9990 chunk 697 optimal weight: 30.0000 chunk 738 optimal weight: 30.0000 chunk 364 optimal weight: 5.9990 chunk 661 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN C 18 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN E 42 GLN G 18 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 18 GLN ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN M 46 GLN N 77 GLN O 12 GLN O 42 GLN P 36 ASN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 42 GLN R 114 ASN S 12 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 GLN W 12 GLN ** W 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 46 GLN Y 18 GLN Y 65 GLN ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 112 ASN ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 123 ASN ** c 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 116 GLN ** d 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN ** g 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 116 GLN m 18 GLN n 42 GLN ** o 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 36 ASN p 116 GLN ** q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 36 ASN ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 43 GLN u 42 GLN ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 43 GLN ** v 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 18 GLN y 18 GLN ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 123 ASN 1 46 GLN 2 36 ASN ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 12 GLN 3 18 GLN 3 77 GLN ** 4 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 116 GLN 6 42 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.6399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 73658 Z= 0.294 Angle : 0.682 11.828 103348 Z= 0.385 Chirality : 0.042 0.352 11716 Planarity : 0.006 0.070 11020 Dihedral : 14.235 86.565 16482 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.97 % Allowed : 13.88 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.09), residues: 7308 helix: 1.49 (0.06), residues: 6264 sheet: None (None), residues: 0 loop : 0.38 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 17 PHE 0.031 0.002 PHE o 45 TYR 0.028 0.002 TYR i 10 ARG 0.014 0.001 ARG Q 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1371 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1190 time to evaluate : 5.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLN cc_start: 0.6432 (tm-30) cc_final: 0.5733 (tp40) REVERT: B 99 MET cc_start: 0.6209 (tpp) cc_final: 0.5911 (tpp) REVERT: E 66 TYR cc_start: 0.6490 (m-10) cc_final: 0.6192 (m-80) REVERT: E 107 TYR cc_start: 0.6436 (OUTLIER) cc_final: 0.5765 (t80) REVERT: G 18 GLN cc_start: 0.7627 (tp40) cc_final: 0.6954 (tp-100) REVERT: G 66 TYR cc_start: 0.7222 (m-10) cc_final: 0.6820 (m-80) REVERT: J 43 GLN cc_start: 0.7058 (pp30) cc_final: 0.6355 (pp30) REVERT: L 46 GLN cc_start: 0.7006 (mm-40) cc_final: 0.6630 (mm-40) REVERT: Q 118 LEU cc_start: 0.7493 (mt) cc_final: 0.7225 (mp) REVERT: S 14 TYR cc_start: 0.7398 (t80) cc_final: 0.7114 (t80) REVERT: W 79 PHE cc_start: 0.7523 (t80) cc_final: 0.7191 (t80) REVERT: X 57 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6852 (mm-30) REVERT: Z 43 GLN cc_start: 0.5741 (pt0) cc_final: 0.5534 (pt0) REVERT: Z 123 ASN cc_start: 0.5894 (t0) cc_final: 0.5525 (t0) REVERT: d 18 GLN cc_start: 0.7563 (tp40) cc_final: 0.7254 (tp-100) REVERT: n 14 TYR cc_start: 0.7859 (t80) cc_final: 0.7583 (t80) REVERT: o 18 GLN cc_start: 0.7988 (tp40) cc_final: 0.7733 (tp40) REVERT: o 43 GLN cc_start: 0.5956 (OUTLIER) cc_final: 0.5729 (tt0) REVERT: o 53 THR cc_start: 0.7161 (m) cc_final: 0.6566 (p) REVERT: s 18 GLN cc_start: 0.7462 (tp40) cc_final: 0.7204 (tp-100) REVERT: u 14 TYR cc_start: 0.7639 (t80) cc_final: 0.7213 (t80) REVERT: u 123 ASN cc_start: 0.5097 (t0) cc_final: 0.4842 (t0) REVERT: x 43 GLN cc_start: 0.5225 (OUTLIER) cc_final: 0.5001 (mt0) REVERT: x 107 TYR cc_start: 0.5340 (OUTLIER) cc_final: 0.4909 (t80) REVERT: 3 124 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7309 (mm) REVERT: 4 43 GLN cc_start: 0.5819 (pp30) cc_final: 0.5607 (pp30) outliers start: 181 outliers final: 96 residues processed: 1276 average time/residue: 0.6133 time to fit residues: 1383.2949 Evaluate side-chains 1066 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 965 time to evaluate : 5.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 66 TYR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 107 TYR Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 92 SER Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 122 VAL Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 97 VAL Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 66 TYR Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain d residue 43 GLN Chi-restraints excluded: chain f residue 116 GLN Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 33 ILE Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 116 GLN Chi-restraints excluded: chain i residue 33 ILE Chi-restraints excluded: chain i residue 124 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain j residue 49 VAL Chi-restraints excluded: chain k residue 124 ILE Chi-restraints excluded: chain l residue 34 LEU Chi-restraints excluded: chain l residue 107 TYR Chi-restraints excluded: chain l residue 116 GLN Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 42 GLN Chi-restraints excluded: chain n residue 107 TYR Chi-restraints excluded: chain o residue 43 GLN Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 92 SER Chi-restraints excluded: chain q residue 28 THR Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain s residue 7 SER Chi-restraints excluded: chain s residue 43 GLN Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain t residue 63 LEU Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain u residue 133 VAL Chi-restraints excluded: chain v residue 123 ASN Chi-restraints excluded: chain w residue 99 MET Chi-restraints excluded: chain w residue 121 VAL Chi-restraints excluded: chain w residue 133 VAL Chi-restraints excluded: chain x residue 43 GLN Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain x residue 124 ILE Chi-restraints excluded: chain y residue 28 THR Chi-restraints excluded: chain y residue 126 THR Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain z residue 124 ILE Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 103 LEU Chi-restraints excluded: chain 2 residue 124 ILE Chi-restraints excluded: chain 2 residue 126 THR Chi-restraints excluded: chain 3 residue 124 ILE Chi-restraints excluded: chain 4 residue 92 SER Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 6 residue 28 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 615 optimal weight: 5.9990 chunk 419 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 549 optimal weight: 6.9990 chunk 304 optimal weight: 6.9990 chunk 630 optimal weight: 8.9990 chunk 510 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 377 optimal weight: 10.0000 chunk 662 optimal weight: 7.9990 chunk 186 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 ASN L 42 GLN O 42 GLN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 12 GLN Q 77 GLN R 42 GLN ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 65 GLN W 12 GLN ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 GLN ** W 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 36 ASN ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 101 ASN Z 77 GLN ** a 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 GLN ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN ** g 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 65 GLN ** j 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 65 GLN ** k 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 46 GLN l 114 ASN l 116 GLN m 114 ASN p 46 GLN s 18 GLN t 18 GLN u 18 GLN v 46 GLN ** w 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 18 GLN ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 43 GLN 1 12 GLN ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 12 GLN 5 116 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.7395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 73658 Z= 0.277 Angle : 0.686 14.996 103348 Z= 0.387 Chirality : 0.043 0.411 11716 Planarity : 0.006 0.072 11020 Dihedral : 14.245 59.736 16470 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.02 % Allowed : 14.71 % Favored : 82.27 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.09), residues: 7308 helix: 1.45 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.61 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP n 17 PHE 0.037 0.002 PHE B 45 TYR 0.042 0.002 TYR B 76 ARG 0.007 0.001 ARG S 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1295 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1111 time to evaluate : 5.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 108 ILE cc_start: 0.6214 (tt) cc_final: 0.6010 (tt) REVERT: E 66 TYR cc_start: 0.6798 (m-10) cc_final: 0.6433 (m-80) REVERT: E 107 TYR cc_start: 0.6475 (OUTLIER) cc_final: 0.5703 (t80) REVERT: G 14 TYR cc_start: 0.7535 (t80) cc_final: 0.7022 (t80) REVERT: G 66 TYR cc_start: 0.7310 (m-10) cc_final: 0.6983 (m-80) REVERT: J 43 GLN cc_start: 0.7127 (pp30) cc_final: 0.6588 (pp30) REVERT: L 18 GLN cc_start: 0.7810 (tp40) cc_final: 0.7362 (tp40) REVERT: R 43 GLN cc_start: 0.6704 (pp30) cc_final: 0.6375 (pp30) REVERT: S 14 TYR cc_start: 0.7732 (t80) cc_final: 0.7397 (t80) REVERT: U 115 PRO cc_start: 0.8710 (Cg_exo) cc_final: 0.8510 (Cg_endo) REVERT: d 18 GLN cc_start: 0.7587 (tp40) cc_final: 0.7378 (tp-100) REVERT: g 116 GLN cc_start: 0.5061 (tm-30) cc_final: 0.4768 (tm-30) REVERT: j 87 LEU cc_start: 0.7257 (mm) cc_final: 0.7002 (tp) REVERT: k 10 TYR cc_start: 0.7451 (t80) cc_final: 0.7185 (t80) REVERT: n 14 TYR cc_start: 0.8094 (t80) cc_final: 0.7722 (t80) REVERT: o 49 VAL cc_start: 0.7928 (m) cc_final: 0.7649 (p) REVERT: p 107 TYR cc_start: 0.6172 (OUTLIER) cc_final: 0.5592 (t80) REVERT: q 49 VAL cc_start: 0.7860 (t) cc_final: 0.7598 (t) REVERT: q 57 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6365 (mp0) REVERT: s 18 GLN cc_start: 0.7617 (tp-100) cc_final: 0.7269 (tp-100) REVERT: s 87 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6726 (tp) REVERT: s 132 TYR cc_start: 0.4304 (m-10) cc_final: 0.4102 (m-80) REVERT: t 107 TYR cc_start: 0.6092 (OUTLIER) cc_final: 0.5474 (t80) REVERT: u 123 ASN cc_start: 0.5217 (t0) cc_final: 0.4846 (t0) REVERT: w 14 TYR cc_start: 0.7526 (t80) cc_final: 0.7291 (t80) REVERT: x 79 PHE cc_start: 0.7981 (t80) cc_final: 0.7619 (t80) REVERT: x 107 TYR cc_start: 0.5680 (OUTLIER) cc_final: 0.5293 (t80) REVERT: 2 33 ILE cc_start: 0.8771 (mm) cc_final: 0.8555 (mm) REVERT: 3 124 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7316 (mm) REVERT: 4 43 GLN cc_start: 0.6174 (pp30) cc_final: 0.5929 (pp30) outliers start: 184 outliers final: 99 residues processed: 1218 average time/residue: 0.6315 time to fit residues: 1358.6552 Evaluate side-chains 1043 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 937 time to evaluate : 5.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 66 TYR Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 77 GLN Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 103 LEU Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 92 SER Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 97 VAL Chi-restraints excluded: chain W residue 55 VAL Chi-restraints excluded: chain X residue 66 TYR Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain d residue 43 GLN Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain f residue 116 GLN Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 42 GLN Chi-restraints excluded: chain h residue 65 GLN Chi-restraints excluded: chain h residue 116 GLN Chi-restraints excluded: chain i residue 124 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain j residue 42 GLN Chi-restraints excluded: chain j residue 49 VAL Chi-restraints excluded: chain k residue 65 GLN Chi-restraints excluded: chain k residue 124 ILE Chi-restraints excluded: chain l residue 34 LEU Chi-restraints excluded: chain l residue 107 TYR Chi-restraints excluded: chain l residue 117 VAL Chi-restraints excluded: chain l residue 119 ASP Chi-restraints excluded: chain m residue 69 THR Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 87 LEU Chi-restraints excluded: chain n residue 107 TYR Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 40 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 57 GLU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain s residue 87 LEU Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain s residue 133 VAL Chi-restraints excluded: chain t residue 63 LEU Chi-restraints excluded: chain t residue 107 TYR Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain u residue 133 VAL Chi-restraints excluded: chain v residue 97 VAL Chi-restraints excluded: chain v residue 123 ASN Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain w residue 99 MET Chi-restraints excluded: chain w residue 133 VAL Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain x residue 124 ILE Chi-restraints excluded: chain y residue 51 LYS Chi-restraints excluded: chain y residue 126 THR Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain 1 residue 134 SER Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 124 ILE Chi-restraints excluded: chain 3 residue 87 LEU Chi-restraints excluded: chain 3 residue 124 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 5 residue 87 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 248 optimal weight: 0.0770 chunk 665 optimal weight: 30.0000 chunk 145 optimal weight: 8.9990 chunk 433 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 739 optimal weight: 30.0000 chunk 613 optimal weight: 5.9990 chunk 342 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 244 optimal weight: 0.3980 chunk 388 optimal weight: 5.9990 overall best weight: 3.6944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 112 ASN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN K 43 GLN M 12 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Q 12 GLN ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 GLN S 123 ASN ** T 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 GLN W 18 GLN W 43 GLN ** W 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 GLN Z 18 GLN ** c 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 116 GLN e 77 GLN f 42 GLN ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 36 ASN i 65 GLN q 42 GLN r 42 GLN v 42 GLN y 36 ASN y 42 GLN ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 123 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.7782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 73658 Z= 0.231 Angle : 0.657 16.703 103348 Z= 0.368 Chirality : 0.041 0.319 11716 Planarity : 0.006 0.070 11020 Dihedral : 14.183 59.983 16468 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.45 % Allowed : 16.34 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.09), residues: 7308 helix: 1.58 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.59 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 17 PHE 0.037 0.002 PHE 2 79 TYR 0.027 0.002 TYR O 10 ARG 0.006 0.001 ARG v 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1072 time to evaluate : 5.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 99 MET cc_start: 0.6759 (mmm) cc_final: 0.6167 (tpp) REVERT: E 107 TYR cc_start: 0.6470 (OUTLIER) cc_final: 0.5843 (t80) REVERT: G 18 GLN cc_start: 0.7314 (tp40) cc_final: 0.6774 (tp40) REVERT: G 66 TYR cc_start: 0.7307 (m-10) cc_final: 0.7012 (m-80) REVERT: J 43 GLN cc_start: 0.7101 (pp30) cc_final: 0.6533 (pp30) REVERT: L 18 GLN cc_start: 0.7837 (tp40) cc_final: 0.7522 (tp40) REVERT: R 43 GLN cc_start: 0.6552 (pp30) cc_final: 0.6218 (pp30) REVERT: W 79 PHE cc_start: 0.7510 (t80) cc_final: 0.7134 (t80) REVERT: d 18 GLN cc_start: 0.7657 (tp40) cc_final: 0.7250 (tp-100) REVERT: g 103 LEU cc_start: 0.7515 (tt) cc_final: 0.7219 (tt) REVERT: h 18 GLN cc_start: 0.7745 (tp40) cc_final: 0.7313 (tp40) REVERT: j 66 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.7180 (t80) REVERT: k 10 TYR cc_start: 0.7426 (t80) cc_final: 0.7214 (t80) REVERT: p 107 TYR cc_start: 0.6165 (OUTLIER) cc_final: 0.5569 (t80) REVERT: q 49 VAL cc_start: 0.8001 (t) cc_final: 0.7738 (t) REVERT: q 57 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6359 (mp0) REVERT: q 87 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6523 (tp) REVERT: s 18 GLN cc_start: 0.7509 (tp-100) cc_final: 0.7225 (tp-100) REVERT: s 57 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6056 (mp0) REVERT: s 87 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6783 (tp) REVERT: t 107 TYR cc_start: 0.6053 (OUTLIER) cc_final: 0.5511 (t80) REVERT: u 123 ASN cc_start: 0.5367 (t0) cc_final: 0.5146 (t0) REVERT: v 107 TYR cc_start: 0.5515 (OUTLIER) cc_final: 0.5101 (t80) REVERT: x 79 PHE cc_start: 0.7944 (t80) cc_final: 0.7574 (t80) REVERT: 3 124 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7337 (mm) outliers start: 149 outliers final: 86 residues processed: 1156 average time/residue: 0.6773 time to fit residues: 1391.5353 Evaluate side-chains 1027 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 931 time to evaluate : 5.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 66 TYR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 107 TYR Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 103 LEU Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain W residue 55 VAL Chi-restraints excluded: chain X residue 66 TYR Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain c residue 116 GLN Chi-restraints excluded: chain d residue 43 GLN Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain f residue 116 GLN Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 65 GLN Chi-restraints excluded: chain h residue 116 GLN Chi-restraints excluded: chain i residue 65 GLN Chi-restraints excluded: chain i residue 124 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain j residue 42 GLN Chi-restraints excluded: chain j residue 49 VAL Chi-restraints excluded: chain j residue 66 TYR Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 124 ILE Chi-restraints excluded: chain l residue 34 LEU Chi-restraints excluded: chain m residue 69 THR Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 107 TYR Chi-restraints excluded: chain n residue 119 ASP Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 57 GLU Chi-restraints excluded: chain q residue 87 LEU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain s residue 57 GLU Chi-restraints excluded: chain s residue 87 LEU Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain s residue 133 VAL Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain t residue 107 TYR Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain u residue 87 LEU Chi-restraints excluded: chain u residue 96 LEU Chi-restraints excluded: chain v residue 107 TYR Chi-restraints excluded: chain v residue 123 ASN Chi-restraints excluded: chain w residue 133 VAL Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain y residue 126 THR Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain z residue 92 SER Chi-restraints excluded: chain z residue 123 ASN Chi-restraints excluded: chain 1 residue 134 SER Chi-restraints excluded: chain 2 residue 124 ILE Chi-restraints excluded: chain 3 residue 87 LEU Chi-restraints excluded: chain 3 residue 124 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 5 residue 87 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 712 optimal weight: 30.0000 chunk 83 optimal weight: 50.0000 chunk 421 optimal weight: 30.0000 chunk 539 optimal weight: 8.9990 chunk 418 optimal weight: 30.0000 chunk 622 optimal weight: 40.0000 chunk 412 optimal weight: 7.9990 chunk 736 optimal weight: 30.0000 chunk 460 optimal weight: 0.7980 chunk 448 optimal weight: 8.9990 chunk 339 optimal weight: 7.9990 overall best weight: 6.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 GLN Q 12 GLN Q 123 ASN R 46 GLN ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 123 ASN T 43 GLN U 12 GLN V 65 GLN W 12 GLN W 43 GLN ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 GLN a 116 GLN ** c 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 116 GLN ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 116 GLN n 43 GLN p 114 ASN ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 42 GLN t 18 GLN w 42 GLN ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 77 GLN z 77 GLN z 123 ASN ** 2 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.8404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 73658 Z= 0.272 Angle : 0.687 17.515 103348 Z= 0.383 Chirality : 0.043 0.336 11716 Planarity : 0.006 0.070 11020 Dihedral : 14.368 62.942 16468 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.53 % Allowed : 17.26 % Favored : 80.21 % 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: 1.79 (0.09), residues: 7308 helix: 1.52 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.80 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 17 PHE 0.026 0.002 PHE N 79 TYR 0.032 0.002 TYR O 10 ARG 0.008 0.001 ARG v 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1010 time to evaluate : 5.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 107 TYR cc_start: 0.6550 (OUTLIER) cc_final: 0.5799 (t80) REVERT: G 66 TYR cc_start: 0.7228 (m-10) cc_final: 0.6984 (m-80) REVERT: I 96 LEU cc_start: 0.7195 (tp) cc_final: 0.6860 (tp) REVERT: J 43 GLN cc_start: 0.6981 (pp30) cc_final: 0.6570 (pp30) REVERT: N 126 THR cc_start: 0.7055 (p) cc_final: 0.6779 (t) REVERT: R 43 GLN cc_start: 0.6564 (pp30) cc_final: 0.6307 (pp30) REVERT: W 79 PHE cc_start: 0.7530 (t80) cc_final: 0.7138 (t80) REVERT: Y 18 GLN cc_start: 0.7719 (tp40) cc_final: 0.7465 (tp40) REVERT: Y 42 GLN cc_start: 0.5780 (OUTLIER) cc_final: 0.5561 (tp40) REVERT: Z 104 LYS cc_start: 0.5194 (tttt) cc_final: 0.4820 (tttt) REVERT: h 18 GLN cc_start: 0.7803 (tp40) cc_final: 0.7398 (tp40) REVERT: k 10 TYR cc_start: 0.7744 (t80) cc_final: 0.7430 (t80) REVERT: l 99 MET cc_start: 0.7288 (tpp) cc_final: 0.7047 (tpp) REVERT: n 43 GLN cc_start: 0.5872 (OUTLIER) cc_final: 0.5657 (tt0) REVERT: p 107 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.5569 (t80) REVERT: q 57 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: q 87 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6943 (tp) REVERT: s 87 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6956 (tp) REVERT: t 107 TYR cc_start: 0.6298 (OUTLIER) cc_final: 0.5594 (t80) REVERT: u 57 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5837 (mp0) REVERT: v 107 TYR cc_start: 0.5719 (OUTLIER) cc_final: 0.5271 (t80) REVERT: 2 43 GLN cc_start: 0.6660 (pm20) cc_final: 0.6427 (pm20) REVERT: 3 124 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7345 (mm) REVERT: 4 28 THR cc_start: 0.8397 (p) cc_final: 0.8183 (p) outliers start: 154 outliers final: 94 residues processed: 1099 average time/residue: 0.6719 time to fit residues: 1308.7392 Evaluate side-chains 1011 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 906 time to evaluate : 5.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 107 TYR Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain Q residue 87 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 97 VAL Chi-restraints excluded: chain W residue 55 VAL Chi-restraints excluded: chain W residue 68 ILE Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Y residue 42 GLN Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain a residue 101 ASN Chi-restraints excluded: chain b residue 68 ILE Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain f residue 116 GLN Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 65 GLN Chi-restraints excluded: chain i residue 124 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain j residue 42 GLN Chi-restraints excluded: chain j residue 49 VAL Chi-restraints excluded: chain j residue 116 GLN Chi-restraints excluded: chain k residue 124 ILE Chi-restraints excluded: chain l residue 34 LEU Chi-restraints excluded: chain l residue 116 GLN Chi-restraints excluded: chain m residue 69 THR Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 43 GLN Chi-restraints excluded: chain n residue 107 TYR Chi-restraints excluded: chain n residue 119 ASP Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 40 VAL Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain p residue 119 ASP Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 57 GLU Chi-restraints excluded: chain q residue 87 LEU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain s residue 57 GLU Chi-restraints excluded: chain s residue 87 LEU Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain s residue 133 VAL Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain t residue 107 TYR Chi-restraints excluded: chain u residue 57 GLU Chi-restraints excluded: chain u residue 87 LEU Chi-restraints excluded: chain u residue 133 VAL Chi-restraints excluded: chain v residue 97 VAL Chi-restraints excluded: chain v residue 107 TYR Chi-restraints excluded: chain w residue 133 VAL Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain x residue 124 ILE Chi-restraints excluded: chain y residue 51 LYS Chi-restraints excluded: chain y residue 77 GLN Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 92 SER Chi-restraints excluded: chain z residue 123 ASN Chi-restraints excluded: chain z residue 126 THR Chi-restraints excluded: chain 1 residue 134 SER Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 2 residue 124 ILE Chi-restraints excluded: chain 3 residue 87 LEU Chi-restraints excluded: chain 3 residue 124 ILE Chi-restraints excluded: chain 4 residue 87 LEU Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 6 residue 87 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 455 optimal weight: 20.0000 chunk 294 optimal weight: 6.9990 chunk 439 optimal weight: 6.9990 chunk 221 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 468 optimal weight: 20.0000 chunk 501 optimal weight: 20.0000 chunk 364 optimal weight: 40.0000 chunk 68 optimal weight: 1.9990 chunk 578 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN R 18 GLN R 42 GLN ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 ASN ** U 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 46 GLN W 43 GLN W 65 GLN ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 GLN ** c 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 116 GLN ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 36 ASN l 116 GLN x 18 GLN ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 46 GLN ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 123 ASN ** 2 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.8823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 73658 Z= 0.251 Angle : 0.697 19.074 103348 Z= 0.382 Chirality : 0.042 0.428 11716 Planarity : 0.006 0.069 11020 Dihedral : 14.395 65.980 16468 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.28 % Allowed : 17.87 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.09), residues: 7308 helix: 1.53 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.87 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 17 PHE 0.028 0.002 PHE r 79 TYR 0.030 0.002 TYR O 10 ARG 0.006 0.001 ARG v 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 997 time to evaluate : 5.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.4973 (ttmt) cc_final: 0.4400 (tptt) REVERT: E 107 TYR cc_start: 0.6492 (OUTLIER) cc_final: 0.5825 (t80) REVERT: J 43 GLN cc_start: 0.7023 (pp30) cc_final: 0.6649 (pp30) REVERT: L 126 THR cc_start: 0.7748 (p) cc_final: 0.7451 (t) REVERT: N 126 THR cc_start: 0.6940 (p) cc_final: 0.6695 (t) REVERT: R 43 GLN cc_start: 0.6646 (pp30) cc_final: 0.6415 (pp30) REVERT: V 103 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8084 (mp) REVERT: Z 104 LYS cc_start: 0.5082 (tttt) cc_final: 0.4730 (tttt) REVERT: h 18 GLN cc_start: 0.7764 (tp40) cc_final: 0.7385 (tp40) REVERT: k 10 TYR cc_start: 0.7680 (t80) cc_final: 0.7431 (t80) REVERT: o 57 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6129 (mp0) REVERT: p 107 TYR cc_start: 0.6093 (OUTLIER) cc_final: 0.5282 (t80) REVERT: q 57 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6502 (mp0) REVERT: q 87 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6882 (tp) REVERT: r 107 TYR cc_start: 0.5909 (OUTLIER) cc_final: 0.5542 (t80) REVERT: s 87 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7000 (tp) REVERT: t 107 TYR cc_start: 0.6154 (OUTLIER) cc_final: 0.5416 (t80) REVERT: u 57 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.5672 (mp0) REVERT: u 89 ARG cc_start: 0.4934 (mmt180) cc_final: 0.4588 (ttm170) REVERT: v 107 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.5033 (t80) REVERT: x 79 PHE cc_start: 0.7971 (t80) cc_final: 0.7672 (t80) REVERT: 2 43 GLN cc_start: 0.6889 (pm20) cc_final: 0.6276 (pm20) REVERT: 4 89 ARG cc_start: 0.5111 (OUTLIER) cc_final: 0.4735 (tpp-160) outliers start: 139 outliers final: 88 residues processed: 1071 average time/residue: 0.6225 time to fit residues: 1178.1724 Evaluate side-chains 988 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 888 time to evaluate : 5.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain Q residue 87 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 103 LEU Chi-restraints excluded: chain W residue 55 VAL Chi-restraints excluded: chain W residue 68 ILE Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain a residue 101 ASN Chi-restraints excluded: chain a residue 116 GLN Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 65 GLN Chi-restraints excluded: chain i residue 124 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain j residue 65 GLN Chi-restraints excluded: chain k residue 65 GLN Chi-restraints excluded: chain k residue 124 ILE Chi-restraints excluded: chain l residue 34 LEU Chi-restraints excluded: chain l residue 119 ASP Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 107 TYR Chi-restraints excluded: chain n residue 119 ASP Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 65 GLN Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 40 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 57 GLU Chi-restraints excluded: chain q residue 87 LEU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 107 TYR Chi-restraints excluded: chain s residue 57 GLU Chi-restraints excluded: chain s residue 87 LEU Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain s residue 133 VAL Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain t residue 107 TYR Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain u residue 57 GLU Chi-restraints excluded: chain u residue 96 LEU Chi-restraints excluded: chain v residue 97 VAL Chi-restraints excluded: chain v residue 107 TYR Chi-restraints excluded: chain w residue 99 MET Chi-restraints excluded: chain w residue 133 VAL Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain x residue 124 ILE Chi-restraints excluded: chain y residue 51 LYS Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain z residue 92 SER Chi-restraints excluded: chain z residue 123 ASN Chi-restraints excluded: chain z residue 126 THR Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 134 SER Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 3 residue 87 LEU Chi-restraints excluded: chain 4 residue 65 GLN Chi-restraints excluded: chain 4 residue 89 ARG Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 6 residue 87 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 669 optimal weight: 9.9990 chunk 705 optimal weight: 30.0000 chunk 643 optimal weight: 6.9990 chunk 686 optimal weight: 10.0000 chunk 413 optimal weight: 8.9990 chunk 298 optimal weight: 20.0000 chunk 538 optimal weight: 9.9990 chunk 210 optimal weight: 20.0000 chunk 620 optimal weight: 40.0000 chunk 649 optimal weight: 7.9990 chunk 683 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 ASN ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 65 GLN Q 36 ASN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 ASN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 42 GLN ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 42 GLN V 18 GLN ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 43 GLN Z 36 ASN ** a 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 GLN c 12 GLN ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 36 ASN ** e 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 116 GLN g 116 GLN ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 36 ASN v 36 ASN x 36 ASN x 43 GLN ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 123 ASN 1 42 GLN ** 2 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 77 GLN 4 36 ASN 5 36 ASN 6 77 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.9397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 73658 Z= 0.302 Angle : 0.737 18.448 103348 Z= 0.403 Chirality : 0.044 0.371 11716 Planarity : 0.006 0.071 11020 Dihedral : 14.599 67.714 16468 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.20 % Allowed : 18.19 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.09), residues: 7308 helix: 1.44 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -1.08 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 17 PHE 0.030 0.002 PHE N 79 TYR 0.031 0.002 TYR O 10 ARG 0.006 0.001 ARG v 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 953 time to evaluate : 5.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 99 MET cc_start: 0.7083 (tpp) cc_final: 0.6596 (tpp) REVERT: E 107 TYR cc_start: 0.6679 (OUTLIER) cc_final: 0.5997 (t80) REVERT: G 66 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6877 (m-80) REVERT: I 76 TYR cc_start: 0.7196 (m-80) cc_final: 0.6946 (m-80) REVERT: J 43 GLN cc_start: 0.6973 (pp30) cc_final: 0.6645 (pp30) REVERT: N 126 THR cc_start: 0.7140 (p) cc_final: 0.6892 (t) REVERT: R 43 GLN cc_start: 0.6598 (pp30) cc_final: 0.6201 (pp30) REVERT: R 126 THR cc_start: 0.6971 (p) cc_final: 0.6545 (t) REVERT: X 129 PRO cc_start: 0.5219 (Cg_exo) cc_final: 0.4984 (Cg_endo) REVERT: Z 46 GLN cc_start: 0.6525 (OUTLIER) cc_final: 0.6254 (mt0) REVERT: Z 104 LYS cc_start: 0.5279 (tttt) cc_final: 0.4937 (tttt) REVERT: h 18 GLN cc_start: 0.7838 (tp40) cc_final: 0.7407 (tp40) REVERT: k 10 TYR cc_start: 0.7714 (t80) cc_final: 0.7443 (t80) REVERT: o 57 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6113 (mp0) REVERT: p 107 TYR cc_start: 0.6157 (OUTLIER) cc_final: 0.5323 (t80) REVERT: q 57 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: r 107 TYR cc_start: 0.6080 (OUTLIER) cc_final: 0.5680 (t80) REVERT: s 87 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7310 (tp) REVERT: t 107 TYR cc_start: 0.6381 (OUTLIER) cc_final: 0.5556 (t80) REVERT: v 107 TYR cc_start: 0.5851 (OUTLIER) cc_final: 0.5463 (t80) REVERT: x 79 PHE cc_start: 0.8037 (t80) cc_final: 0.7742 (t80) REVERT: 2 43 GLN cc_start: 0.6926 (pm20) cc_final: 0.6505 (pm20) REVERT: 4 89 ARG cc_start: 0.5023 (OUTLIER) cc_final: 0.4507 (tpp-160) outliers start: 134 outliers final: 91 residues processed: 1030 average time/residue: 0.6183 time to fit residues: 1121.8050 Evaluate side-chains 958 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 856 time to evaluate : 5.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain Q residue 77 GLN Chi-restraints excluded: chain Q residue 87 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain W residue 55 VAL Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain a residue 116 GLN Chi-restraints excluded: chain b residue 68 ILE Chi-restraints excluded: chain d residue 46 GLN Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 65 GLN Chi-restraints excluded: chain i residue 124 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain j residue 116 GLN Chi-restraints excluded: chain j residue 117 VAL Chi-restraints excluded: chain k residue 124 ILE Chi-restraints excluded: chain l residue 34 LEU Chi-restraints excluded: chain l residue 87 LEU Chi-restraints excluded: chain l residue 119 ASP Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 107 TYR Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 40 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain q residue 57 GLU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 107 TYR Chi-restraints excluded: chain s residue 57 GLU Chi-restraints excluded: chain s residue 87 LEU Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain s residue 133 VAL Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain t residue 107 TYR Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain u residue 96 LEU Chi-restraints excluded: chain u residue 133 VAL Chi-restraints excluded: chain v residue 97 VAL Chi-restraints excluded: chain v residue 107 TYR Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain w residue 99 MET Chi-restraints excluded: chain x residue 97 VAL Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain x residue 124 ILE Chi-restraints excluded: chain y residue 51 LYS Chi-restraints excluded: chain y residue 134 SER Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain z residue 92 SER Chi-restraints excluded: chain z residue 123 ASN Chi-restraints excluded: chain z residue 126 THR Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 134 SER Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 3 residue 87 LEU Chi-restraints excluded: chain 4 residue 65 GLN Chi-restraints excluded: chain 4 residue 89 ARG Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 6 residue 87 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 450 optimal weight: 10.0000 chunk 725 optimal weight: 30.0000 chunk 442 optimal weight: 20.0000 chunk 344 optimal weight: 30.0000 chunk 504 optimal weight: 10.0000 chunk 761 optimal weight: 30.0000 chunk 700 optimal weight: 30.0000 chunk 606 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 468 optimal weight: 6.9990 chunk 371 optimal weight: 2.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 GLN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 123 ASN ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 43 GLN ** X 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 GLN b 42 GLN c 12 GLN ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 114 ASN k 116 GLN t 42 GLN x 12 GLN x 43 GLN ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 123 ASN 2 18 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.9730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 73658 Z= 0.281 Angle : 0.735 18.639 103348 Z= 0.400 Chirality : 0.044 0.374 11716 Planarity : 0.006 0.071 11020 Dihedral : 14.632 70.798 16468 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.87 % Allowed : 18.95 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.09), residues: 7308 helix: 1.47 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -1.17 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 17 PHE 0.030 0.002 PHE H 79 TYR 0.033 0.002 TYR O 10 ARG 0.006 0.001 ARG R 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 942 time to evaluate : 5.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 GLN cc_start: 0.5649 (pt0) cc_final: 0.5397 (pt0) REVERT: B 96 LEU cc_start: 0.6409 (tp) cc_final: 0.5895 (tt) REVERT: B 99 MET cc_start: 0.6977 (tpp) cc_final: 0.6489 (tpt) REVERT: D 99 MET cc_start: 0.7095 (tpp) cc_final: 0.6540 (tpp) REVERT: E 107 TYR cc_start: 0.6544 (OUTLIER) cc_final: 0.5872 (t80) REVERT: J 18 GLN cc_start: 0.8113 (tp40) cc_final: 0.7761 (tp40) REVERT: J 43 GLN cc_start: 0.6911 (pp30) cc_final: 0.6452 (pp30) REVERT: N 126 THR cc_start: 0.7278 (p) cc_final: 0.7039 (t) REVERT: R 43 GLN cc_start: 0.6570 (pp30) cc_final: 0.6324 (pp30) REVERT: R 126 THR cc_start: 0.7003 (p) cc_final: 0.6659 (t) REVERT: d 126 THR cc_start: 0.7781 (p) cc_final: 0.7511 (t) REVERT: f 43 GLN cc_start: 0.6850 (pp30) cc_final: 0.6564 (pp30) REVERT: h 18 GLN cc_start: 0.7726 (tp40) cc_final: 0.7364 (tp40) REVERT: k 10 TYR cc_start: 0.7741 (t80) cc_final: 0.7534 (t80) REVERT: o 49 VAL cc_start: 0.8382 (m) cc_final: 0.8092 (p) REVERT: o 57 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6070 (mp0) REVERT: p 107 TYR cc_start: 0.6146 (OUTLIER) cc_final: 0.5253 (t80) REVERT: q 57 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: q 99 MET cc_start: 0.6594 (mmm) cc_final: 0.6320 (tpp) REVERT: r 107 TYR cc_start: 0.6066 (OUTLIER) cc_final: 0.5725 (t80) REVERT: s 87 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7263 (tp) REVERT: t 107 TYR cc_start: 0.6385 (OUTLIER) cc_final: 0.5594 (t80) REVERT: v 107 TYR cc_start: 0.5796 (OUTLIER) cc_final: 0.5308 (t80) REVERT: x 79 PHE cc_start: 0.7974 (t80) cc_final: 0.7688 (t80) REVERT: 2 43 GLN cc_start: 0.6778 (pm20) cc_final: 0.6368 (pm20) REVERT: 4 89 ARG cc_start: 0.4976 (OUTLIER) cc_final: 0.4378 (tpp-160) outliers start: 114 outliers final: 88 residues processed: 1005 average time/residue: 0.6284 time to fit residues: 1116.8010 Evaluate side-chains 959 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 862 time to evaluate : 5.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain Q residue 77 GLN Chi-restraints excluded: chain Q residue 87 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 92 SER Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain V residue 66 TYR Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 97 VAL Chi-restraints excluded: chain W residue 55 VAL Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain a residue 116 GLN Chi-restraints excluded: chain b residue 68 ILE Chi-restraints excluded: chain d residue 46 GLN Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain i residue 124 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain j residue 116 GLN Chi-restraints excluded: chain j residue 117 VAL Chi-restraints excluded: chain k residue 124 ILE Chi-restraints excluded: chain l residue 34 LEU Chi-restraints excluded: chain l residue 87 LEU Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 107 TYR Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 40 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain q residue 57 GLU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 107 TYR Chi-restraints excluded: chain s residue 57 GLU Chi-restraints excluded: chain s residue 87 LEU Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain s residue 133 VAL Chi-restraints excluded: chain t residue 42 GLN Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain t residue 107 TYR Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain u residue 96 LEU Chi-restraints excluded: chain u residue 133 VAL Chi-restraints excluded: chain v residue 97 VAL Chi-restraints excluded: chain v residue 107 TYR Chi-restraints excluded: chain w residue 99 MET Chi-restraints excluded: chain x residue 87 LEU Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain x residue 124 ILE Chi-restraints excluded: chain y residue 51 LYS Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain z residue 92 SER Chi-restraints excluded: chain z residue 123 ASN Chi-restraints excluded: chain z residue 126 THR Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 134 SER Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 3 residue 87 LEU Chi-restraints excluded: chain 4 residue 68 ILE Chi-restraints excluded: chain 4 residue 89 ARG Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 6 residue 87 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 481 optimal weight: 20.0000 chunk 645 optimal weight: 7.9990 chunk 185 optimal weight: 8.9990 chunk 558 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 168 optimal weight: 0.0060 chunk 607 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 623 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 overall best weight: 5.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN F 42 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 ASN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 GLN ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 114 ASN U 123 ASN W 43 GLN ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN a 12 GLN a 65 GLN a 116 GLN b 42 GLN ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 12 GLN ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 123 ASN 4 18 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.075975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.071302 restraints weight = 290980.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.072652 restraints weight = 140741.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.073457 restraints weight = 78546.916| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.9912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 73658 Z= 0.255 Angle : 0.736 18.508 103348 Z= 0.398 Chirality : 0.043 0.359 11716 Planarity : 0.006 0.070 11020 Dihedral : 14.636 72.267 16468 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.79 % Allowed : 19.28 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.09), residues: 7308 helix: 1.51 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -1.20 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 17 PHE 0.041 0.002 PHE v 79 TYR 0.032 0.002 TYR O 10 ARG 0.007 0.001 ARG R 8 =============================================================================== Job complete usr+sys time: 19358.60 seconds wall clock time: 335 minutes 12.72 seconds (20112.72 seconds total)