Starting phenix.real_space_refine on Tue Mar 12 02:50:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc6_4381/03_2024/6gc6_4381.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc6_4381/03_2024/6gc6_4381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc6_4381/03_2024/6gc6_4381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc6_4381/03_2024/6gc6_4381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc6_4381/03_2024/6gc6_4381.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc6_4381/03_2024/6gc6_4381.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.070 sd= 0.487 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 2092 5.49 5 S 47 5.16 5 C 30355 2.51 5 N 11491 2.21 5 O 17419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 10": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 37": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 61404 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 44960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2092, 44960 Classifications: {'RNA': 2092} Modifications used: {'rna2p_pur': 206, 'rna2p_pyr': 111, 'rna3p_pur': 1025, 'rna3p_pyr': 750} Link IDs: {'rna2p': 317, 'rna3p': 1774} Chain breaks: 6 Chain: "C" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1561 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} Chain breaks: 1 Chain: "D" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1366 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 1 Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 778 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain breaks: 1 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Time building chain proxies: 23.75, per 1000 atoms: 0.39 Number of scatterers: 61404 At special positions: 0 Unit cell: (209.56, 166.16, 223.2, 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 47 16.00 P 2092 15.00 O 17419 8.00 N 11491 7.00 C 30355 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.57 Conformation dependent library (CDL) restraints added in 2.6 seconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3872 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 29 sheets defined 27.4% alpha, 20.1% beta 599 base pairs and 1090 stacking pairs defined. Time for finding SS restraints: 21.31 Creating SS restraints... Processing helix chain 'C' and resid 29 through 33 Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.017A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'D' and resid 61 through 72 removed outlier: 4.026A pdb=" N HIS D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.510A pdb=" N VAL E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 178 through 183 removed outlier: 3.740A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 removed outlier: 4.159A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 80 removed outlier: 4.625A pdb=" N THR G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA G 67 " --> pdb=" O GLN G 63 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR G 79 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 removed outlier: 3.549A pdb=" N ILE G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU G 147 " --> pdb=" O VAL G 143 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA G 149 " --> pdb=" O ALA G 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.717A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.678A pdb=" N LYS J 61 " --> pdb=" O ASN J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 96 through 109 removed outlier: 4.475A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.671A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.585A pdb=" N GLN J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 33 removed outlier: 3.862A pdb=" N GLY L 32 " --> pdb=" O LYS L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 99 Processing helix chain 'L' and resid 130 through 135 removed outlier: 4.331A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE L 135 " --> pdb=" O ALA L 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 130 through 135' Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.944A pdb=" N ARG N 17 " --> pdb=" O ASN N 13 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 55 removed outlier: 4.195A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 67 removed outlier: 3.799A pdb=" N ARG N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU N 65 " --> pdb=" O ALA N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 79 removed outlier: 3.666A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 removed outlier: 3.914A pdb=" N ARG N 86 " --> pdb=" O GLU N 82 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 82 through 87' Processing helix chain 'P' and resid 2 through 10 Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 removed outlier: 3.704A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU P 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 108 removed outlier: 3.612A pdb=" N ALA P 106 " --> pdb=" O THR P 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 18 removed outlier: 3.921A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 28 removed outlier: 4.052A pdb=" N ARG Q 27 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.048A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.597A pdb=" N LEU Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP Q 101 " --> pdb=" O ILE Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 115 removed outlier: 3.720A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 22 removed outlier: 3.694A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 4.457A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE S 35 " --> pdb=" O GLN S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 61 removed outlier: 3.647A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 3 through 9 removed outlier: 3.771A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.528A pdb=" N THR T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'Y' and resid 2 through 7 Processing helix chain 'Y' and resid 9 through 32 removed outlier: 3.819A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 56 Processing helix chain '0' and resid 8 through 16 Processing helix chain '0' and resid 17 through 20 removed outlier: 4.199A pdb=" N ALA 0 20 " --> pdb=" O SER 0 17 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 17 through 20' Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 26 through 38 Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.887A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 3 removed outlier: 4.132A pdb=" N VAL C 3 " --> pdb=" O LYS C 17 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS C 17 " --> pdb=" O VAL C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 100 through 104 removed outlier: 3.591A pdb=" N ARG C 101 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 128 through 130 removed outlier: 7.468A pdb=" N ARG C 188 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL C 143 " --> pdb=" O ARG C 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.780A pdb=" N GLN C 162 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL C 164 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 15 removed outlier: 5.749A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR D 25 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 33 through 38 removed outlier: 3.861A pdb=" N ARG D 33 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 120 removed outlier: 7.007A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 8 through 9 removed outlier: 4.291A pdb=" N VAL G 8 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 23 through 25 Processing sheet with id=AB1, first strand: chain 'G' and resid 82 through 87 Processing sheet with id=AB2, first strand: chain 'G' and resid 95 through 98 removed outlier: 3.897A pdb=" N LEU G 104 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL G 112 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.650A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN J 138 " --> pdb=" O TRP J 15 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 73 through 77 Processing sheet with id=AB5, first strand: chain 'K' and resid 6 through 10 removed outlier: 3.728A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL K 63 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.523A pdb=" N VAL K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.523A pdb=" N VAL K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.606A pdb=" N ILE N 34 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE N 113 " --> pdb=" O ILE N 34 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 2 through 6 Processing sheet with id=AC1, first strand: chain 'R' and resid 19 through 22 removed outlier: 3.566A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP R 95 " --> pdb=" O ALA R 65 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS R 97 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL R 63 " --> pdb=" O LYS R 97 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N THR R 99 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ALA R 61 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE R 101 " --> pdb=" O ILE R 59 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE R 59 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 72 through 78 removed outlier: 3.967A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 3 through 8 removed outlier: 6.869A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 82 through 87 removed outlier: 3.845A pdb=" N ARG S 84 " --> pdb=" O ILE S 96 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE S 96 " --> pdb=" O ARG S 84 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'T' and resid 13 through 14 removed outlier: 3.726A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP T 80 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'U' and resid 63 through 65 removed outlier: 6.134A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE U 11 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA U 70 " --> pdb=" O ILE U 11 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN U 73 " --> pdb=" O LYS U 78 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS U 78 " --> pdb=" O ASN U 73 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 40 through 41 removed outlier: 3.689A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 83 through 87 removed outlier: 3.839A pdb=" N GLY U 83 " --> pdb=" O PHE U 94 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE U 94 " --> pdb=" O GLY U 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG U 85 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS U 90 " --> pdb=" O GLU U 87 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AD1, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AD2, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.575A pdb=" N ARG Z 37 " --> pdb=" O ILE Z 4 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE Z 4 " --> pdb=" O ARG Z 37 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1503 hydrogen bonds 2356 hydrogen bond angles 0 basepair planarities 599 basepair parallelities 1090 stacking parallelities Total time for adding SS restraints: 71.25 Time building geometry restraints manager: 27.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8552 1.33 - 1.45: 28364 1.45 - 1.57: 25831 1.57 - 1.69: 4177 1.69 - 1.81: 88 Bond restraints: 67012 Sorted by residual: bond pdb=" C ILE K 47 " pdb=" N PRO K 48 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.30e-02 5.92e+03 5.79e+00 bond pdb=" CA ASN U 98 " pdb=" CB ASN U 98 " ideal model delta sigma weight residual 1.532 1.563 -0.031 1.33e-02 5.65e+03 5.50e+00 bond pdb=" CB ASN U 98 " pdb=" CG ASN U 98 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.20e+00 bond pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.14e+00 bond pdb=" C3' G A 271 " pdb=" O3' G A 271 " ideal model delta sigma weight residual 1.427 1.455 -0.028 1.50e-02 4.44e+03 3.55e+00 ... (remaining 67007 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.56: 12725 106.56 - 113.62: 40542 113.62 - 120.68: 26231 120.68 - 127.74: 17423 127.74 - 134.79: 3972 Bond angle restraints: 100893 Sorted by residual: angle pdb=" C ILE T 2 " pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 121.70 133.71 -12.01 1.80e+00 3.09e-01 4.46e+01 angle pdb=" N VAL D 98 " pdb=" CA VAL D 98 " pdb=" C VAL D 98 " ideal model delta sigma weight residual 112.83 107.10 5.73 9.90e-01 1.02e+00 3.35e+01 angle pdb=" C SER U 97 " pdb=" N ASN U 98 " pdb=" CA ASN U 98 " ideal model delta sigma weight residual 124.82 134.79 -9.97 1.78e+00 3.16e-01 3.14e+01 angle pdb=" C VAL 0 53 " pdb=" N ILE 0 54 " pdb=" CA ILE 0 54 " ideal model delta sigma weight residual 120.77 127.99 -7.22 1.31e+00 5.83e-01 3.04e+01 angle pdb=" C ASP S 65 " pdb=" N ILE S 66 " pdb=" CA ILE S 66 " ideal model delta sigma weight residual 120.46 127.36 -6.90 1.37e+00 5.33e-01 2.54e+01 ... (remaining 100888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 37705 35.30 - 70.60: 4543 70.60 - 105.90: 542 105.90 - 141.20: 2 141.20 - 176.50: 6 Dihedral angle restraints: 42798 sinusoidal: 36792 harmonic: 6006 Sorted by residual: dihedral pdb=" CA GLY C 11 " pdb=" C GLY C 11 " pdb=" N ARG C 12 " pdb=" CA ARG C 12 " ideal model delta harmonic sigma weight residual -180.00 -129.02 -50.98 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" O4' U A1174 " pdb=" C1' U A1174 " pdb=" N1 U A1174 " pdb=" C2 U A1174 " ideal model delta sinusoidal sigma weight residual 200.00 46.03 153.97 1 1.50e+01 4.44e-03 8.10e+01 dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 61.18 138.82 1 1.50e+01 4.44e-03 7.48e+01 ... (remaining 42795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 12060 0.057 - 0.113: 803 0.113 - 0.170: 122 0.170 - 0.227: 16 0.227 - 0.284: 4 Chirality restraints: 13005 Sorted by residual: chirality pdb=" C3' G A 271 " pdb=" C4' G A 271 " pdb=" O3' G A 271 " pdb=" C2' G A 271 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' A A1378 " pdb=" C4' A A1378 " pdb=" O3' A A1378 " pdb=" C2' A A1378 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ASN U 98 " pdb=" N ASN U 98 " pdb=" C ASN U 98 " pdb=" CB ASN U 98 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 13002 not shown) Planarity restraints: 4966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL L 110 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C VAL L 110 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL L 110 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE L 111 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 11 " -0.015 2.00e-02 2.50e+03 3.13e-02 9.81e+00 pdb=" C GLY C 11 " 0.054 2.00e-02 2.50e+03 pdb=" O GLY C 11 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG C 12 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A1736 " -0.029 2.00e-02 2.50e+03 1.63e-02 5.97e+00 pdb=" N1 U A1736 " 0.037 2.00e-02 2.50e+03 pdb=" C2 U A1736 " -0.000 2.00e-02 2.50e+03 pdb=" O2 U A1736 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U A1736 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U A1736 " -0.008 2.00e-02 2.50e+03 pdb=" O4 U A1736 " -0.005 2.00e-02 2.50e+03 pdb=" C5 U A1736 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U A1736 " 0.004 2.00e-02 2.50e+03 ... (remaining 4963 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 9744 2.76 - 3.30: 49531 3.30 - 3.83: 127930 3.83 - 4.37: 148474 4.37 - 4.90: 199079 Nonbonded interactions: 534758 Sorted by model distance: nonbonded pdb=" O2' C A1351 " pdb=" O2' A A1571 " model vdw 2.229 2.440 nonbonded pdb=" O2 C A 269 " pdb=" N2 G A 370 " model vdw 2.230 2.496 nonbonded pdb=" O2' C A 239 " pdb=" O2' G A 622 " model vdw 2.257 2.440 nonbonded pdb=" O ILE S 35 " pdb=" OG1 THR S 39 " model vdw 2.273 2.440 nonbonded pdb=" O LEU S 33 " pdb=" OG1 THR S 37 " model vdw 2.281 2.440 ... (remaining 534753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.880 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: 0.040 Extract box with map and model: 6.330 Check model and map are aligned: 0.680 Set scattering table: 0.410 Process input model: 185.730 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.130 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:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 197.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 67012 Z= 0.160 Angle : 0.662 12.014 100893 Z= 0.339 Chirality : 0.031 0.284 13005 Planarity : 0.005 0.053 4966 Dihedral : 22.325 176.501 38926 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.97 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.14), residues: 2076 helix: -4.21 (0.10), residues: 514 sheet: -1.27 (0.27), residues: 339 loop : -2.34 (0.14), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 60 HIS 0.006 0.001 HIS R 82 PHE 0.016 0.002 PHE R 5 TYR 0.013 0.001 TYR Q 24 ARG 0.007 0.001 ARG R 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 851 time to evaluate : 2.370 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 LEU cc_start: 0.4040 (mt) cc_final: 0.3759 (mt) REVERT: G 74 MET cc_start: 0.0153 (mtt) cc_final: -0.0828 (ptm) REVERT: J 93 ILE cc_start: 0.7287 (mm) cc_final: 0.6840 (tp) REVERT: J 101 ILE cc_start: 0.7570 (mm) cc_final: 0.7190 (mm) REVERT: J 114 LEU cc_start: 0.7468 (tp) cc_final: 0.7229 (tt) REVERT: K 73 ASP cc_start: 0.5516 (p0) cc_final: 0.5237 (p0) REVERT: N 28 LEU cc_start: 0.6479 (tp) cc_final: 0.6224 (tp) REVERT: N 53 THR cc_start: 0.7507 (m) cc_final: 0.6363 (m) REVERT: N 57 THR cc_start: 0.7554 (m) cc_final: 0.7082 (m) REVERT: N 65 LEU cc_start: 0.7373 (tp) cc_final: 0.7085 (tp) REVERT: Q 90 ASP cc_start: 0.7017 (p0) cc_final: 0.6365 (p0) REVERT: R 63 VAL cc_start: 0.6919 (t) cc_final: 0.6336 (t) REVERT: S 30 SER cc_start: 0.7783 (m) cc_final: 0.6969 (t) REVERT: S 72 THR cc_start: 0.6664 (p) cc_final: 0.6380 (t) REVERT: S 75 PHE cc_start: 0.6629 (p90) cc_final: 0.6428 (p90) REVERT: S 76 VAL cc_start: 0.8409 (t) cc_final: 0.7799 (t) REVERT: S 106 VAL cc_start: 0.7238 (t) cc_final: 0.6796 (t) REVERT: T 50 LEU cc_start: 0.7468 (mp) cc_final: 0.7242 (mt) REVERT: U 30 SER cc_start: 0.6945 (p) cc_final: 0.6737 (m) REVERT: U 34 ILE cc_start: 0.6997 (mm) cc_final: 0.6365 (mm) REVERT: Z 13 ILE cc_start: 0.6604 (mt) cc_final: 0.6255 (mm) REVERT: Z 26 LEU cc_start: 0.7239 (mt) cc_final: 0.5870 (mt) outliers start: 0 outliers final: 0 residues processed: 851 average time/residue: 0.7308 time to fit residues: 978.4766 Evaluate side-chains 500 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 349 optimal weight: 10.0000 chunk 313 optimal weight: 30.0000 chunk 174 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 167 optimal weight: 30.0000 chunk 324 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 197 optimal weight: 20.0000 chunk 241 optimal weight: 9.9990 chunk 375 optimal weight: 20.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 42 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN G 127 GLN J 76 HIS K 93 GLN L 4 ASN ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 ASN U 65 GLN U 68 ASN Y 20 ASN ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN 2 6 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.210 67012 Z= 0.382 Angle : 0.825 14.091 100893 Z= 0.417 Chirality : 0.041 0.260 13005 Planarity : 0.007 0.147 4966 Dihedral : 23.668 179.074 34819 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 31.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.84 % Favored : 93.06 % Rotamer: Outliers : 0.23 % Allowed : 5.01 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.16), residues: 2076 helix: -2.10 (0.18), residues: 556 sheet: -1.01 (0.26), residues: 361 loop : -1.97 (0.16), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP R 92 HIS 0.011 0.003 HIS J 40 PHE 0.027 0.003 PHE S 75 TYR 0.021 0.003 TYR E 101 ARG 0.028 0.001 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 557 time to evaluate : 2.388 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: 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: C 180 MET cc_start: 0.4995 (mmt) cc_final: 0.4692 (mmm) REVERT: D 21 SER cc_start: 0.7105 (t) cc_final: 0.6432 (p) REVERT: D 58 ASN cc_start: 0.6683 (p0) cc_final: 0.6344 (m-40) REVERT: E 43 THR cc_start: 0.7018 (p) cc_final: 0.6640 (p) REVERT: E 191 ASP cc_start: 0.5851 (p0) cc_final: 0.5644 (p0) REVERT: G 74 MET cc_start: 0.0432 (mtt) cc_final: -0.0164 (ttp) REVERT: K 47 ILE cc_start: 0.6452 (pt) cc_final: 0.6206 (pt) REVERT: K 73 ASP cc_start: 0.6711 (p0) cc_final: 0.6438 (p0) REVERT: L 3 LEU cc_start: 0.7242 (mm) cc_final: 0.6982 (mm) REVERT: N 57 THR cc_start: 0.7827 (m) cc_final: 0.7472 (m) REVERT: N 81 ASN cc_start: 0.7977 (p0) cc_final: 0.7448 (p0) REVERT: N 94 TYR cc_start: 0.6519 (m-80) cc_final: 0.6178 (m-80) REVERT: Q 46 TYR cc_start: 0.7254 (t80) cc_final: 0.7027 (t80) REVERT: S 30 SER cc_start: 0.7432 (m) cc_final: 0.6938 (t) REVERT: S 67 ASP cc_start: 0.6723 (t0) cc_final: 0.6497 (t0) REVERT: S 69 LEU cc_start: 0.6550 (mm) cc_final: 0.6267 (mm) REVERT: T 1 MET cc_start: 0.2512 (mtt) cc_final: 0.2195 (mtt) REVERT: Y 8 GLU cc_start: 0.6525 (pt0) cc_final: 0.5682 (pt0) REVERT: 0 18 HIS cc_start: 0.6531 (m-70) cc_final: 0.6290 (m90) outliers start: 4 outliers final: 1 residues processed: 559 average time/residue: 0.6549 time to fit residues: 590.5799 Evaluate side-chains 422 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 421 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 208 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 312 optimal weight: 0.9990 chunk 256 optimal weight: 0.2980 chunk 103 optimal weight: 10.0000 chunk 376 optimal weight: 0.2980 chunk 406 optimal weight: 1.9990 chunk 335 optimal weight: 6.9990 chunk 373 optimal weight: 7.9990 chunk 128 optimal weight: 20.0000 chunk 302 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN C 152 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS J 86 GLN J 135 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS Q 19 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN 0 41 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 67012 Z= 0.141 Angle : 0.505 10.195 100893 Z= 0.262 Chirality : 0.030 0.243 13005 Planarity : 0.004 0.044 4966 Dihedral : 23.368 178.280 34819 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.78 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.17), residues: 2076 helix: -1.14 (0.21), residues: 551 sheet: -0.66 (0.25), residues: 389 loop : -1.70 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 15 HIS 0.006 0.001 HIS S 60 PHE 0.016 0.001 PHE S 75 TYR 0.018 0.001 TYR C 61 ARG 0.012 0.001 ARG J 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 549 time to evaluate : 2.395 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: 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: D 18 ASP cc_start: 0.7688 (p0) cc_final: 0.7164 (p0) REVERT: E 43 THR cc_start: 0.7195 (p) cc_final: 0.6656 (p) REVERT: E 173 THR cc_start: 0.7226 (m) cc_final: 0.6960 (p) REVERT: G 74 MET cc_start: 0.0564 (mtt) cc_final: -0.0327 (mtm) REVERT: J 101 ILE cc_start: 0.7342 (tp) cc_final: 0.7052 (tp) REVERT: K 1 MET cc_start: 0.4684 (pmm) cc_final: 0.4344 (pmm) REVERT: K 73 ASP cc_start: 0.6440 (p0) cc_final: 0.6090 (p0) REVERT: N 53 THR cc_start: 0.8267 (m) cc_final: 0.7943 (m) REVERT: N 57 THR cc_start: 0.8049 (m) cc_final: 0.7796 (m) REVERT: N 81 ASN cc_start: 0.7717 (p0) cc_final: 0.7079 (p0) REVERT: P 5 LYS cc_start: 0.7935 (mttm) cc_final: 0.7498 (mttm) REVERT: Q 109 VAL cc_start: 0.7705 (t) cc_final: 0.7324 (t) REVERT: Q 116 LEU cc_start: 0.6681 (tt) cc_final: 0.6280 (tt) REVERT: R 82 HIS cc_start: 0.6538 (t70) cc_final: 0.6227 (t70) REVERT: S 61 ASN cc_start: 0.5725 (m110) cc_final: 0.5127 (m110) REVERT: S 106 VAL cc_start: 0.7652 (t) cc_final: 0.7416 (t) REVERT: T 50 LEU cc_start: 0.7042 (mm) cc_final: 0.6559 (mm) REVERT: Y 26 PHE cc_start: 0.6277 (t80) cc_final: 0.5325 (t80) REVERT: Y 49 ASP cc_start: 0.6296 (m-30) cc_final: 0.5468 (m-30) REVERT: 0 3 GLN cc_start: 0.6915 (mp10) cc_final: 0.6548 (mt0) REVERT: 0 18 HIS cc_start: 0.6278 (m-70) cc_final: 0.6040 (m90) outliers start: 0 outliers final: 0 residues processed: 549 average time/residue: 0.6542 time to fit residues: 578.9647 Evaluate side-chains 420 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 372 optimal weight: 8.9990 chunk 283 optimal weight: 0.0980 chunk 195 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 179 optimal weight: 30.0000 chunk 252 optimal weight: 8.9990 chunk 377 optimal weight: 20.0000 chunk 400 optimal weight: 20.0000 chunk 197 optimal weight: 20.0000 chunk 358 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN G 127 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 67012 Z= 0.258 Angle : 0.612 8.473 100893 Z= 0.318 Chirality : 0.035 0.249 13005 Planarity : 0.005 0.073 4966 Dihedral : 23.546 176.788 34819 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 25.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.37 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.17), residues: 2076 helix: -1.01 (0.21), residues: 553 sheet: -0.70 (0.25), residues: 385 loop : -1.58 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 15 HIS 0.007 0.002 HIS Q 13 PHE 0.025 0.002 PHE E 85 TYR 0.016 0.002 TYR N 94 ARG 0.011 0.001 ARG J 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 3.626 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: 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: E 43 THR cc_start: 0.7040 (p) cc_final: 0.6653 (p) REVERT: G 74 MET cc_start: 0.0351 (mtt) cc_final: -0.0044 (mtm) REVERT: K 1 MET cc_start: 0.4973 (pmm) cc_final: 0.4511 (pmm) REVERT: K 8 LEU cc_start: 0.7449 (mm) cc_final: 0.7234 (mm) REVERT: K 73 ASP cc_start: 0.6840 (p0) cc_final: 0.6338 (p0) REVERT: N 20 MET cc_start: 0.6757 (tpp) cc_final: 0.6493 (tpp) REVERT: N 49 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6862 (mm-30) REVERT: N 53 THR cc_start: 0.8593 (m) cc_final: 0.8364 (m) REVERT: N 57 THR cc_start: 0.8171 (m) cc_final: 0.7849 (m) REVERT: P 5 LYS cc_start: 0.7712 (mttm) cc_final: 0.7224 (mttm) REVERT: Q 63 ARG cc_start: 0.5877 (mtt180) cc_final: 0.5661 (mtt180) REVERT: S 24 ILE cc_start: 0.8912 (mm) cc_final: 0.8561 (mm) REVERT: S 51 LEU cc_start: 0.7789 (pp) cc_final: 0.7467 (pp) REVERT: S 61 ASN cc_start: 0.6517 (m110) cc_final: 0.5960 (m110) REVERT: S 106 VAL cc_start: 0.7877 (t) cc_final: 0.7601 (t) REVERT: T 1 MET cc_start: 0.3084 (mtt) cc_final: 0.2788 (mtt) REVERT: T 50 LEU cc_start: 0.7243 (mm) cc_final: 0.6824 (mm) REVERT: Y 26 PHE cc_start: 0.7408 (t80) cc_final: 0.6620 (t80) REVERT: 0 3 GLN cc_start: 0.6886 (mp10) cc_final: 0.6411 (mt0) REVERT: 0 18 HIS cc_start: 0.6756 (m-70) cc_final: 0.6369 (m-70) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.6721 time to fit residues: 559.7384 Evaluate side-chains 388 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 333 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 297 optimal weight: 5.9990 chunk 165 optimal weight: 50.0000 chunk 341 optimal weight: 6.9990 chunk 276 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 359 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 42 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS E 30 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN J 40 HIS ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 HIS N 73 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.6610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 67012 Z= 0.266 Angle : 0.623 8.884 100893 Z= 0.324 Chirality : 0.035 0.247 13005 Planarity : 0.005 0.082 4966 Dihedral : 23.718 174.949 34819 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 26.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.29 % Favored : 91.62 % Rotamer: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.88 (0.17), residues: 2076 helix: -0.79 (0.21), residues: 542 sheet: -0.88 (0.25), residues: 376 loop : -1.60 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 15 HIS 0.009 0.002 HIS C 24 PHE 0.021 0.002 PHE D 127 TYR 0.017 0.002 TYR N 94 ARG 0.012 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 474 time to evaluate : 2.411 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 ILE cc_start: 0.8074 (pt) cc_final: 0.7772 (pt) REVERT: D 18 ASP cc_start: 0.8280 (p0) cc_final: 0.7813 (p0) REVERT: D 108 ASP cc_start: 0.6034 (t70) cc_final: 0.5682 (t0) REVERT: G 74 MET cc_start: 0.0242 (mtt) cc_final: -0.0227 (mtm) REVERT: J 132 HIS cc_start: 0.4834 (OUTLIER) cc_final: 0.4609 (m170) REVERT: K 1 MET cc_start: 0.5366 (pmm) cc_final: 0.4882 (pmm) REVERT: K 8 LEU cc_start: 0.7712 (mm) cc_final: 0.7125 (mm) REVERT: K 73 ASP cc_start: 0.6998 (p0) cc_final: 0.6502 (p0) REVERT: K 112 PHE cc_start: 0.4268 (m-80) cc_final: 0.3803 (m-80) REVERT: L 3 LEU cc_start: 0.7674 (mm) cc_final: 0.7444 (mt) REVERT: N 20 MET cc_start: 0.6728 (tpp) cc_final: 0.6051 (tpp) REVERT: N 23 ASN cc_start: 0.8314 (p0) cc_final: 0.8108 (p0) REVERT: N 53 THR cc_start: 0.8682 (m) cc_final: 0.8411 (m) REVERT: P 5 LYS cc_start: 0.7583 (mttm) cc_final: 0.7099 (mttm) REVERT: P 8 GLU cc_start: 0.6894 (pt0) cc_final: 0.6572 (pt0) REVERT: Q 88 GLU cc_start: 0.5450 (pm20) cc_final: 0.5013 (pm20) REVERT: S 24 ILE cc_start: 0.8870 (mm) cc_final: 0.8473 (mm) REVERT: S 74 ILE cc_start: 0.8184 (pt) cc_final: 0.7753 (pt) REVERT: 0 3 GLN cc_start: 0.6683 (mp10) cc_final: 0.6444 (mt0) REVERT: 0 18 HIS cc_start: 0.6916 (m-70) cc_final: 0.6247 (m-70) outliers start: 1 outliers final: 0 residues processed: 474 average time/residue: 0.6195 time to fit residues: 484.5863 Evaluate side-chains 381 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 380 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 134 optimal weight: 10.0000 chunk 360 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 400 optimal weight: 0.4980 chunk 332 optimal weight: 0.8980 chunk 185 optimal weight: 40.0000 chunk 33 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 overall best weight: 6.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 4 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.7194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 67012 Z= 0.271 Angle : 0.634 9.020 100893 Z= 0.329 Chirality : 0.036 0.248 13005 Planarity : 0.005 0.064 4966 Dihedral : 23.808 175.762 34819 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 27.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.38 % Favored : 91.52 % Rotamer: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.17), residues: 2076 helix: -1.03 (0.20), residues: 546 sheet: -1.02 (0.25), residues: 401 loop : -1.58 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 15 HIS 0.008 0.002 HIS J 76 PHE 0.030 0.002 PHE K 112 TYR 0.015 0.002 TYR N 112 ARG 0.030 0.001 ARG T 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 467 time to evaluate : 2.428 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: 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 2 ILE cc_start: 0.8161 (pt) cc_final: 0.7724 (pt) REVERT: D 18 ASP cc_start: 0.8284 (p0) cc_final: 0.7918 (p0) REVERT: D 164 GLN cc_start: 0.6731 (tm-30) cc_final: 0.6453 (tm-30) REVERT: G 74 MET cc_start: 0.0125 (mtt) cc_final: -0.0274 (mtm) REVERT: J 16 TYR cc_start: 0.6436 (m-80) cc_final: 0.5715 (m-80) REVERT: K 1 MET cc_start: 0.5583 (pmm) cc_final: 0.5193 (pmm) REVERT: K 73 ASP cc_start: 0.7177 (p0) cc_final: 0.6413 (p0) REVERT: L 3 LEU cc_start: 0.7161 (mm) cc_final: 0.6894 (mp) REVERT: P 5 LYS cc_start: 0.7332 (mttm) cc_final: 0.7041 (mttm) REVERT: S 24 ILE cc_start: 0.8953 (mm) cc_final: 0.8697 (mm) REVERT: S 51 LEU cc_start: 0.7849 (pp) cc_final: 0.7608 (pp) REVERT: S 69 LEU cc_start: 0.6217 (mm) cc_final: 0.5919 (mm) REVERT: S 109 ASP cc_start: 0.7158 (p0) cc_final: 0.6795 (p0) REVERT: U 21 ARG cc_start: 0.7127 (tpp-160) cc_final: 0.6599 (mmm-85) REVERT: 0 3 GLN cc_start: 0.6452 (mp10) cc_final: 0.6100 (mt0) REVERT: 0 18 HIS cc_start: 0.7191 (m-70) cc_final: 0.6505 (m-70) REVERT: 0 54 ILE cc_start: 0.8285 (tp) cc_final: 0.8020 (tp) outliers start: 1 outliers final: 0 residues processed: 467 average time/residue: 0.6221 time to fit residues: 480.3733 Evaluate side-chains 374 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 386 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 292 optimal weight: 30.0000 chunk 226 optimal weight: 6.9990 chunk 337 optimal weight: 20.0000 chunk 223 optimal weight: 8.9990 chunk 399 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 184 optimal weight: 40.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN G 72 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.8059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 67012 Z= 0.322 Angle : 0.707 12.419 100893 Z= 0.365 Chirality : 0.039 0.265 13005 Planarity : 0.006 0.106 4966 Dihedral : 24.060 176.120 34819 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 32.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.92 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.17), residues: 2076 helix: -1.32 (0.20), residues: 534 sheet: -1.20 (0.25), residues: 387 loop : -1.67 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 125 HIS 0.014 0.002 HIS C 24 PHE 0.030 0.003 PHE K 112 TYR 0.025 0.002 TYR N 94 ARG 0.017 0.001 ARG Z 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 2.448 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 ILE cc_start: 0.8270 (pt) cc_final: 0.7883 (pt) REVERT: D 18 ASP cc_start: 0.8443 (p0) cc_final: 0.7887 (p0) REVERT: D 80 TRP cc_start: 0.7674 (m-90) cc_final: 0.7313 (m100) REVERT: D 183 GLU cc_start: 0.8386 (pp20) cc_final: 0.7583 (pp20) REVERT: G 74 MET cc_start: 0.0860 (mtt) cc_final: 0.0135 (mtm) REVERT: J 136 GLN cc_start: 0.7235 (tm-30) cc_final: 0.6969 (tm-30) REVERT: K 14 SER cc_start: 0.5285 (m) cc_final: 0.4879 (m) REVERT: K 73 ASP cc_start: 0.6733 (p0) cc_final: 0.6379 (p0) REVERT: N 23 ASN cc_start: 0.7776 (p0) cc_final: 0.7226 (p0) REVERT: N 53 THR cc_start: 0.8610 (m) cc_final: 0.8405 (m) REVERT: P 5 LYS cc_start: 0.7464 (mttm) cc_final: 0.6939 (mttm) REVERT: P 8 GLU cc_start: 0.7072 (pt0) cc_final: 0.6750 (pt0) REVERT: P 112 ARG cc_start: 0.7321 (ttm170) cc_final: 0.6489 (ttm170) REVERT: S 51 LEU cc_start: 0.7868 (pp) cc_final: 0.7662 (pp) REVERT: S 72 THR cc_start: 0.8083 (p) cc_final: 0.7748 (p) REVERT: S 74 ILE cc_start: 0.8332 (pt) cc_final: 0.7887 (pt) REVERT: S 109 ASP cc_start: 0.6943 (p0) cc_final: 0.6678 (p0) REVERT: T 92 ASN cc_start: 0.8786 (t0) cc_final: 0.8341 (t0) REVERT: U 21 ARG cc_start: 0.6750 (tpp-160) cc_final: 0.6359 (mmm-85) REVERT: Y 34 SER cc_start: 0.5331 (p) cc_final: 0.5120 (p) REVERT: 0 18 HIS cc_start: 0.7304 (m-70) cc_final: 0.6817 (m-70) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.6327 time to fit residues: 498.3041 Evaluate side-chains 385 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 246 optimal weight: 0.8980 chunk 159 optimal weight: 20.0000 chunk 238 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 78 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 253 optimal weight: 30.0000 chunk 271 optimal weight: 8.9990 chunk 197 optimal weight: 20.0000 chunk 37 optimal weight: 30.0000 chunk 313 optimal weight: 9.9990 overall best weight: 7.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.8476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 67012 Z= 0.331 Angle : 0.701 8.849 100893 Z= 0.362 Chirality : 0.039 0.287 13005 Planarity : 0.006 0.085 4966 Dihedral : 24.113 175.263 34819 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 32.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.92 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.17), residues: 2076 helix: -1.33 (0.20), residues: 523 sheet: -1.21 (0.26), residues: 396 loop : -1.75 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 15 HIS 0.008 0.002 HIS P 76 PHE 0.026 0.003 PHE K 112 TYR 0.029 0.002 TYR Q 23 ARG 0.013 0.001 ARG Y 7 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 2.440 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 ILE cc_start: 0.8221 (pt) cc_final: 0.7853 (pt) REVERT: D 18 ASP cc_start: 0.8550 (p0) cc_final: 0.8033 (p0) REVERT: D 80 TRP cc_start: 0.7611 (m-90) cc_final: 0.7052 (m100) REVERT: G 74 MET cc_start: 0.1083 (mtt) cc_final: 0.0125 (mtm) REVERT: K 73 ASP cc_start: 0.7147 (p0) cc_final: 0.6725 (p0) REVERT: K 112 PHE cc_start: 0.4945 (m-80) cc_final: 0.4493 (m-80) REVERT: N 23 ASN cc_start: 0.7991 (p0) cc_final: 0.7413 (p0) REVERT: N 40 LYS cc_start: 0.7758 (mtpp) cc_final: 0.7511 (mtpp) REVERT: P 5 LYS cc_start: 0.7537 (mttm) cc_final: 0.7035 (mttm) REVERT: P 112 ARG cc_start: 0.7617 (ttm170) cc_final: 0.6864 (ttm170) REVERT: R 81 LYS cc_start: 0.7906 (mmmt) cc_final: 0.7591 (mmtm) REVERT: S 45 VAL cc_start: 0.7833 (t) cc_final: 0.7540 (p) REVERT: S 51 LEU cc_start: 0.7943 (pp) cc_final: 0.7603 (pp) REVERT: S 68 ASP cc_start: 0.7451 (p0) cc_final: 0.7153 (p0) REVERT: S 72 THR cc_start: 0.8331 (p) cc_final: 0.8065 (p) REVERT: S 74 ILE cc_start: 0.8316 (pt) cc_final: 0.8032 (pt) REVERT: S 109 ASP cc_start: 0.6880 (p0) cc_final: 0.6424 (p0) REVERT: 0 3 GLN cc_start: 0.6221 (mp10) cc_final: 0.5538 (mt0) REVERT: 0 18 HIS cc_start: 0.7374 (m-70) cc_final: 0.6899 (m-70) REVERT: 0 53 VAL cc_start: 0.7810 (m) cc_final: 0.7373 (p) REVERT: Z 55 LYS cc_start: 0.6203 (mmtm) cc_final: 0.5863 (mmtm) outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.6384 time to fit residues: 508.0656 Evaluate side-chains 384 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 362 optimal weight: 9.9990 chunk 382 optimal weight: 8.9990 chunk 348 optimal weight: 2.9990 chunk 371 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 291 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 351 optimal weight: 10.0000 chunk 370 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN J 132 HIS ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.8532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 67012 Z= 0.255 Angle : 0.635 13.666 100893 Z= 0.329 Chirality : 0.036 0.282 13005 Planarity : 0.005 0.064 4966 Dihedral : 24.029 172.405 34819 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 27.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.91 % Favored : 90.94 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.17), residues: 2076 helix: -1.16 (0.21), residues: 527 sheet: -1.03 (0.26), residues: 391 loop : -1.72 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 15 HIS 0.009 0.002 HIS C 24 PHE 0.035 0.002 PHE K 112 TYR 0.023 0.002 TYR Q 46 ARG 0.010 0.001 ARG K 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 2.468 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 ILE cc_start: 0.8148 (pt) cc_final: 0.7795 (pt) REVERT: D 18 ASP cc_start: 0.8372 (p0) cc_final: 0.7793 (p0) REVERT: D 80 TRP cc_start: 0.7624 (m-90) cc_final: 0.7246 (m100) REVERT: E 17 THR cc_start: 0.8057 (p) cc_final: 0.7039 (p) REVERT: G 74 MET cc_start: 0.1140 (mtt) cc_final: 0.0134 (mtm) REVERT: J 57 LEU cc_start: 0.6976 (mt) cc_final: 0.6756 (mp) REVERT: J 108 MET cc_start: 0.6926 (tpt) cc_final: 0.6674 (tpt) REVERT: K 73 ASP cc_start: 0.6783 (p0) cc_final: 0.6459 (p0) REVERT: N 23 ASN cc_start: 0.7816 (p0) cc_final: 0.7348 (p0) REVERT: N 40 LYS cc_start: 0.7612 (mtpp) cc_final: 0.7167 (mtpp) REVERT: P 5 LYS cc_start: 0.7439 (mttm) cc_final: 0.7015 (mttm) REVERT: P 8 GLU cc_start: 0.6137 (pt0) cc_final: 0.5931 (pt0) REVERT: P 112 ARG cc_start: 0.7565 (ttm170) cc_final: 0.6645 (ttm170) REVERT: R 81 LYS cc_start: 0.7822 (mmmt) cc_final: 0.7467 (mmtt) REVERT: S 74 ILE cc_start: 0.8372 (pt) cc_final: 0.7991 (pt) REVERT: Y 1 MET cc_start: 0.6623 (ppp) cc_final: 0.6126 (ppp) REVERT: Y 7 ARG cc_start: 0.7753 (pmt-80) cc_final: 0.7424 (pmt-80) REVERT: Y 8 GLU cc_start: 0.6410 (tt0) cc_final: 0.5958 (tt0) REVERT: Y 24 GLU cc_start: 0.6116 (mp0) cc_final: 0.5869 (mp0) REVERT: Y 34 SER cc_start: 0.5301 (p) cc_final: 0.4946 (p) REVERT: 0 3 GLN cc_start: 0.6360 (mp10) cc_final: 0.5773 (mt0) REVERT: 0 18 HIS cc_start: 0.7291 (m-70) cc_final: 0.6796 (m-70) REVERT: 0 45 ASP cc_start: 0.7975 (p0) cc_final: 0.7695 (p0) REVERT: 0 53 VAL cc_start: 0.7881 (m) cc_final: 0.7486 (p) outliers start: 0 outliers final: 0 residues processed: 483 average time/residue: 0.6403 time to fit residues: 506.4608 Evaluate side-chains 383 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 244 optimal weight: 0.7980 chunk 393 optimal weight: 8.9990 chunk 239 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 273 optimal weight: 30.0000 chunk 412 optimal weight: 5.9990 chunk 379 optimal weight: 5.9990 chunk 328 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 253 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 GLN ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN Y 27 ASN 2 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.8381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 67012 Z= 0.168 Angle : 0.562 11.834 100893 Z= 0.290 Chirality : 0.032 0.261 13005 Planarity : 0.005 0.097 4966 Dihedral : 23.815 171.783 34819 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.85 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.84 (0.18), residues: 2076 helix: -0.80 (0.22), residues: 526 sheet: -0.87 (0.26), residues: 394 loop : -1.54 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.003 TRP J 15 HIS 0.008 0.001 HIS Z 19 PHE 0.043 0.002 PHE K 112 TYR 0.017 0.002 TYR C 160 ARG 0.010 0.001 ARG J 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 491 time to evaluate : 2.502 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: D 18 ASP cc_start: 0.8026 (p0) cc_final: 0.7356 (p0) REVERT: D 80 TRP cc_start: 0.7372 (m-90) cc_final: 0.7070 (m100) REVERT: E 43 THR cc_start: 0.7272 (p) cc_final: 0.6982 (p) REVERT: G 74 MET cc_start: 0.1265 (mtt) cc_final: 0.0400 (mtm) REVERT: J 57 LEU cc_start: 0.7021 (mt) cc_final: 0.6779 (mp) REVERT: J 108 MET cc_start: 0.6495 (tpt) cc_final: 0.6120 (mmm) REVERT: K 73 ASP cc_start: 0.6354 (p0) cc_final: 0.6070 (p0) REVERT: N 42 LYS cc_start: 0.7877 (mmtt) cc_final: 0.7377 (mmtt) REVERT: N 118 ARG cc_start: 0.6750 (ptm-80) cc_final: 0.5753 (ttp80) REVERT: P 5 LYS cc_start: 0.7340 (mttm) cc_final: 0.7046 (mttm) REVERT: R 81 LYS cc_start: 0.7846 (mmmt) cc_final: 0.7476 (mmtt) REVERT: S 33 LEU cc_start: 0.7291 (mm) cc_final: 0.6989 (mt) REVERT: S 36 LEU cc_start: 0.8388 (pp) cc_final: 0.8167 (pp) REVERT: S 72 THR cc_start: 0.7875 (p) cc_final: 0.7557 (p) REVERT: S 74 ILE cc_start: 0.8281 (pt) cc_final: 0.7830 (pt) REVERT: T 92 ASN cc_start: 0.8534 (t0) cc_final: 0.7966 (t0) REVERT: Y 1 MET cc_start: 0.6429 (ppp) cc_final: 0.6181 (ppp) REVERT: Y 7 ARG cc_start: 0.7618 (pmt-80) cc_final: 0.7339 (pmt-80) REVERT: Y 24 GLU cc_start: 0.6026 (mp0) cc_final: 0.5711 (mp0) REVERT: 0 3 GLN cc_start: 0.6619 (mp10) cc_final: 0.5987 (mt0) REVERT: 0 18 HIS cc_start: 0.7403 (m-70) cc_final: 0.6742 (m-70) REVERT: 0 53 VAL cc_start: 0.7370 (m) cc_final: 0.7167 (p) outliers start: 0 outliers final: 0 residues processed: 491 average time/residue: 0.6452 time to fit residues: 518.4905 Evaluate side-chains 382 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 260 optimal weight: 5.9990 chunk 349 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 302 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 91 optimal weight: 30.0000 chunk 328 optimal weight: 0.0970 chunk 137 optimal weight: 20.0000 chunk 337 optimal weight: 8.9990 chunk 41 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN J 86 GLN J 135 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.069663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.049585 restraints weight = 356152.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.051354 restraints weight = 138074.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.052386 restraints weight = 80873.834| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.8483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 67012 Z= 0.192 Angle : 0.571 10.681 100893 Z= 0.294 Chirality : 0.033 0.254 13005 Planarity : 0.005 0.077 4966 Dihedral : 23.810 170.199 34819 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.82 % Favored : 91.14 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.84 (0.18), residues: 2076 helix: -0.74 (0.22), residues: 524 sheet: -0.97 (0.25), residues: 416 loop : -1.54 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP J 15 HIS 0.007 0.001 HIS R 82 PHE 0.036 0.002 PHE K 112 TYR 0.026 0.002 TYR J 16 ARG 0.010 0.001 ARG D 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9909.52 seconds wall clock time: 178 minutes 30.98 seconds (10710.98 seconds total)