Starting phenix.real_space_refine on Mon Mar 18 11:19:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gbz_4378/03_2024/6gbz_4378.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gbz_4378/03_2024/6gbz_4378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gbz_4378/03_2024/6gbz_4378.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gbz_4378/03_2024/6gbz_4378.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gbz_4378/03_2024/6gbz_4378.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gbz_4378/03_2024/6gbz_4378.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.158 sd= 1.483 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 2907 5.49 5 S 69 5.16 5 C 42877 2.51 5 N 16121 2.21 5 O 24427 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 132": "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 169": "NH1" <-> "NH2" Residue "D ARG 179": "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 "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "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 "H ARG 27": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 20": "NH1" <-> "NH2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "L ARG 46": "NH1" <-> "NH2" Residue "L ARG 59": "NH1" <-> "NH2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L ARG 125": "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 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 "O ARG 9": "NH1" <-> "NH2" Residue "O ARG 15": "NH1" <-> "NH2" Residue "O ARG 24": "NH1" <-> "NH2" Residue "O ARG 80": "NH1" <-> "NH2" Residue "O ARG 93": "NH1" <-> "NH2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "O ARG 110": "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 "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" 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 "X ARG 2": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X ARG 17": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ARG 56": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 41": "NH1" <-> "NH2" Residue "2 ARG 3": "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 "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 86401 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 59885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2789, 59885 Classifications: {'RNA': 2789} Modifications used: {'rna2p_pur': 263, 'rna2p_pyr': 141, 'rna3p_pur': 1351, 'rna3p_pyr': 1034} Link IDs: {'rna2p': 404, 'rna3p': 2384} Chain breaks: 2 Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} 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: "F" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} 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: "H" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 384 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} 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: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} 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: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} 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: "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} 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: "1" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "B" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2546 Classifications: {'RNA': 119} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "M" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 984 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 100 residue: pdb=" P C A 840 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C A 840 " occ=0.00 residue: pdb=" P G A 841 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G A 841 " occ=0.00 residue: pdb=" P U A 842 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U A 842 " occ=0.00 residue: pdb=" P G A 843 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G A 843 " occ=0.00 residue: pdb=" P A A 844 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A A 844 " occ=0.00 residue: pdb=" P A A 845 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A A 845 " occ=0.00 residue: pdb=" P U A 846 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U A 846 " occ=0.00 residue: pdb=" P U A 847 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U A 847 " occ=0.00 residue: pdb=" P C A 848 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C A 848 " occ=0.00 residue: pdb=" P A A 849 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A A 849 " occ=0.00 residue: pdb=" P U A 850 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U A 850 " occ=0.00 residue: pdb=" P C A 851 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C A 851 " occ=0.00 ... (remaining 88 not shown) Time building chain proxies: 33.70, per 1000 atoms: 0.39 Number of scatterers: 86401 At special positions: 0 Unit cell: (214.52, 207.08, 221.96, 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 69 16.00 P 2907 15.00 O 24427 8.00 N 16121 7.00 C 42877 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: 34.86 Conformation dependent library (CDL) restraints added in 3.9 seconds 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5600 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 48 sheets defined 27.3% alpha, 20.4% beta 765 base pairs and 1682 stacking pairs defined. Time for finding SS restraints: 29.91 Creating SS restraints... Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.066A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.978A pdb=" N ARG C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.620A pdb=" N HIS D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.959A pdb=" N ALA D 102 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASP D 103 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 37 removed outlier: 3.523A pdb=" N GLN E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 115 removed outlier: 3.724A pdb=" N SER E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.631A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 178 through 183 removed outlier: 4.066A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 removed outlier: 3.888A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 10 Processing helix chain 'F' and resid 10 through 17 removed outlier: 3.534A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 removed outlier: 3.890A pdb=" N VAL F 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 44 removed outlier: 3.783A pdb=" N ILE F 43 " --> pdb=" O GLY F 40 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA F 44 " --> pdb=" O GLU F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 44' Processing helix chain 'F' and resid 48 through 60 Processing helix chain 'F' and resid 92 through 104 Processing helix chain 'F' and resid 106 through 110 Processing helix chain 'F' and resid 133 through 137 removed outlier: 3.837A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.568A pdb=" N GLY F 165 " --> pdb=" O SER F 161 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.660A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 60 through 77 removed outlier: 3.800A pdb=" N THR G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 removed outlier: 3.567A pdb=" N ALA G 144 " --> pdb=" O ILE G 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 27 Processing helix chain 'H' and resid 42 through 47 removed outlier: 3.809A pdb=" N PHE H 46 " --> pdb=" O LYS H 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.024A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.744A pdb=" N LYS J 72 " --> pdb=" O LYS J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 removed outlier: 3.936A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 109 removed outlier: 4.386A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 120 removed outlier: 3.655A pdb=" N ALA J 117 " --> pdb=" O PRO J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.559A pdb=" N GLN J 135 " --> pdb=" O HIS J 132 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 132 through 136' Processing helix chain 'K' and resid 109 through 113 removed outlier: 3.702A pdb=" N MET K 113 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 60 removed outlier: 3.879A pdb=" N LEU L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 137 removed outlier: 3.855A pdb=" N ALA L 132 " --> pdb=" O LYS L 128 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA L 136 " --> pdb=" O ALA L 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.683A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE N 21 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG N 22 " --> pdb=" O GLN N 18 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 55 removed outlier: 3.649A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 60 through 69 removed outlier: 3.657A pdb=" N ARG N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 79 removed outlier: 3.864A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 Processing helix chain 'O' and resid 3 through 21 removed outlier: 3.870A pdb=" N ILE O 7 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG O 8 " --> pdb=" O SER O 4 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG O 12 " --> pdb=" O ARG O 8 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU O 20 " --> pdb=" O LYS O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 54 through 59 removed outlier: 3.872A pdb=" N GLU O 59 " --> pdb=" O LYS O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 83 removed outlier: 3.948A pdb=" N ALA O 72 " --> pdb=" O ASP O 68 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG O 80 " --> pdb=" O ALA O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 113 removed outlier: 3.571A pdb=" N ALA O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 10 removed outlier: 3.654A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 removed outlier: 3.774A pdb=" N LEU P 99 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU P 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 101' Processing helix chain 'Q' and resid 7 through 19 removed outlier: 3.842A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.189A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE Q 39 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS Q 40 " --> pdb=" O GLN Q 36 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN Q 70 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.659A pdb=" N ALA Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 115 removed outlier: 3.598A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.721A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 4.067A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR S 37 " --> pdb=" O LEU S 33 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 60 removed outlier: 3.588A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.540A 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 8 removed outlier: 3.959A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 49 removed outlier: 3.634A pdb=" N VAL T 47 " --> pdb=" O ILE T 43 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 12 through 22 removed outlier: 4.213A pdb=" N ALA V 16 " --> pdb=" O GLN V 12 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 51 removed outlier: 3.602A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 57 removed outlier: 4.141A pdb=" N TYR V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 62 removed outlier: 3.515A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS X 60 " --> pdb=" O ARG X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 73 removed outlier: 3.558A pdb=" N VAL X 66 " --> pdb=" O GLY X 62 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU X 67 " --> pdb=" O ILE X 63 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU X 69 " --> pdb=" O THR X 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 23 removed outlier: 3.557A pdb=" N LEU Y 22 " --> pdb=" O LEU Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 34 removed outlier: 3.609A pdb=" N ASN Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU Y 28 " --> pdb=" O GLU Y 24 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 42 No H-bonds generated for 'chain 'Y' and resid 40 through 42' Processing helix chain 'Y' and resid 43 through 56 removed outlier: 4.121A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASP Y 49 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG Y 52 " --> pdb=" O ARG Y 48 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL Y 53 " --> pdb=" O ASP Y 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.531A pdb=" N ALA Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 16 Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 23 removed outlier: 3.599A pdb=" N ARG 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 removed outlier: 3.554A pdb=" N VAL 2 30 " --> pdb=" O ASN 2 26 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU 2 31 " --> pdb=" O GLY 2 27 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA 2 36 " --> pdb=" O ALA 2 32 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS 2 37 " --> pdb=" O ARG 2 33 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 11 removed outlier: 3.501A pdb=" N LYS 3 11 " --> pdb=" O ARG 3 7 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 42 removed outlier: 3.610A pdb=" N HIS 3 42 " --> pdb=" O LYS 3 38 " (cutoff:3.500A) Processing helix chain '3' and resid 50 through 52 No H-bonds generated for 'chain '3' and resid 50 through 52' Processing helix chain '3' and resid 53 through 61 removed outlier: 3.768A pdb=" N VAL 3 57 " --> pdb=" O ASP 3 53 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE 3 58 " --> pdb=" O LEU 3 54 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA 3 59 " --> pdb=" O GLY 3 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 55 removed outlier: 3.705A pdb=" N GLU M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET M 53 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG M 55 " --> pdb=" O ARG M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 122 removed outlier: 4.038A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4 removed outlier: 3.610A pdb=" N VAL C 3 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.693A pdb=" N GLU C 34 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR C 61 " --> pdb=" O GLU C 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 104 removed outlier: 3.569A pdb=" N ARG C 101 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 128 through 130 Processing sheet with id=AA5, first strand: chain 'C' and resid 162 through 165 removed outlier: 5.879A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG C 268 " --> pdb=" O MET C 180 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS C 182 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE C 266 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 15 removed outlier: 3.884A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 80 through 83 removed outlier: 6.722A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 117 through 119 removed outlier: 3.555A pdb=" N GLY D 117 " --> pdb=" O MET D 165 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY D 163 " --> pdb=" O ALA D 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 3 removed outlier: 3.512A pdb=" N LEU E 3 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 12 " --> pdb=" O LEU E 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.101A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.529A pdb=" N LEU F 90 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE F 33 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 17 through 18 removed outlier: 3.673A pdb=" N ARG G 34 " --> pdb=" O ILE G 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 40 through 42 Processing sheet with id=AB5, first strand: chain 'G' and resid 121 through 123 Processing sheet with id=AB6, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.558A pdb=" N ARG G 94 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL G 101 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.604A pdb=" N VAL H 37 " --> pdb=" O ILE H 4 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.662A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU J 140 " --> pdb=" O TRP J 15 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL J 17 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 73 through 77 removed outlier: 3.578A pdb=" N HIS J 76 " --> pdb=" O LYS J 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 7 through 10 removed outlier: 3.729A pdb=" N LEU K 8 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ARG K 17 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA K 46 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL K 19 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LYS K 44 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N CYS K 21 " --> pdb=" O THR K 42 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR K 42 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL K 63 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 77 through 78 removed outlier: 3.796A pdb=" N PHE P 58 " --> pdb=" O PHE P 73 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 77 through 78 removed outlier: 3.796A pdb=" N PHE P 58 " --> pdb=" O PHE P 73 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 73 through 75 removed outlier: 3.818A pdb=" N LYS L 108 " --> pdb=" O ALA L 74 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 88 through 89 removed outlier: 6.105A pdb=" N VAL L 121 " --> pdb=" O GLU L 142 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.698A pdb=" N THR N 36 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 46 through 49 removed outlier: 3.648A pdb=" N VAL O 48 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG O 24 " --> pdb=" O ILE O 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 89 through 90 removed outlier: 3.988A pdb=" N LYS P 110 " --> pdb=" O ALA P 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 2 through 6 removed outlier: 3.673A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'R' and resid 19 through 22 removed outlier: 3.783A pdb=" N VAL R 20 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL R 96 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE R 101 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL R 58 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 40 through 42 Processing sheet with id=AD3, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.330A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 3 through 10 removed outlier: 5.782A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 82 through 87 removed outlier: 3.607A pdb=" N LYS S 98 " --> pdb=" O MET S 82 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG S 84 " --> pdb=" O ILE S 96 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 11 through 14 removed outlier: 4.139A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 64 through 65 removed outlier: 4.269A pdb=" N ASN U 26 " --> pdb=" O ILE U 34 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS U 78 " --> pdb=" O ASN U 73 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 40 through 45 removed outlier: 3.773A pdb=" N GLN U 45 " --> pdb=" O GLY U 56 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY U 56 " --> pdb=" O GLN U 45 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 82 through 85 removed outlier: 3.982A pdb=" N ARG U 85 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 3 through 5 removed outlier: 6.233A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA V 74 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL V 92 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 10.074A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 13 through 14 removed outlier: 6.979A pdb=" N LEU W 50 " --> pdb=" O ILE W 28 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 21 through 22 removed outlier: 3.970A pdb=" N GLY W 56 " --> pdb=" O VAL W 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 12 through 15 removed outlier: 3.645A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'X' and resid 33 through 38 Processing sheet with id=AE6, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.883A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU Z 57 " --> pdb=" O LYS Z 5 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AE8, first strand: chain '1' and resid 4 through 6 removed outlier: 3.705A pdb=" N GLU 1 4 " --> pdb=" O LYS 1 22 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '1' and resid 9 through 10 removed outlier: 3.585A pdb=" N GLN 1 42 " --> pdb=" O ASP 1 37 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU 1 33 " --> pdb=" O TYR 1 46 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '3' and resid 14 through 15 removed outlier: 3.581A pdb=" N LYS 3 14 " --> pdb=" O LYS 3 22 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 62 through 65 removed outlier: 5.986A pdb=" N VAL M 101 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA M 35 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL M 131 " --> pdb=" O GLY M 32 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 39 through 42 removed outlier: 3.561A pdb=" N GLY M 39 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE M 96 " --> pdb=" O GLY M 39 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR M 91 " --> pdb=" O ILE M 73 " (cutoff:3.500A) 687 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1862 hydrogen bonds 2952 hydrogen bond angles 0 basepair planarities 765 basepair parallelities 1682 stacking parallelities Total time for adding SS restraints: 142.98 Time building geometry restraints manager: 37.86 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: 15372 1.33 - 1.46: 38920 1.46 - 1.58: 33988 1.58 - 1.70: 5811 1.70 - 1.82: 128 Bond restraints: 94219 Sorted by residual: bond pdb=" C ALA C 30 " pdb=" N PRO C 31 " ideal model delta sigma weight residual 1.337 1.382 -0.046 9.80e-03 1.04e+04 2.18e+01 bond pdb=" C GLN U 53 " pdb=" N PRO U 54 " ideal model delta sigma weight residual 1.336 1.390 -0.055 1.23e-02 6.61e+03 1.97e+01 bond pdb=" C LYS V 83 " pdb=" N PRO V 84 " ideal model delta sigma weight residual 1.334 1.431 -0.097 2.34e-02 1.83e+03 1.73e+01 bond pdb=" C ARG 3 44 " pdb=" N PRO 3 45 " ideal model delta sigma weight residual 1.326 1.385 -0.059 1.44e-02 4.82e+03 1.70e+01 bond pdb=" C LYS D 62 " pdb=" N PRO D 63 " ideal model delta sigma weight residual 1.336 1.384 -0.048 1.23e-02 6.61e+03 1.52e+01 ... (remaining 94214 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.83: 17765 106.83 - 114.32: 59768 114.32 - 121.81: 42063 121.81 - 129.30: 20164 129.30 - 136.79: 1883 Bond angle restraints: 141643 Sorted by residual: angle pdb=" C SER U 97 " pdb=" N ASN U 98 " pdb=" CA ASN U 98 " ideal model delta sigma weight residual 121.54 136.79 -15.25 1.91e+00 2.74e-01 6.38e+01 angle pdb=" C ILE T 2 " pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 121.70 133.08 -11.38 1.80e+00 3.09e-01 3.99e+01 angle pdb=" C ALA F 106 " pdb=" N VAL F 107 " pdb=" CA VAL F 107 " ideal model delta sigma weight residual 120.24 124.08 -3.84 6.30e-01 2.52e+00 3.72e+01 angle pdb=" N GLN H 33 " pdb=" CA GLN H 33 " pdb=" C GLN H 33 " ideal model delta sigma weight residual 114.12 105.98 8.14 1.39e+00 5.18e-01 3.43e+01 angle pdb=" C3' U A2457 " pdb=" O3' U A2457 " pdb=" P G A2458 " ideal model delta sigma weight residual 120.20 128.27 -8.07 1.50e+00 4.44e-01 2.90e+01 ... (remaining 141638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 53196 35.94 - 71.88: 6350 71.88 - 107.81: 768 107.81 - 143.75: 7 143.75 - 179.69: 17 Dihedral angle restraints: 60338 sinusoidal: 51635 harmonic: 8703 Sorted by residual: dihedral pdb=" CA VAL H 31 " pdb=" C VAL H 31 " pdb=" N PRO H 32 " pdb=" CA PRO H 32 " ideal model delta harmonic sigma weight residual 180.00 -118.09 -61.91 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA THR D 151 " pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta harmonic sigma weight residual -180.00 -118.75 -61.25 0 5.00e+00 4.00e-02 1.50e+02 dihedral pdb=" CA PHE F 174 " pdb=" C PHE F 174 " pdb=" N PRO F 175 " pdb=" CA PRO F 175 " ideal model delta harmonic sigma weight residual -180.00 -127.42 -52.58 0 5.00e+00 4.00e-02 1.11e+02 ... (remaining 60335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 17695 0.085 - 0.170: 450 0.170 - 0.256: 27 0.256 - 0.341: 11 0.341 - 0.426: 1 Chirality restraints: 18184 Sorted by residual: chirality pdb=" C3' A A1966 " pdb=" C4' A A1966 " pdb=" O3' A A1966 " pdb=" C2' A A1966 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" C3' G A 60 " pdb=" C4' G A 60 " pdb=" O3' G A 60 " pdb=" C2' G A 60 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C3' C A 995 " pdb=" C4' C A 995 " pdb=" O3' C A 995 " pdb=" C2' C A 995 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 18181 not shown) Planarity restraints: 7113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL M 57 " 0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C VAL M 57 " -0.057 2.00e-02 2.50e+03 pdb=" O VAL M 57 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS M 58 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 11 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.16e+00 pdb=" C GLY C 11 " 0.049 2.00e-02 2.50e+03 pdb=" O GLY C 11 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG C 12 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL H 31 " 0.046 5.00e-02 4.00e+02 6.93e-02 7.69e+00 pdb=" N PRO H 32 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO H 32 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO H 32 " 0.039 5.00e-02 4.00e+02 ... (remaining 7110 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 14953 2.77 - 3.30: 68662 3.30 - 3.83: 180953 3.83 - 4.37: 217169 4.37 - 4.90: 287294 Nonbonded interactions: 769031 Sorted by model distance: nonbonded pdb=" O2' G A1945 " pdb=" O2 C A1965 " model vdw 2.235 2.440 nonbonded pdb=" O2' U A2404 " pdb=" OG SER L 67 " model vdw 2.263 2.440 nonbonded pdb=" O2' G B 13 " pdb=" OP2 A B 15 " model vdw 2.270 2.440 nonbonded pdb=" OP1 G A1296 " pdb=" O2' G A2709 " model vdw 2.276 2.440 nonbonded pdb=" O2' G A1826 " pdb=" OP2 U A1971 " model vdw 2.277 2.440 ... (remaining 769026 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=0.00 max=1.00 mean=0.98 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: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 7.410 Check model and map are aligned: 0.930 Set scattering table: 0.580 Process input model: 303.050 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.230 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 317.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 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 : 0.002 0.097 94219 Z= 0.155 Angle : 0.609 15.253 141643 Z= 0.346 Chirality : 0.030 0.426 18184 Planarity : 0.005 0.069 7113 Dihedral : 22.522 179.690 54738 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.23 % Favored : 93.44 % Rotamer: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 4.17 % Twisted General : 0.34 % 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: -4.24 (0.12), residues: 3018 helix: -4.55 (0.07), residues: 736 sheet: -1.43 (0.21), residues: 554 loop : -2.53 (0.12), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP C 212 HIS 0.007 0.001 HIS O 99 PHE 0.033 0.002 PHE F 176 TYR 0.017 0.002 TYR M 103 ARG 0.007 0.001 ARG Q 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1161 time to evaluate : 3.415 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: C 212 TRP cc_start: 0.6542 (p90) cc_final: 0.6065 (p90) REVERT: D 40 LEU cc_start: 0.7903 (mt) cc_final: 0.7517 (mp) REVERT: E 43 THR cc_start: 0.8150 (p) cc_final: 0.7716 (p) REVERT: E 49 ARG cc_start: 0.8223 (ptm160) cc_final: 0.7680 (ttt180) REVERT: L 3 ASN cc_start: 0.6013 (p0) cc_final: 0.5809 (p0) REVERT: N 29 VAL cc_start: 0.8909 (t) cc_final: 0.8700 (t) REVERT: O 94 SER cc_start: 0.8165 (m) cc_final: 0.7603 (t) REVERT: Q 54 ARG cc_start: 0.7490 (mtt180) cc_final: 0.7220 (mtm180) REVERT: Q 109 VAL cc_start: 0.7388 (t) cc_final: 0.7166 (t) REVERT: T 1 MET cc_start: 0.3291 (mtt) cc_final: 0.2953 (mtt) REVERT: X 3 VAL cc_start: 0.8504 (t) cc_final: 0.8074 (t) REVERT: X 31 ASN cc_start: 0.6609 (t0) cc_final: 0.6070 (t0) REVERT: X 51 SER cc_start: 0.8346 (p) cc_final: 0.8084 (p) REVERT: 3 28 LEU cc_start: 0.8050 (tp) cc_final: 0.7813 (tt) outliers start: 2 outliers final: 0 residues processed: 1162 average time/residue: 0.9485 time to fit residues: 1764.1198 Evaluate side-chains 673 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 673 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 494 optimal weight: 0.6980 chunk 444 optimal weight: 6.9990 chunk 246 optimal weight: 30.0000 chunk 151 optimal weight: 10.0000 chunk 299 optimal weight: 7.9990 chunk 237 optimal weight: 10.0000 chunk 459 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 279 optimal weight: 3.9990 chunk 341 optimal weight: 10.0000 chunk 532 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN C 114 GLN C 152 GLN C 238 ASN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 149 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN G 19 ASN G 29 ASN G 72 ASN G 103 ASN J 67 ASN ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN N 107 ASN O 37 GLN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 13 HIS Q 36 GLN Q 71 ASN R 43 ASN R 89 HIS ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN T 28 ASN U 73 ASN U 98 ASN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 3 ASN Z 19 HIS 0 3 GLN 0 5 ASN 0 18 HIS 1 43 HIS 2 13 ASN 2 16 HIS M 97 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 94219 Z= 0.289 Angle : 0.695 10.507 141643 Z= 0.355 Chirality : 0.038 0.290 18184 Planarity : 0.006 0.164 7113 Dihedral : 23.356 178.304 48725 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.26 % Favored : 92.48 % Rotamer: Outliers : 4.58 % Allowed : 15.98 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 3.12 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.13), residues: 3018 helix: -2.44 (0.15), residues: 751 sheet: -1.18 (0.21), residues: 581 loop : -2.19 (0.13), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP X 38 HIS 0.017 0.002 HIS Q 13 PHE 0.027 0.003 PHE K 79 TYR 0.022 0.003 TYR O 98 ARG 0.032 0.001 ARG O 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 754 time to evaluate : 3.434 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: C 87 SER cc_start: 0.8251 (p) cc_final: 0.7978 (t) REVERT: C 212 TRP cc_start: 0.7032 (p90) cc_final: 0.6813 (p90) REVERT: D 13 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.7114 (mtp-110) REVERT: E 136 GLN cc_start: 0.7216 (tm-30) cc_final: 0.6904 (tp-100) REVERT: E 175 ILE cc_start: 0.6805 (pt) cc_final: 0.6604 (tt) REVERT: F 19 PHE cc_start: 0.4046 (m-10) cc_final: 0.3710 (m-10) REVERT: F 76 PHE cc_start: 0.5998 (m-80) cc_final: 0.5583 (m-10) REVERT: H 29 PHE cc_start: 0.4505 (t80) cc_final: 0.4058 (t80) REVERT: L 16 LYS cc_start: 0.7764 (mtmt) cc_final: 0.7389 (mtmt) REVERT: R 1 MET cc_start: 0.7098 (tmm) cc_final: 0.5464 (ttt) REVERT: R 68 ARG cc_start: 0.7186 (mtm-85) cc_final: 0.6632 (mtm110) REVERT: S 15 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7590 (tm-30) REVERT: S 75 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.8069 (p90) REVERT: T 25 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6215 (mp0) REVERT: U 46 LYS cc_start: 0.8012 (tptt) cc_final: 0.7763 (tptt) REVERT: U 73 ASN cc_start: 0.7160 (OUTLIER) cc_final: 0.6692 (m-40) REVERT: W 67 ASN cc_start: 0.5001 (t0) cc_final: 0.4773 (t0) REVERT: X 3 VAL cc_start: 0.8986 (t) cc_final: 0.8666 (t) REVERT: X 10 ARG cc_start: 0.7954 (ttm110) cc_final: 0.7594 (ttm110) REVERT: 3 28 LEU cc_start: 0.8241 (tp) cc_final: 0.7648 (tt) REVERT: 3 48 MET cc_start: 0.8192 (mmp) cc_final: 0.7759 (mmm) outliers start: 114 outliers final: 64 residues processed: 801 average time/residue: 0.8903 time to fit residues: 1181.9740 Evaluate side-chains 716 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 649 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 75 PHE Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 18 LYS Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 44 VAL Chi-restraints excluded: chain 1 residue 45 ILE Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 42 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 295 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 442 optimal weight: 7.9990 chunk 362 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 533 optimal weight: 7.9990 chunk 575 optimal weight: 5.9990 chunk 474 optimal weight: 20.0000 chunk 528 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 427 optimal weight: 3.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 GLN J 67 ASN ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 HIS P 76 HIS Q 58 GLN R 66 HIS ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 92 ASN U 65 GLN V 78 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 94219 Z= 0.373 Angle : 0.773 9.994 141643 Z= 0.394 Chirality : 0.042 0.310 18184 Planarity : 0.007 0.169 7113 Dihedral : 23.591 179.606 48725 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.78 % Favored : 90.89 % Rotamer: Outliers : 6.22 % Allowed : 18.19 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 3.12 % Twisted General : 0.20 % 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: -2.87 (0.13), residues: 3018 helix: -1.77 (0.17), residues: 781 sheet: -1.46 (0.20), residues: 560 loop : -2.15 (0.13), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP T 80 HIS 0.012 0.003 HIS Q 13 PHE 0.040 0.003 PHE U 95 TYR 0.034 0.003 TYR H 25 ARG 0.027 0.001 ARG L 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 690 time to evaluate : 3.515 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: C 87 SER cc_start: 0.8342 (p) cc_final: 0.8081 (t) REVERT: C 244 VAL cc_start: 0.8316 (m) cc_final: 0.8049 (t) REVERT: D 165 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7369 (tpp) REVERT: E 195 GLN cc_start: 0.7547 (tm-30) cc_final: 0.7297 (tm-30) REVERT: F 37 MET cc_start: 0.6814 (tpt) cc_final: 0.6220 (tpp) REVERT: F 51 ASN cc_start: 0.5581 (OUTLIER) cc_final: 0.4602 (t0) REVERT: J 60 ASP cc_start: 0.6162 (p0) cc_final: 0.5599 (p0) REVERT: J 67 ASN cc_start: 0.6477 (t0) cc_final: 0.6152 (t0) REVERT: L 54 MET cc_start: 0.7818 (tpp) cc_final: 0.7369 (mmp) REVERT: N 43 GLU cc_start: 0.7223 (tp30) cc_final: 0.6985 (tp30) REVERT: O 86 ILE cc_start: 0.7345 (mt) cc_final: 0.7075 (mt) REVERT: R 1 MET cc_start: 0.6918 (tmm) cc_final: 0.5238 (ttt) REVERT: S 1 MET cc_start: 0.5251 (ttm) cc_final: 0.5033 (ttp) REVERT: V 82 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6959 (p90) REVERT: Y 41 HIS cc_start: 0.7592 (p-80) cc_final: 0.7247 (p-80) REVERT: Z 23 LEU cc_start: 0.9279 (mm) cc_final: 0.9074 (mm) REVERT: 3 28 LEU cc_start: 0.8419 (tp) cc_final: 0.8013 (tp) REVERT: 3 53 ASP cc_start: 0.6312 (p0) cc_final: 0.5996 (p0) REVERT: M 9 PHE cc_start: 0.6129 (m-80) cc_final: 0.5908 (m-10) REVERT: M 44 ARG cc_start: 0.6291 (mtt180) cc_final: 0.6090 (mtt90) outliers start: 155 outliers final: 99 residues processed: 768 average time/residue: 0.9120 time to fit residues: 1196.0971 Evaluate side-chains 708 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 606 time to evaluate : 3.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 11 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 93 LYS Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 82 TYR Chi-restraints excluded: chain W residue 41 ASN Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 58 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 526 optimal weight: 10.0000 chunk 400 optimal weight: 8.9990 chunk 276 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 254 optimal weight: 40.0000 chunk 357 optimal weight: 6.9990 chunk 535 optimal weight: 0.9990 chunk 566 optimal weight: 20.0000 chunk 279 optimal weight: 0.5980 chunk 507 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 overall best weight: 5.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 HIS ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 GLN N 107 ASN P 6 GLN P 9 GLN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 3 ASN Y 39 GLN 0 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 94219 Z= 0.303 Angle : 0.677 11.590 141643 Z= 0.347 Chirality : 0.038 0.297 18184 Planarity : 0.006 0.141 7113 Dihedral : 23.522 179.772 48725 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.61 % Favored : 91.09 % Rotamer: Outliers : 5.86 % Allowed : 21.04 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 3.12 % Twisted General : 0.24 % 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: -2.62 (0.14), residues: 3018 helix: -1.33 (0.18), residues: 774 sheet: -1.39 (0.20), residues: 626 loop : -2.11 (0.13), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP T 80 HIS 0.043 0.002 HIS R 66 PHE 0.038 0.002 PHE M 117 TYR 0.025 0.002 TYR X 77 ARG 0.016 0.001 ARG O 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 653 time to evaluate : 3.472 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: C 87 SER cc_start: 0.8336 (p) cc_final: 0.8080 (t) REVERT: D 165 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7176 (tpp) REVERT: E 175 ILE cc_start: 0.7721 (tt) cc_final: 0.7417 (tt) REVERT: F 135 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6370 (mm) REVERT: J 60 ASP cc_start: 0.6444 (p0) cc_final: 0.5918 (p0) REVERT: J 67 ASN cc_start: 0.6202 (t0) cc_final: 0.5738 (t0) REVERT: J 118 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.6950 (mpp) REVERT: L 54 MET cc_start: 0.7566 (tpp) cc_final: 0.7323 (mmp) REVERT: N 74 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6663 (tm-30) REVERT: O 14 ARG cc_start: 0.6615 (mmm-85) cc_final: 0.6363 (mtt-85) REVERT: T 88 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6906 (pttm) REVERT: Y 41 HIS cc_start: 0.7473 (p-80) cc_final: 0.7246 (t70) REVERT: 3 28 LEU cc_start: 0.8369 (tp) cc_final: 0.7903 (tp) REVERT: 3 53 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.6358 (p0) outliers start: 146 outliers final: 101 residues processed: 729 average time/residue: 0.8393 time to fit residues: 1035.8215 Evaluate side-chains 725 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 619 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 42 LYS Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 1 ASP Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 18 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain W residue 41 ASN Chi-restraints excluded: chain W residue 73 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 45 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 471 optimal weight: 0.9980 chunk 321 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 421 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 chunk 483 optimal weight: 0.9980 chunk 391 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 508 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN Q 58 GLN ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN 2 13 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 94219 Z= 0.194 Angle : 0.583 10.986 141643 Z= 0.301 Chirality : 0.034 0.273 18184 Planarity : 0.005 0.102 7113 Dihedral : 23.439 179.218 48725 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.75 % Favored : 91.12 % Rotamer: Outliers : 5.86 % Allowed : 22.17 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 3.12 % Twisted General : 0.24 % 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: -2.23 (0.14), residues: 3018 helix: -0.96 (0.18), residues: 776 sheet: -1.15 (0.21), residues: 551 loop : -1.87 (0.13), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP M 92 HIS 0.010 0.001 HIS R 66 PHE 0.023 0.002 PHE M 117 TYR 0.036 0.002 TYR H 25 ARG 0.017 0.001 ARG T 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 660 time to evaluate : 3.458 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: C 87 SER cc_start: 0.8316 (p) cc_final: 0.8100 (t) REVERT: D 165 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7100 (tpp) REVERT: E 175 ILE cc_start: 0.7776 (tt) cc_final: 0.7530 (tt) REVERT: J 31 GLU cc_start: 0.4824 (tp30) cc_final: 0.4612 (tp30) REVERT: J 60 ASP cc_start: 0.6654 (p0) cc_final: 0.6003 (p0) REVERT: J 67 ASN cc_start: 0.6165 (t0) cc_final: 0.5656 (t0) REVERT: J 118 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.6991 (mpp) REVERT: L 16 LYS cc_start: 0.7727 (mtmt) cc_final: 0.7486 (mtmm) REVERT: L 54 MET cc_start: 0.7588 (tpp) cc_final: 0.7356 (mmp) REVERT: N 74 GLU cc_start: 0.6794 (tm-30) cc_final: 0.6528 (tm-30) REVERT: O 14 ARG cc_start: 0.6770 (mmm-85) cc_final: 0.6475 (mtt-85) REVERT: R 99 THR cc_start: 0.8307 (p) cc_final: 0.8083 (p) REVERT: S 25 ARG cc_start: 0.7159 (ttm110) cc_final: 0.6778 (ttm-80) REVERT: T 88 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6506 (pttm) REVERT: U 43 LYS cc_start: 0.7205 (mttp) cc_final: 0.7005 (ptpp) REVERT: V 1 MET cc_start: 0.6004 (ppp) cc_final: 0.5590 (pmm) REVERT: 3 27 ASN cc_start: 0.8388 (m-40) cc_final: 0.7829 (m-40) REVERT: 3 28 LEU cc_start: 0.8240 (tp) cc_final: 0.7744 (tp) REVERT: 3 48 MET cc_start: 0.8410 (mmm) cc_final: 0.7223 (mmm) REVERT: 3 53 ASP cc_start: 0.6442 (OUTLIER) cc_final: 0.6181 (p0) outliers start: 146 outliers final: 105 residues processed: 736 average time/residue: 0.8300 time to fit residues: 1030.8393 Evaluate side-chains 727 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 618 time to evaluate : 3.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 18 GLN Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain P residue 2 ASN Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 45 GLN Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain W residue 41 ASN Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 52 ARG Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 39 VAL Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 3 residue 58 ILE Chi-restraints excluded: chain M residue 42 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 190 optimal weight: 20.0000 chunk 510 optimal weight: 6.9990 chunk 111 optimal weight: 30.0000 chunk 332 optimal weight: 0.4980 chunk 139 optimal weight: 10.0000 chunk 566 optimal weight: 20.0000 chunk 470 optimal weight: 9.9990 chunk 262 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 297 optimal weight: 9.9990 overall best weight: 7.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 51 ASN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS L 34 HIS ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN Q 80 ASN ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 35 HIS ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 94219 Z= 0.393 Angle : 0.773 8.952 141643 Z= 0.390 Chirality : 0.041 0.291 18184 Planarity : 0.006 0.134 7113 Dihedral : 23.626 179.817 48725 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.30 % Favored : 89.40 % Rotamer: Outliers : 7.15 % Allowed : 21.89 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 3.12 % Twisted General : 0.20 % 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: -2.42 (0.14), residues: 3018 helix: -1.23 (0.17), residues: 785 sheet: -1.29 (0.21), residues: 562 loop : -1.92 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP M 92 HIS 0.008 0.002 HIS N 3 PHE 0.033 0.003 PHE D 118 TYR 0.031 0.003 TYR Q 31 ARG 0.015 0.001 ARG O 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 631 time to evaluate : 3.464 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: C 87 SER cc_start: 0.8493 (p) cc_final: 0.8233 (t) REVERT: D 8 LYS cc_start: 0.7065 (tptm) cc_final: 0.6858 (tptm) REVERT: D 11 MET cc_start: 0.7561 (mpp) cc_final: 0.7348 (mmm) REVERT: D 95 SER cc_start: 0.7925 (t) cc_final: 0.7704 (t) REVERT: D 165 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7296 (tpp) REVERT: E 16 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6267 (mm-30) REVERT: E 175 ILE cc_start: 0.7974 (tt) cc_final: 0.7754 (tt) REVERT: F 37 MET cc_start: 0.6927 (tpt) cc_final: 0.6498 (mmm) REVERT: F 51 ASN cc_start: 0.5624 (OUTLIER) cc_final: 0.5097 (t0) REVERT: F 133 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.5882 (tm-30) REVERT: J 1 MET cc_start: 0.6509 (mmt) cc_final: 0.6220 (mtm) REVERT: J 60 ASP cc_start: 0.6748 (p0) cc_final: 0.6120 (p0) REVERT: J 118 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.6952 (mpp) REVERT: O 67 LYS cc_start: 0.6890 (mmmm) cc_final: 0.6292 (mmtm) REVERT: S 109 ASP cc_start: 0.8647 (p0) cc_final: 0.8271 (p0) REVERT: T 88 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6786 (pttm) REVERT: U 73 ASN cc_start: 0.7209 (m-40) cc_final: 0.7006 (m-40) REVERT: Y 28 LEU cc_start: 0.8217 (mp) cc_final: 0.8003 (mp) REVERT: 3 28 LEU cc_start: 0.8418 (tp) cc_final: 0.7935 (tp) REVERT: 3 48 MET cc_start: 0.8467 (mmm) cc_final: 0.7391 (mmm) outliers start: 178 outliers final: 142 residues processed: 723 average time/residue: 0.8423 time to fit residues: 1036.0013 Evaluate side-chains 744 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 596 time to evaluate : 3.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 16 GLU Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 1 ASP Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 99 HIS Chi-restraints excluded: chain P residue 2 ASN Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 80 ASN Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 87 GLN Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 45 GLN Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain W residue 41 ASN Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain 0 residue 30 ASP Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 39 VAL Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 58 ILE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 546 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 323 optimal weight: 9.9990 chunk 414 optimal weight: 0.4980 chunk 320 optimal weight: 8.9990 chunk 477 optimal weight: 6.9990 chunk 316 optimal weight: 6.9990 chunk 564 optimal weight: 20.0000 chunk 353 optimal weight: 4.9990 chunk 344 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 51 ASN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN J 76 HIS K 9 ASN N 31 HIS ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN Q 80 ASN ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 94219 Z= 0.230 Angle : 0.627 11.140 141643 Z= 0.322 Chirality : 0.036 0.266 18184 Planarity : 0.005 0.104 7113 Dihedral : 23.533 179.700 48725 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.15 % Favored : 90.62 % Rotamer: Outliers : 6.22 % Allowed : 23.86 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.08 % Twisted General : 0.24 % 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: -2.14 (0.14), residues: 3018 helix: -0.87 (0.18), residues: 778 sheet: -1.13 (0.21), residues: 590 loop : -1.82 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP M 92 HIS 0.008 0.001 HIS 3 30 PHE 0.029 0.002 PHE F 98 TYR 0.017 0.002 TYR Q 31 ARG 0.013 0.001 ARG O 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 616 time to evaluate : 3.464 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: D 8 LYS cc_start: 0.7026 (tptm) cc_final: 0.6789 (tptm) REVERT: D 11 MET cc_start: 0.7463 (mpp) cc_final: 0.7166 (mmm) REVERT: D 165 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7204 (tpp) REVERT: E 175 ILE cc_start: 0.7907 (tt) cc_final: 0.7689 (tt) REVERT: F 51 ASN cc_start: 0.5727 (OUTLIER) cc_final: 0.5156 (t0) REVERT: F 133 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.5859 (tm-30) REVERT: J 1 MET cc_start: 0.6605 (mmt) cc_final: 0.6284 (mtm) REVERT: J 60 ASP cc_start: 0.6671 (p0) cc_final: 0.6265 (p0) REVERT: J 67 ASN cc_start: 0.6364 (t0) cc_final: 0.6079 (t0) REVERT: J 118 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.6901 (mpp) REVERT: L 17 ARG cc_start: 0.8143 (mtp85) cc_final: 0.7912 (mtp180) REVERT: L 81 LEU cc_start: 0.8047 (tt) cc_final: 0.7806 (tp) REVERT: L 131 ARG cc_start: 0.5390 (OUTLIER) cc_final: 0.5094 (mtt90) REVERT: N 74 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6717 (tm-30) REVERT: O 75 LYS cc_start: 0.7238 (mtpp) cc_final: 0.6938 (ttmm) REVERT: S 25 ARG cc_start: 0.7169 (ttm110) cc_final: 0.6932 (ttp-110) REVERT: S 109 ASP cc_start: 0.8657 (p0) cc_final: 0.8296 (p0) REVERT: T 88 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6519 (pttm) REVERT: U 43 LYS cc_start: 0.7361 (mttp) cc_final: 0.7074 (ptpp) REVERT: U 73 ASN cc_start: 0.7336 (m-40) cc_final: 0.6782 (m-40) REVERT: 3 28 LEU cc_start: 0.8301 (tp) cc_final: 0.7792 (tp) REVERT: 3 48 MET cc_start: 0.8458 (mmm) cc_final: 0.7187 (mmm) REVERT: 3 53 ASP cc_start: 0.6654 (OUTLIER) cc_final: 0.6322 (p0) outliers start: 155 outliers final: 121 residues processed: 699 average time/residue: 0.8400 time to fit residues: 1000.3270 Evaluate side-chains 716 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 588 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 131 ARG Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 18 GLN Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 97 GLN Chi-restraints excluded: chain P residue 2 ASN Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 80 ASN Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 45 GLN Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 66 LYS Chi-restraints excluded: chain W residue 73 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 52 ARG Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 3 residue 58 ILE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 349 optimal weight: 0.6980 chunk 225 optimal weight: 20.0000 chunk 337 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 110 optimal weight: 50.0000 chunk 109 optimal weight: 50.0000 chunk 359 optimal weight: 2.9990 chunk 384 optimal weight: 5.9990 chunk 279 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 443 optimal weight: 1.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS K 9 ASN L 98 ASN N 73 ASN P 9 GLN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN Q 80 ASN ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.6042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 94219 Z= 0.250 Angle : 0.640 11.052 141643 Z= 0.328 Chirality : 0.036 0.269 18184 Planarity : 0.005 0.103 7113 Dihedral : 23.521 179.352 48725 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.91 % Favored : 89.89 % Rotamer: Outliers : 6.31 % Allowed : 24.22 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.08 % Twisted General : 0.20 % 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: -2.08 (0.14), residues: 3018 helix: -0.82 (0.18), residues: 780 sheet: -1.06 (0.21), residues: 555 loop : -1.79 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP M 92 HIS 0.008 0.001 HIS J 130 PHE 0.026 0.002 PHE V 56 TYR 0.017 0.002 TYR M 103 ARG 0.015 0.001 ARG Y 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 610 time to evaluate : 3.446 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: C 47 ARG cc_start: 0.8024 (mtt90) cc_final: 0.7808 (mtt180) REVERT: D 1 MET cc_start: 0.7476 (tmm) cc_final: 0.6647 (tpp) REVERT: D 8 LYS cc_start: 0.7008 (tptm) cc_final: 0.6703 (tptm) REVERT: D 165 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7207 (tpp) REVERT: E 175 ILE cc_start: 0.7895 (tt) cc_final: 0.7678 (tt) REVERT: F 37 MET cc_start: 0.6930 (mmm) cc_final: 0.6581 (mmm) REVERT: F 133 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5852 (tm-30) REVERT: F 146 ASP cc_start: 0.3389 (OUTLIER) cc_final: 0.0427 (t0) REVERT: J 1 MET cc_start: 0.6544 (mmt) cc_final: 0.6342 (mtm) REVERT: J 60 ASP cc_start: 0.6677 (p0) cc_final: 0.6169 (p0) REVERT: J 118 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.6890 (mpp) REVERT: O 75 LYS cc_start: 0.7251 (mtpp) cc_final: 0.6992 (ttmm) REVERT: S 109 ASP cc_start: 0.8710 (p0) cc_final: 0.8334 (p0) REVERT: T 88 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6544 (pttm) REVERT: U 43 LYS cc_start: 0.7360 (mttp) cc_final: 0.7015 (ptpp) REVERT: U 73 ASN cc_start: 0.7505 (m-40) cc_final: 0.6953 (m-40) REVERT: Y 47 ARG cc_start: 0.7706 (ptp-170) cc_final: 0.7488 (ptp-170) REVERT: Y 52 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.6041 (ttm170) REVERT: 3 28 LEU cc_start: 0.8298 (tp) cc_final: 0.7800 (tp) REVERT: 3 48 MET cc_start: 0.8451 (mmm) cc_final: 0.7201 (mmm) REVERT: 3 53 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6306 (p0) outliers start: 157 outliers final: 129 residues processed: 686 average time/residue: 0.8458 time to fit residues: 987.7883 Evaluate side-chains 725 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 589 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 9 GLN Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 18 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 97 GLN Chi-restraints excluded: chain O residue 99 HIS Chi-restraints excluded: chain P residue 2 ASN Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 45 GLN Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 73 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 52 ARG Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 3 residue 58 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 513 optimal weight: 6.9990 chunk 541 optimal weight: 5.9990 chunk 493 optimal weight: 9.9990 chunk 526 optimal weight: 9.9990 chunk 540 optimal weight: 6.9990 chunk 316 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 413 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 475 optimal weight: 8.9990 chunk 497 optimal weight: 0.2980 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS K 9 ASN N 73 ASN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 ASN ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 94219 Z= 0.301 Angle : 0.689 11.902 141643 Z= 0.351 Chirality : 0.038 0.283 18184 Planarity : 0.005 0.115 7113 Dihedral : 23.562 179.665 48725 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.60 % Favored : 89.20 % Rotamer: Outliers : 6.59 % Allowed : 24.26 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.08 % Twisted General : 0.17 % 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: -2.16 (0.14), residues: 3018 helix: -0.88 (0.18), residues: 778 sheet: -1.25 (0.21), residues: 575 loop : -1.78 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP M 92 HIS 0.009 0.002 HIS E 165 PHE 0.054 0.003 PHE F 98 TYR 0.014 0.002 TYR M 91 ARG 0.013 0.001 ARG O 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 604 time to evaluate : 3.677 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: C 47 ARG cc_start: 0.8056 (mtt90) cc_final: 0.7827 (mtt180) REVERT: D 1 MET cc_start: 0.7487 (tmm) cc_final: 0.6615 (tpp) REVERT: D 165 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7208 (tpp) REVERT: F 37 MET cc_start: 0.7073 (mmm) cc_final: 0.6767 (mmm) REVERT: F 133 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.5909 (tm-30) REVERT: J 60 ASP cc_start: 0.6780 (p0) cc_final: 0.6224 (p0) REVERT: J 118 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.6918 (mpp) REVERT: L 17 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7530 (mtp85) REVERT: O 67 LYS cc_start: 0.6830 (mmmt) cc_final: 0.6387 (mmtm) REVERT: O 75 LYS cc_start: 0.7282 (mtpp) cc_final: 0.7021 (ttmm) REVERT: S 109 ASP cc_start: 0.8599 (p0) cc_final: 0.8294 (p0) REVERT: T 88 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6593 (pttm) REVERT: U 73 ASN cc_start: 0.7715 (m-40) cc_final: 0.7168 (m-40) REVERT: Y 1 MET cc_start: 0.6094 (tpt) cc_final: 0.5857 (tpt) REVERT: 3 28 LEU cc_start: 0.8320 (tp) cc_final: 0.7834 (tp) REVERT: 3 53 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6315 (p0) REVERT: M 12 MET cc_start: 0.8351 (tpp) cc_final: 0.7958 (mtp) REVERT: M 92 TRP cc_start: 0.6794 (m100) cc_final: 0.6395 (m100) outliers start: 164 outliers final: 139 residues processed: 693 average time/residue: 0.8982 time to fit residues: 1071.5119 Evaluate side-chains 735 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 591 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 9 GLN Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 18 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 97 GLN Chi-restraints excluded: chain O residue 99 HIS Chi-restraints excluded: chain P residue 2 ASN Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 80 ASN Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 45 GLN Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 41 ASN Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 73 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 52 ARG Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 39 VAL Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 3 residue 58 ILE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 524 optimal weight: 1.9990 chunk 345 optimal weight: 20.0000 chunk 556 optimal weight: 5.9990 chunk 339 optimal weight: 3.9990 chunk 264 optimal weight: 30.0000 chunk 386 optimal weight: 4.9990 chunk 583 optimal weight: 10.0000 chunk 537 optimal weight: 6.9990 chunk 464 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 359 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS J 131 ASN K 9 ASN N 73 ASN N 107 ASN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN Q 80 ASN ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 GLN ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.6325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 94219 Z= 0.232 Angle : 0.628 12.072 141643 Z= 0.321 Chirality : 0.035 0.267 18184 Planarity : 0.005 0.096 7113 Dihedral : 23.526 179.570 48725 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.61 % Favored : 90.23 % Rotamer: Outliers : 6.02 % Allowed : 25.38 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.08 % Twisted General : 0.20 % 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: -2.02 (0.15), residues: 3018 helix: -0.77 (0.18), residues: 780 sheet: -1.02 (0.22), residues: 533 loop : -1.74 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP M 92 HIS 0.007 0.001 HIS 3 30 PHE 0.020 0.002 PHE R 53 TYR 0.018 0.002 TYR M 103 ARG 0.012 0.001 ARG O 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 619 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.7435 (tmm) cc_final: 0.6601 (tpp) REVERT: D 8 LYS cc_start: 0.7300 (tptm) cc_final: 0.7003 (tptm) REVERT: D 165 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7039 (tpp) REVERT: F 37 MET cc_start: 0.7022 (mmm) cc_final: 0.6730 (mmm) REVERT: F 51 ASN cc_start: 0.6514 (p0) cc_final: 0.6121 (p0) REVERT: F 133 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.6103 (tm-30) REVERT: F 135 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6185 (mm) REVERT: F 173 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.6940 (t70) REVERT: J 60 ASP cc_start: 0.6785 (p0) cc_final: 0.6179 (p0) REVERT: J 118 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.6857 (mpp) REVERT: L 17 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7580 (mtp85) REVERT: O 67 LYS cc_start: 0.6979 (mmmt) cc_final: 0.6341 (mmmt) REVERT: O 75 LYS cc_start: 0.7221 (mtpp) cc_final: 0.6960 (ttmm) REVERT: S 78 GLU cc_start: 0.5845 (mm-30) cc_final: 0.5621 (mm-30) REVERT: S 109 ASP cc_start: 0.8578 (p0) cc_final: 0.8251 (p0) REVERT: T 77 ARG cc_start: 0.6374 (mtt180) cc_final: 0.5854 (mtp85) REVERT: T 88 LYS cc_start: 0.6776 (OUTLIER) cc_final: 0.6313 (pttm) REVERT: U 73 ASN cc_start: 0.7658 (m-40) cc_final: 0.7098 (m-40) REVERT: 1 30 LYS cc_start: 0.7712 (tttm) cc_final: 0.7458 (mptt) REVERT: 3 27 ASN cc_start: 0.8339 (m-40) cc_final: 0.7808 (m-40) REVERT: 3 28 LEU cc_start: 0.8272 (tp) cc_final: 0.7757 (tp) REVERT: 3 48 MET cc_start: 0.8479 (mmm) cc_final: 0.7256 (mmm) REVERT: 3 53 ASP cc_start: 0.6624 (OUTLIER) cc_final: 0.6204 (p0) REVERT: M 6 ARG cc_start: 0.6144 (tpt-90) cc_final: 0.5795 (tpt90) REVERT: M 90 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6518 (mt-10) outliers start: 150 outliers final: 127 residues processed: 698 average time/residue: 0.8378 time to fit residues: 994.1259 Evaluate side-chains 737 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 603 time to evaluate : 3.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 9 GLN Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 18 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 97 GLN Chi-restraints excluded: chain P residue 2 ASN Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 80 ASN Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 45 GLN Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain W residue 41 ASN Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 73 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 52 ARG Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 3 residue 58 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 285 optimal weight: 0.0020 chunk 369 optimal weight: 0.6980 chunk 495 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 428 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 465 optimal weight: 2.9990 chunk 194 optimal weight: 40.0000 chunk 478 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS K 13 ASN N 107 ASN Q 80 ASN R 91 GLN S 31 GLN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.134790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.106405 restraints weight = 195811.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.109039 restraints weight = 68002.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110633 restraints weight = 37433.750| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 94219 Z= 0.160 Angle : 0.587 26.034 141643 Z= 0.300 Chirality : 0.032 0.258 18184 Planarity : 0.005 0.084 7113 Dihedral : 23.488 179.430 48725 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.58 % Favored : 91.32 % Rotamer: Outliers : 4.10 % Allowed : 27.71 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.08 % Twisted General : 0.17 % 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: -1.87 (0.15), residues: 3018 helix: -0.62 (0.19), residues: 785 sheet: -1.00 (0.21), residues: 571 loop : -1.63 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP M 92 HIS 0.008 0.001 HIS Y 41 PHE 0.055 0.002 PHE F 98 TYR 0.040 0.002 TYR O 98 ARG 0.012 0.001 ARG T 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17291.31 seconds wall clock time: 307 minutes 36.46 seconds (18456.46 seconds total)