Starting phenix.real_space_refine (version: dev) on Fri Dec 16 06:59:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gbz_4378/12_2022/6gbz_4378.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gbz_4378/12_2022/6gbz_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_4378/12_2022/6gbz_4378.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gbz_4378/12_2022/6gbz_4378.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gbz_4378/12_2022/6gbz_4378.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gbz_4378/12_2022/6gbz_4378.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.158 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 Convert atoms to be neutral 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 40.26, per 1000 atoms: 0.47 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: 37.40 Conformation dependent library (CDL) restraints added in 3.6 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: 29.41 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: 145.47 Time building geometry restraints manager: 40.97 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 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 angle pdb=" C3' A A1938 " pdb=" O3' A A1938 " pdb=" P U A1939 " ideal model delta sigma weight residual 120.20 128.14 -7.94 1.50e+00 4.44e-01 2.80e+01 ... (remaining 141638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 48342 35.94 - 71.88: 1428 71.88 - 107.81: 118 107.81 - 143.75: 7 143.75 - 179.69: 17 Dihedral angle restraints: 49912 sinusoidal: 41209 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 49909 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 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. 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: 1.540 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: 0.090 Extract box with map and model: 10.390 Check model and map are aligned: 0.960 Convert atoms to be neutral: 0.610 Process input model: 317.140 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 334.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 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 : 13.325 179.690 44312 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.23 % Favored : 93.44 % Rotamer Outliers : 0.08 % 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 *********************** 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 : 3.685 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 outliers start: 2 outliers final: 0 residues processed: 1162 average time/residue: 0.9141 time to fit residues: 1700.2739 Evaluate side-chains 669 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 669 time to evaluate : 3.645 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7482 ------------------------------------------------------------------------------- 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: 4.9990 chunk 237 optimal weight: 10.0000 chunk 459 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 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 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.095 94219 Z= 0.301 Angle : 0.706 11.004 141643 Z= 0.360 Chirality : 0.039 0.312 18184 Planarity : 0.006 0.156 7113 Dihedral : 14.063 177.626 38299 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.39 % Favored : 92.38 % Rotamer Outliers : 4.66 % 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: -3.01 (0.13), residues: 3018 helix: -2.32 (0.15), residues: 745 sheet: -1.17 (0.21), residues: 575 loop : -2.18 (0.13), residues: 1698 *********************** 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 871 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 755 time to evaluate : 3.780 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 outliers start: 116 outliers final: 67 residues processed: 803 average time/residue: 0.8820 time to fit residues: 1173.0536 Evaluate side-chains 713 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 646 time to evaluate : 3.630 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.6258 time to fit residues: 83.4319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 295 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 442 optimal weight: 8.9990 chunk 362 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 533 optimal weight: 5.9990 chunk 575 optimal weight: 5.9990 chunk 474 optimal weight: 10.0000 chunk 528 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 427 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 GLN J 67 ASN ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 HIS ** O 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN Q 58 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 92 ASN U 65 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN 2 13 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 94219 Z= 0.306 Angle : 0.686 11.142 141643 Z= 0.351 Chirality : 0.038 0.304 18184 Planarity : 0.006 0.146 7113 Dihedral : 14.581 178.841 38299 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.45 % Favored : 91.29 % Rotamer Outliers : 3.94 % 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: -2.69 (0.13), residues: 3018 helix: -1.56 (0.17), residues: 781 sheet: -1.39 (0.20), residues: 563 loop : -2.05 (0.13), residues: 1674 *********************** 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 782 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 684 time to evaluate : 3.649 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 outliers start: 98 outliers final: 50 residues processed: 726 average time/residue: 0.8567 time to fit residues: 1061.0264 Evaluate side-chains 660 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 610 time to evaluate : 3.610 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.6694 time to fit residues: 66.8092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 526 optimal weight: 6.9990 chunk 400 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 254 optimal weight: 40.0000 chunk 357 optimal weight: 20.0000 chunk 535 optimal weight: 2.9990 chunk 566 optimal weight: 20.0000 chunk 279 optimal weight: 0.8980 chunk 507 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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** D 67 HIS ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 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 67 ASN ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN P 76 HIS ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** 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: 0.7265 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.098 94219 Z= 0.335 Angle : 0.700 11.142 141643 Z= 0.360 Chirality : 0.039 0.375 18184 Planarity : 0.006 0.146 7113 Dihedral : 14.861 179.390 38299 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.05 % Favored : 90.62 % Rotamer Outliers : 3.98 % 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: -2.57 (0.14), residues: 3018 helix: -1.28 (0.18), residues: 769 sheet: -1.41 (0.20), residues: 622 loop : -2.05 (0.13), residues: 1627 *********************** 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 745 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 646 time to evaluate : 3.744 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 outliers start: 99 outliers final: 48 residues processed: 693 average time/residue: 0.8099 time to fit residues: 953.6323 Evaluate side-chains 655 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 607 time to evaluate : 3.708 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.6442 time to fit residues: 61.3893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 471 optimal weight: 4.9990 chunk 321 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 421 optimal weight: 7.9990 chunk 233 optimal weight: 10.0000 chunk 483 optimal weight: 0.9990 chunk 391 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 289 optimal weight: 0.0030 chunk 508 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 overall best weight: 3.7998 ------------------------------------------------------------------------------- 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 156 ASN ** F 51 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 ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS N 107 ASN Q 36 GLN Q 58 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** 0 18 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 94219 Z= 0.223 Angle : 0.604 11.223 141643 Z= 0.312 Chirality : 0.035 0.298 18184 Planarity : 0.005 0.109 7113 Dihedral : 14.681 179.702 38299 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.71 % Favored : 91.12 % Rotamer Outliers : 3.01 % 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: -2.27 (0.14), residues: 3018 helix: -0.97 (0.18), residues: 777 sheet: -1.29 (0.20), residues: 605 loop : -1.86 (0.14), residues: 1636 *********************** 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 725 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 650 time to evaluate : 3.774 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 outliers start: 75 outliers final: 44 residues processed: 685 average time/residue: 0.8452 time to fit residues: 987.5041 Evaluate side-chains 666 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 622 time to evaluate : 3.653 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.6573 time to fit residues: 58.0888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 111 optimal weight: 30.0000 chunk 332 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 566 optimal weight: 20.0000 chunk 470 optimal weight: 5.9990 chunk 262 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 297 optimal weight: 7.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- 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** G 87 GLN J 67 ASN J 76 HIS ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN 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 ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 94219 Z= 0.355 Angle : 0.728 12.273 141643 Z= 0.370 Chirality : 0.040 0.329 18184 Planarity : 0.006 0.120 7113 Dihedral : 15.115 179.686 38299 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.71 % Favored : 89.96 % Rotamer Outliers : 3.29 % 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: -2.37 (0.14), residues: 3018 helix: -1.17 (0.18), residues: 785 sheet: -1.32 (0.20), residues: 594 loop : -1.88 (0.14), residues: 1639 *********************** 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 708 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 626 time to evaluate : 4.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 49 residues processed: 659 average time/residue: 0.8217 time to fit residues: 916.4236 Evaluate side-chains 635 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 586 time to evaluate : 3.625 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.6353 time to fit residues: 62.3605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 546 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 323 optimal weight: 7.9990 chunk 414 optimal weight: 6.9990 chunk 320 optimal weight: 5.9990 chunk 477 optimal weight: 7.9990 chunk 316 optimal weight: 4.9990 chunk 564 optimal weight: 20.0000 chunk 353 optimal weight: 8.9990 chunk 344 optimal weight: 5.9990 chunk 260 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN J 76 HIS L 34 HIS ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 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** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.103 94219 Z= 0.341 Angle : 0.720 13.171 141643 Z= 0.367 Chirality : 0.040 0.307 18184 Planarity : 0.006 0.112 7113 Dihedral : 15.259 179.700 38299 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.01 % Favored : 89.73 % Rotamer Outliers : 2.97 % 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: -2.38 (0.14), residues: 3018 helix: -1.16 (0.17), residues: 788 sheet: -1.36 (0.21), residues: 574 loop : -1.88 (0.14), residues: 1656 *********************** 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 694 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 620 time to evaluate : 3.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 41 residues processed: 662 average time/residue: 0.8276 time to fit residues: 934.1004 Evaluate side-chains 634 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 593 time to evaluate : 3.716 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.6316 time to fit residues: 53.5296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 349 optimal weight: 5.9990 chunk 225 optimal weight: 20.0000 chunk 337 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 110 optimal weight: 50.0000 chunk 109 optimal weight: 40.0000 chunk 359 optimal weight: 10.0000 chunk 384 optimal weight: 2.9990 chunk 279 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 443 optimal weight: 0.9980 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN Q 36 GLN ** 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 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.6314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 94219 Z= 0.316 Angle : 0.704 13.235 141643 Z= 0.359 Chirality : 0.039 0.301 18184 Planarity : 0.006 0.111 7113 Dihedral : 15.278 179.750 38299 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.57 % Favored : 89.23 % Rotamer Outliers : 2.49 % 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: -2.34 (0.14), residues: 3018 helix: -1.09 (0.18), residues: 779 sheet: -1.26 (0.21), residues: 562 loop : -1.91 (0.14), residues: 1677 *********************** 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 684 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 622 time to evaluate : 3.724 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 outliers start: 62 outliers final: 30 residues processed: 654 average time/residue: 0.8406 time to fit residues: 942.0328 Evaluate side-chains 610 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 580 time to evaluate : 3.709 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.6301 time to fit residues: 39.7928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 513 optimal weight: 10.0000 chunk 541 optimal weight: 10.0000 chunk 493 optimal weight: 20.0000 chunk 526 optimal weight: 5.9990 chunk 540 optimal weight: 7.9990 chunk 316 optimal weight: 1.9990 chunk 229 optimal weight: 10.0000 chunk 413 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 475 optimal weight: 8.9990 chunk 497 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 58 ASN ** J 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS K 13 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN R 66 HIS ** 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 75 GLN ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 HIS Y 20 ASN ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 13 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.6505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 94219 Z= 0.316 Angle : 0.706 13.482 141643 Z= 0.360 Chirality : 0.039 0.297 18184 Planarity : 0.005 0.109 7113 Dihedral : 15.318 179.022 38299 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.17 % Favored : 88.67 % Rotamer Outliers : 1.65 % 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: -2.35 (0.14), residues: 3018 helix: -1.02 (0.18), residues: 779 sheet: -1.38 (0.21), residues: 569 loop : -1.90 (0.14), residues: 1670 *********************** 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 643 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 602 time to evaluate : 3.712 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 outliers start: 41 outliers final: 27 residues processed: 621 average time/residue: 0.8298 time to fit residues: 878.6798 Evaluate side-chains 612 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 585 time to evaluate : 3.796 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.6561 time to fit residues: 36.9095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 524 optimal weight: 0.0570 chunk 345 optimal weight: 20.0000 chunk 556 optimal weight: 4.9990 chunk 339 optimal weight: 2.9990 chunk 264 optimal weight: 30.0000 chunk 386 optimal weight: 7.9990 chunk 583 optimal weight: 4.9990 chunk 537 optimal weight: 10.0000 chunk 464 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 359 optimal weight: 0.0040 overall best weight: 1.8114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 GLN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN G 63 GLN J 76 HIS J 131 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN R 91 GLN S 31 GLN T 70 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.6458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 94219 Z= 0.155 Angle : 0.579 14.065 141643 Z= 0.297 Chirality : 0.032 0.278 18184 Planarity : 0.005 0.090 7113 Dihedral : 14.804 178.774 38299 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.45 % Favored : 91.45 % Rotamer Outliers : 0.36 % 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: -1.93 (0.15), residues: 3018 helix: -0.60 (0.19), residues: 766 sheet: -1.01 (0.21), residues: 546 loop : -1.71 (0.14), residues: 1706 ********************** 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 648 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 639 time to evaluate : 3.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 642 average time/residue: 0.8236 time to fit residues: 900.3786 Evaluate side-chains 600 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 596 time to evaluate : 3.664 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.8722 time to fit residues: 9.4989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 586 random chunks: chunk 285 optimal weight: 20.0000 chunk 369 optimal weight: 0.7980 chunk 495 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 428 optimal weight: 4.9990 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: 10.0000 chunk 58 optimal weight: 10.0000 overall best weight: 5.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 GLN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 62 GLN J 76 HIS J 131 ASN K 9 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.130966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102550 restraints weight = 199594.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105078 restraints weight = 70533.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106599 restraints weight = 39411.927| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.6652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 94219 Z= 0.299 Angle : 0.691 15.579 141643 Z= 0.351 Chirality : 0.037 0.290 18184 Planarity : 0.005 0.102 7113 Dihedral : 15.102 179.765 38299 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.77 % Favored : 89.10 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 1.04 % 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: -2.14 (0.14), residues: 3018 helix: -0.85 (0.18), residues: 784 sheet: -1.12 (0.22), residues: 534 loop : -1.82 (0.14), residues: 1700 =============================================================================== Job complete usr+sys time: 16039.11 seconds wall clock time: 285 minutes 56.97 seconds (17156.97 seconds total)