Starting phenix.real_space_refine (version: dev) on Mon May 16 04:05:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc0_4379/05_2022/6gc0_4379.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc0_4379/05_2022/6gc0_4379.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/6gc0_4379/05_2022/6gc0_4379.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc0_4379/05_2022/6gc0_4379.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc0_4379/05_2022/6gc0_4379.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc0_4379/05_2022/6gc0_4379.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= 0.157 sd= 1.409 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 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 69": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 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 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 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 43": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 84138 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 58604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2729, 58604 Classifications: {'RNA': 2729} Modifications used: {'rna3p_pyr': 1005, 'rna2p_pur': 260, 'rna3p_pur': 1323, 'rna2p_pyr': 141} Link IDs: {'rna3p': 2327, 'rna2p': 401} Chain breaks: 2 Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2548 Classifications: {'RNA': 119} Modifications used: {'rna3p_pyr': 49, 'rna2p_pur': 7, 'rna3p_pur': 57, 'rna2p_pyr': 6} Link IDs: {'rna3p': 105, 'rna2p': 13} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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} 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: 35.35, per 1000 atoms: 0.42 Number of scatterers: 84138 At special positions: 0 Unit cell: (243.04, 209.56, 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 64 16.00 P 2847 15.00 O 23844 8.00 N 15706 7.00 C 41677 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: 30.65 Conformation dependent library (CDL) restraints added in 3.3 seconds 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5374 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 44 sheets defined 27.2% alpha, 21.5% beta 659 base pairs and 1635 stacking pairs defined. Time for finding SS restraints: 28.18 Creating SS restraints... Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.096A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.797A pdb=" N HIS D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 removed outlier: 4.054A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASP D 103 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 37 removed outlier: 3.652A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 115 removed outlier: 3.512A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.532A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 removed outlier: 4.350A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 183 removed outlier: 3.789A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 removed outlier: 3.833A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 10 Processing helix chain 'F' and resid 10 through 19 removed outlier: 4.231A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 removed outlier: 3.721A pdb=" N VAL F 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 60 removed outlier: 3.713A pdb=" N ASP F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 104 removed outlier: 3.790A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 137 Processing helix chain 'F' and resid 161 through 171 removed outlier: 3.543A pdb=" N GLY F 165 " --> pdb=" O SER F 161 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 80 removed outlier: 3.838A pdb=" N ALA G 67 " --> pdb=" O GLN G 63 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 removed outlier: 3.668A pdb=" N GLY G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) removed outlier: 3.601A 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 Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.677A pdb=" N ALA J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 removed outlier: 3.812A pdb=" N ILE J 93 " --> pdb=" O PHE J 89 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 108 removed outlier: 4.375A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 120 Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.565A pdb=" N GLN J 135 " --> pdb=" O HIS J 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 111 No H-bonds generated for 'chain 'K' and resid 109 through 111' Processing helix chain 'K' and resid 112 through 118 removed outlier: 3.668A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.776A pdb=" N THR L 5 " --> pdb=" O ARG L 2 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU L 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2 through 6' Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.795A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 74 removed outlier: 3.592A pdb=" N THR L 74 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.559A pdb=" N ARG L 132 " --> pdb=" O THR L 128 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.759A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE N 21 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA N 25 " --> pdb=" O PHE N 21 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 45 removed outlier: 3.546A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 55 Processing helix chain 'N' and resid 59 through 69 removed outlier: 3.608A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 79 removed outlier: 3.599A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 removed outlier: 3.985A pdb=" N ARG N 86 " --> pdb=" O GLU N 82 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 82 through 87' Processing helix chain 'O' and resid 5 through 11 removed outlier: 3.768A pdb=" N ARG O 9 " --> pdb=" O SER O 5 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA O 11 " --> pdb=" O ARG O 7 " (cutoff:3.500A) Processing helix chain 'O' and resid 11 through 22 removed outlier: 3.634A pdb=" N LEU O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 removed outlier: 3.870A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 84 removed outlier: 3.518A pdb=" N ALA O 72 " --> pdb=" O LYS O 68 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS O 76 " --> pdb=" O ALA O 72 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 113 removed outlier: 3.634A pdb=" N ALA O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 10 removed outlier: 3.807A 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: 3.723A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU P 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.907A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS Q 13 " --> pdb=" O ALA Q 9 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 29 removed outlier: 4.191A pdb=" N ARG Q 27 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 71 removed outlier: 3.969A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE Q 39 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS Q 40 " --> pdb=" O GLN Q 36 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA Q 62 " --> pdb=" O GLN Q 58 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN Q 70 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 92 through 101 removed outlier: 3.540A pdb=" N ALA Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.725A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.591A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 36 removed outlier: 4.649A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.534A pdb=" N ASN S 61 " --> pdb=" O ASN S 57 " (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: 3.745A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 3 through 8' Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.521A pdb=" N THR T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'V' and resid 12 through 23 removed outlier: 4.246A pdb=" N ALA V 16 " --> pdb=" O GLN V 12 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA V 22 " --> pdb=" O ARG V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 51 Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.214A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 62 removed outlier: 3.852A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 74 removed outlier: 3.503A pdb=" N LEU X 67 " --> pdb=" O ILE X 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 23 removed outlier: 3.519A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 32 removed outlier: 3.698A pdb=" N LEU Y 28 " --> pdb=" O GLU Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 56 removed outlier: 3.686A pdb=" N ARG Y 48 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.526A pdb=" N GLY Z 45 " --> pdb=" O PRO Z 41 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 14 Processing helix chain '0' and resid 15 through 19 removed outlier: 4.397A pdb=" N HIS 0 18 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 16 removed outlier: 3.523A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 24 through 38 removed outlier: 3.842A pdb=" N VAL 2 30 " --> pdb=" O ASN 2 26 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 2 31 " --> pdb=" O GLY 2 27 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 11 Processing helix chain '3' and resid 36 through 43 removed outlier: 3.706A pdb=" N HIS 3 42 " --> pdb=" O LYS 3 38 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU 3 43 " --> pdb=" O ARG 3 39 " (cutoff:3.500A) Processing helix chain '3' and resid 50 through 53 removed outlier: 3.536A pdb=" N ASP 3 53 " --> pdb=" O SER 3 50 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 50 through 53' Processing helix chain '3' and resid 54 through 59 removed outlier: 3.939A pdb=" N ALA 3 59 " --> pdb=" O GLY 3 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.624A pdb=" N GLU C 34 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 3.636A 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: 3.670A pdb=" N ARG C 101 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.798A 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: 6.756A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET C 180 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 14 removed outlier: 5.692A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.234A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.748A 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 118 removed outlier: 3.735A pdb=" N GLY D 117 " --> pdb=" O MET D 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.392A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU E 147 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N THR E 189 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE E 149 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 65 through 67 removed outlier: 4.337A pdb=" N CYS F 86 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET F 37 " --> pdb=" O CYS F 86 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 90 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE F 33 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR F 34 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR F 154 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR F 127 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 8 through 9 removed outlier: 3.638A pdb=" N VAL G 8 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR G 50 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 16 through 18 removed outlier: 3.649A pdb=" N LYS G 17 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR G 24 " --> pdb=" O LYS G 17 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG G 34 " --> pdb=" O ILE G 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 121 through 123 removed outlier: 3.569A pdb=" N GLY G 134 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN G 87 " --> pdb=" O ARG G 162 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG G 162 " --> pdb=" O GLN G 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 95 through 98 removed outlier: 3.964A pdb=" N LYS G 98 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.325A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 73 through 76 removed outlier: 3.548A pdb=" N LYS J 85 " --> pdb=" O HIS J 76 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 7 through 10 removed outlier: 3.896A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU K 45 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL K 19 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE K 43 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N CYS K 21 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE K 41 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS K 23 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE K 39 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL K 63 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 69 through 70 removed outlier: 4.115A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 69 through 70 removed outlier: 4.115A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR P 24 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL P 85 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLU P 26 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE P 83 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS P 28 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 89 through 90 Processing sheet with id=AC4, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.542A pdb=" N ILE N 113 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU N 114 " --> pdb=" O ARG N 96 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 25 through 30 removed outlier: 3.724A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN O 38 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 89 through 90 removed outlier: 4.261A pdb=" N LYS P 110 " --> pdb=" O ALA P 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.783A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA R 42 " --> pdb=" O TYR R 2 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 19 through 22 removed outlier: 7.403A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.164A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 2 through 10 removed outlier: 3.526A pdb=" N HIS S 9 " --> pdb=" O SER S 101 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP S 94 " --> pdb=" O ILE S 85 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE S 85 " --> pdb=" O ASP S 94 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE S 96 " --> pdb=" O LYS S 83 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS S 83 " --> pdb=" O ILE S 96 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS S 98 " --> pdb=" O SER S 81 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER S 81 " --> pdb=" O LYS S 98 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'T' and resid 11 through 14 removed outlier: 4.152A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 11 through 14 removed outlier: 4.152A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.900A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 40 through 44 Processing sheet with id=AD6, first strand: chain 'U' and resid 82 through 86 removed outlier: 3.920A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 2 through 8 removed outlier: 8.346A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU V 7 " --> pdb=" O GLU V 41 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU V 38 " --> pdb=" O ILE V 30 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE V 30 " --> pdb=" O LEU V 38 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN V 87 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN V 78 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ILE V 89 " --> pdb=" O ASP V 76 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASP V 76 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N PHE V 91 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA V 74 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG V 93 " --> pdb=" O VAL V 72 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL V 72 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N PHE V 2 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL V 64 " --> pdb=" O PHE V 2 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 18 through 19 removed outlier: 3.501A pdb=" N GLY W 18 " --> pdb=" O ARG W 35 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'W' and resid 26 through 27 removed outlier: 3.739A pdb=" N GLY W 61 " --> pdb=" O VAL W 27 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS W 68 " --> pdb=" O ARG W 73 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG W 73 " --> pdb=" O LYS W 68 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N HIS W 42 " --> pdb=" O ILE W 76 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N ILE W 78 " --> pdb=" O HIS W 42 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'X' and resid 12 through 17 removed outlier: 3.640A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'X' and resid 32 through 38 Processing sheet with id=AE3, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.533A pdb=" N VAL Z 35 " --> pdb=" O ILE Z 6 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU Z 57 " --> pdb=" O LYS Z 5 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AE5, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AE6, first strand: chain '1' and resid 6 through 11 removed outlier: 3.766A pdb=" N GLU 1 6 " --> pdb=" O LYS 1 24 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR 1 20 " --> pdb=" O LEU 1 10 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '1' and resid 36 through 39 removed outlier: 3.620A pdb=" N LYS 1 37 " --> pdb=" O VAL 1 46 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '3' and resid 14 through 15 removed outlier: 3.609A pdb=" N LYS 3 14 " --> pdb=" O LYS 3 22 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS 3 23 " --> pdb=" O ALA 3 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA 3 47 " --> pdb=" O HIS 3 23 " (cutoff:3.500A) 659 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1553 hydrogen bonds 2414 hydrogen bond angles 0 basepair planarities 659 basepair parallelities 1635 stacking parallelities Total time for adding SS restraints: 139.31 Time building geometry restraints manager: 33.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15650 1.34 - 1.46: 37866 1.46 - 1.58: 32461 1.58 - 1.70: 5691 1.70 - 1.82: 118 Bond restraints: 91786 Sorted by residual: bond pdb=" C ALA E 128 " pdb=" N PRO E 129 " ideal model delta sigma weight residual 1.334 1.483 -0.149 2.34e-02 1.83e+03 4.03e+01 bond pdb=" C ARG 3 44 " pdb=" N PRO 3 45 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.91e+00 bond pdb=" N PHE F 176 " pdb=" CA PHE F 176 " ideal model delta sigma weight residual 1.459 1.484 -0.026 1.16e-02 7.43e+03 4.90e+00 bond pdb=" CB ASN U 98 " pdb=" CG ASN U 98 " ideal model delta sigma weight residual 1.516 1.570 -0.054 2.50e-02 1.60e+03 4.64e+00 bond pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.34e+00 ... (remaining 91781 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.43: 17081 106.43 - 113.71: 56387 113.71 - 120.99: 38731 120.99 - 128.27: 21460 128.27 - 135.55: 4411 Bond angle restraints: 138070 Sorted by residual: angle pdb=" C LYS 1 49 " pdb=" N GLU 1 50 " pdb=" CA GLU 1 50 " ideal model delta sigma weight residual 121.31 132.48 -11.17 1.49e+00 4.50e-01 5.62e+01 angle pdb=" C SER U 97 " pdb=" N ASN U 98 " pdb=" CA ASN U 98 " ideal model delta sigma weight residual 121.54 135.55 -14.01 1.91e+00 2.74e-01 5.38e+01 angle pdb=" C CYS N 100 " pdb=" N GLY N 101 " pdb=" CA GLY N 101 " ideal model delta sigma weight residual 121.41 132.57 -11.16 1.96e+00 2.60e-01 3.24e+01 angle pdb=" C GLN P 14 " pdb=" N ASP P 15 " pdb=" CA ASP P 15 " ideal model delta sigma weight residual 124.82 134.63 -9.81 1.78e+00 3.16e-01 3.04e+01 angle pdb=" C ASN U 52 " pdb=" N GLN U 53 " pdb=" CA GLN U 53 " ideal model delta sigma weight residual 120.06 126.59 -6.53 1.19e+00 7.06e-01 3.01e+01 ... (remaining 138065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 47296 35.93 - 71.86: 1173 71.86 - 107.80: 88 107.80 - 143.73: 4 143.73 - 179.66: 14 Dihedral angle restraints: 48575 sinusoidal: 40222 harmonic: 8353 Sorted by residual: 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 -116.29 -63.71 0 5.00e+00 4.00e-02 1.62e+02 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 -119.84 -60.16 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA GLY C 11 " pdb=" C GLY C 11 " pdb=" N ARG C 12 " pdb=" CA ARG C 12 " ideal model delta harmonic sigma weight residual -180.00 -131.52 -48.48 0 5.00e+00 4.00e-02 9.40e+01 ... (remaining 48572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 16879 0.060 - 0.119: 722 0.119 - 0.179: 117 0.179 - 0.238: 11 0.238 - 0.298: 8 Chirality restraints: 17737 Sorted by residual: chirality pdb=" C3' A A1938 " pdb=" C4' A A1938 " pdb=" O3' A A1938 " pdb=" C2' A A1938 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE E 149 " pdb=" CA ILE E 149 " pdb=" CG1 ILE E 149 " pdb=" CG2 ILE E 149 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C3' G A 271 " pdb=" C4' G A 271 " pdb=" O3' G A 271 " pdb=" C2' G A 271 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 17734 not shown) Planarity restraints: 6884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO H 32 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C PRO H 32 " -0.070 2.00e-02 2.50e+03 pdb=" O PRO H 32 " 0.027 2.00e-02 2.50e+03 pdb=" N GLN H 33 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL H 31 " 0.060 5.00e-02 4.00e+02 9.00e-02 1.29e+01 pdb=" N PRO H 32 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO H 32 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO H 32 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 151 " 0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO D 152 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO D 152 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 152 " 0.048 5.00e-02 4.00e+02 ... (remaining 6881 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 20276 2.81 - 3.33: 65993 3.33 - 3.85: 176196 3.85 - 4.38: 208195 4.38 - 4.90: 272397 Nonbonded interactions: 743057 Sorted by model distance: nonbonded pdb=" OD1 ASN D 136 " pdb=" OG SER D 139 " model vdw 2.283 2.440 nonbonded pdb=" O2' A A 911 " pdb=" O2' C A2263 " model vdw 2.290 2.440 nonbonded pdb=" O2' G A1792 " pdb=" OP1 C A1830 " model vdw 2.292 2.440 nonbonded pdb=" OP1 G A1296 " pdb=" O2' G A2709 " model vdw 2.294 2.440 nonbonded pdb=" O2' U A2343 " pdb=" O2' G A2373 " model vdw 2.301 2.440 ... (remaining 743052 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 2847 5.49 5 S 64 5.16 5 C 41677 2.51 5 N 15706 2.21 5 O 23844 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=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.070 Extract box with map and model: 9.490 Check model and map are aligned: 0.910 Convert atoms to be neutral: 0.540 Process input model: 292.390 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 307.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 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 0.149 91786 Z= 0.133 Angle : 0.523 16.019 138070 Z= 0.290 Chirality : 0.028 0.298 17737 Planarity : 0.005 0.090 6884 Dihedral : 12.294 179.660 43201 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.94 % Favored : 94.00 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.28 % 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: 2898 helix: -4.74 (0.06), residues: 675 sheet: -1.43 (0.20), residues: 586 loop : -2.51 (0.12), residues: 1637 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1114 time to evaluate : 4.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1115 average time/residue: 0.9878 time to fit residues: 1792.4257 Evaluate side-chains 651 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 651 time to evaluate : 3.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 479 optimal weight: 2.9990 chunk 430 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 290 optimal weight: 20.0000 chunk 230 optimal weight: 10.0000 chunk 445 optimal weight: 1.9990 chunk 172 optimal weight: 20.0000 chunk 270 optimal weight: 10.0000 chunk 331 optimal weight: 0.7980 chunk 515 optimal weight: 20.0000 overall best weight: 5.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 116 GLN C 199 HIS ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 242 HIS D 67 HIS D 134 HIS ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 62 GLN E 165 HIS F 4 HIS F 62 GLN H 2 GLN J 58 ASN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN O 38 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN Q 71 ASN R 87 GLN R 91 GLN S 9 HIS T 48 GLN U 68 ASN V 75 GLN W 8 ASN W 53 HIS X 35 HIS Z 19 HIS 2 26 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.100 91786 Z= 0.286 Angle : 0.659 14.662 138070 Z= 0.338 Chirality : 0.037 0.299 17737 Planarity : 0.006 0.117 6884 Dihedral : 13.383 178.549 37441 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.49 % Favored : 93.44 % Rotamer Outliers : 5.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.18 % 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: -2.90 (0.13), residues: 2898 helix: -2.62 (0.14), residues: 707 sheet: -1.02 (0.20), residues: 595 loop : -1.94 (0.13), residues: 1596 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 717 time to evaluate : 3.420 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 outliers start: 127 outliers final: 93 residues processed: 774 average time/residue: 0.8055 time to fit residues: 1053.5228 Evaluate side-chains 707 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 614 time to evaluate : 3.346 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 0 residues processed: 93 average time/residue: 0.6052 time to fit residues: 109.5409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 286 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 429 optimal weight: 10.0000 chunk 351 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 516 optimal weight: 9.9990 chunk 558 optimal weight: 0.9990 chunk 460 optimal weight: 6.9990 chunk 512 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 414 optimal weight: 0.3980 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN C 199 HIS ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN J 138 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN N 107 ASN O 38 GLN P 40 GLN R 12 HIS S 61 ASN T 28 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN Y 58 ASN 0 18 HIS 1 45 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.115 91786 Z= 0.281 Angle : 0.646 14.568 138070 Z= 0.332 Chirality : 0.037 0.271 17737 Planarity : 0.006 0.105 6884 Dihedral : 13.908 178.886 37441 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.49 % Favored : 92.48 % Rotamer Outliers : 3.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.18 % 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: 2898 helix: -1.65 (0.17), residues: 721 sheet: -0.95 (0.20), residues: 580 loop : -1.79 (0.14), residues: 1597 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 685 time to evaluate : 3.439 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 outliers start: 87 outliers final: 61 residues processed: 730 average time/residue: 0.8266 time to fit residues: 1028.5749 Evaluate side-chains 661 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 600 time to evaluate : 3.381 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.6173 time to fit residues: 74.0466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 510 optimal weight: 0.0270 chunk 388 optimal weight: 2.9990 chunk 268 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 346 optimal weight: 0.2980 chunk 518 optimal weight: 7.9990 chunk 549 optimal weight: 2.9990 chunk 270 optimal weight: 10.0000 chunk 491 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 overall best weight: 1.6644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN H 33 GLN J 47 HIS K 88 ASN N 107 ASN T 28 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 42 HIS Y 58 ASN 3 27 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.101 91786 Z= 0.145 Angle : 0.517 13.178 138070 Z= 0.268 Chirality : 0.031 0.245 17737 Planarity : 0.005 0.103 6884 Dihedral : 13.570 179.730 37441 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.42 % Favored : 93.55 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.18 % 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: -1.89 (0.15), residues: 2898 helix: -1.08 (0.18), residues: 725 sheet: -0.83 (0.20), residues: 593 loop : -1.49 (0.15), residues: 1580 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 676 time to evaluate : 3.435 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 outliers start: 73 outliers final: 43 residues processed: 704 average time/residue: 0.7935 time to fit residues: 954.7164 Evaluate side-chains 648 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 605 time to evaluate : 3.542 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.6168 time to fit residues: 54.1567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 457 optimal weight: 10.0000 chunk 311 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 408 optimal weight: 7.9990 chunk 226 optimal weight: 10.0000 chunk 468 optimal weight: 5.9990 chunk 379 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 280 optimal weight: 10.0000 chunk 492 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN J 135 GLN J 138 GLN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN P 9 GLN P 40 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN Y 58 ASN ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.086 91786 Z= 0.382 Angle : 0.751 13.303 138070 Z= 0.378 Chirality : 0.040 0.272 17737 Planarity : 0.006 0.105 6884 Dihedral : 14.434 175.838 37441 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.73 % Favored : 91.20 % Rotamer Outliers : 4.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.18 % 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: -2.09 (0.15), residues: 2898 helix: -1.05 (0.18), residues: 721 sheet: -0.96 (0.20), residues: 595 loop : -1.72 (0.14), residues: 1582 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 637 time to evaluate : 3.467 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 outliers start: 100 outliers final: 67 residues processed: 688 average time/residue: 0.8442 time to fit residues: 993.6230 Evaluate side-chains 672 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 605 time to evaluate : 3.414 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.7000 time to fit residues: 91.8694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 184 optimal weight: 20.0000 chunk 494 optimal weight: 9.9990 chunk 108 optimal weight: 50.0000 chunk 322 optimal weight: 0.5980 chunk 135 optimal weight: 10.0000 chunk 549 optimal weight: 10.0000 chunk 456 optimal weight: 7.9990 chunk 254 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 overall best weight: 7.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN J 135 GLN L 35 HIS ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 ASN ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN Z 33 HIS ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.148 91786 Z= 0.388 Angle : 0.765 12.516 138070 Z= 0.390 Chirality : 0.042 0.299 17737 Planarity : 0.007 0.106 6884 Dihedral : 15.062 178.891 37441 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.73 % Favored : 90.20 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.14 % 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: -2.30 (0.14), residues: 2898 helix: -1.15 (0.18), residues: 703 sheet: -1.03 (0.21), residues: 560 loop : -1.91 (0.14), residues: 1635 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 648 time to evaluate : 3.482 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 outliers start: 85 outliers final: 54 residues processed: 684 average time/residue: 0.8057 time to fit residues: 930.4589 Evaluate side-chains 648 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 594 time to evaluate : 3.376 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.5883 time to fit residues: 64.5704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 529 optimal weight: 0.0020 chunk 61 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 401 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 462 optimal weight: 4.9990 chunk 306 optimal weight: 30.0000 chunk 547 optimal weight: 2.9990 chunk 342 optimal weight: 0.0000 chunk 333 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN J 135 GLN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN T 28 ASN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS Y 15 ASN Y 58 ASN 0 3 GLN 0 18 HIS 1 25 ASN 3 27 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.148 91786 Z= 0.190 Angle : 0.580 12.410 138070 Z= 0.302 Chirality : 0.033 0.282 17737 Planarity : 0.006 0.111 6884 Dihedral : 14.449 178.035 37441 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.04 % Favored : 91.89 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.15), residues: 2898 helix: -0.61 (0.20), residues: 692 sheet: -1.01 (0.22), residues: 553 loop : -1.66 (0.14), residues: 1653 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 651 time to evaluate : 3.377 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: 50 outliers final: 23 residues processed: 673 average time/residue: 0.7962 time to fit residues: 908.6239 Evaluate side-chains 618 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 595 time to evaluate : 3.360 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.6171 time to fit residues: 30.3641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 338 optimal weight: 0.9990 chunk 218 optimal weight: 20.0000 chunk 326 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 107 optimal weight: 50.0000 chunk 106 optimal weight: 30.0000 chunk 348 optimal weight: 9.9990 chunk 372 optimal weight: 5.9990 chunk 270 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 430 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN J 135 GLN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN P 11 GLN P 40 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 25 ASN ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.130 91786 Z= 0.272 Angle : 0.645 12.268 138070 Z= 0.333 Chirality : 0.036 0.283 17737 Planarity : 0.006 0.130 6884 Dihedral : 14.572 177.019 37441 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.04 % Favored : 90.89 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.18 % 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: -1.96 (0.15), residues: 2898 helix: -0.74 (0.19), residues: 707 sheet: -0.96 (0.22), residues: 540 loop : -1.70 (0.14), residues: 1651 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 610 time to evaluate : 3.461 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: 57 outliers final: 45 residues processed: 628 average time/residue: 0.8142 time to fit residues: 873.7505 Evaluate side-chains 634 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 589 time to evaluate : 3.511 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.6844 time to fit residues: 61.7038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 498 optimal weight: 0.2980 chunk 524 optimal weight: 4.9990 chunk 478 optimal weight: 7.9990 chunk 510 optimal weight: 0.9990 chunk 307 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 400 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 461 optimal weight: 0.9990 chunk 482 optimal weight: 6.9990 chunk 508 optimal weight: 30.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN P 11 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 25 ASN ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.174 91786 Z= 0.181 Angle : 0.562 12.787 138070 Z= 0.291 Chirality : 0.032 0.287 17737 Planarity : 0.006 0.144 6884 Dihedral : 14.247 178.769 37441 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.01 % Favored : 91.93 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.14 % 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: -1.71 (0.15), residues: 2898 helix: -0.40 (0.20), residues: 688 sheet: -0.94 (0.22), residues: 547 loop : -1.54 (0.15), residues: 1663 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 612 time to evaluate : 3.410 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 outliers start: 20 outliers final: 9 residues processed: 624 average time/residue: 0.8024 time to fit residues: 855.4257 Evaluate side-chains 596 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 587 time to evaluate : 3.390 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5842 time to fit residues: 13.6313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 335 optimal weight: 10.0000 chunk 539 optimal weight: 6.9990 chunk 329 optimal weight: 0.5980 chunk 255 optimal weight: 9.9990 chunk 375 optimal weight: 5.9990 chunk 565 optimal weight: 9.9990 chunk 520 optimal weight: 20.0000 chunk 450 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 348 optimal weight: 5.9990 chunk 276 optimal weight: 20.0000 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS D 36 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN J 135 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN P 40 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 25 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.139 91786 Z= 0.313 Angle : 0.691 16.203 138070 Z= 0.354 Chirality : 0.037 0.271 17737 Planarity : 0.007 0.176 6884 Dihedral : 14.701 175.948 37441 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.11 % Favored : 89.79 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.07 % 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: -1.96 (0.15), residues: 2898 helix: -0.66 (0.19), residues: 696 sheet: -0.99 (0.22), residues: 545 loop : -1.72 (0.14), residues: 1657 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 592 time to evaluate : 3.399 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 outliers start: 26 outliers final: 20 residues processed: 600 average time/residue: 0.8272 time to fit residues: 848.1178 Evaluate side-chains 598 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 578 time to evaluate : 3.408 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.6289 time to fit residues: 27.7292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 357 optimal weight: 4.9990 chunk 480 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 415 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 451 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 463 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.127568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.100824 restraints weight = 208053.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.103409 restraints weight = 71253.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.104949 restraints weight = 38273.180| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.229 91786 Z= 0.353 Angle : 0.729 17.803 138070 Z= 0.372 Chirality : 0.039 0.270 17737 Planarity : 0.007 0.146 6884 Dihedral : 14.818 176.593 37441 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.04 % Favored : 88.85 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.11 % 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: -2.13 (0.15), residues: 2898 helix: -0.78 (0.19), residues: 700 sheet: -1.11 (0.21), residues: 558 loop : -1.83 (0.14), residues: 1640 =============================================================================== Job complete usr+sys time: 15925.53 seconds wall clock time: 283 minutes 35.49 seconds (17015.49 seconds total)