Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 12:35:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc4_4380/04_2023/6gc4_4380.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc4_4380/04_2023/6gc4_4380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc4_4380/04_2023/6gc4_4380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc4_4380/04_2023/6gc4_4380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc4_4380/04_2023/6gc4_4380.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc4_4380/04_2023/6gc4_4380.pdb" } resolution = 4.3 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= 0.164 sd= 1.303 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2705 5.49 5 S 62 5.16 5 C 39724 2.51 5 N 14967 2.21 5 O 22707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ARG 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 174": "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 "C ARG 237": "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 128": "NH1" <-> "NH2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 98": "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 48": "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 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 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 "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 "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "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 "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 "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 80165 Number of models: 1 Model: "" Number of chains: 26 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: "A" Number of atoms: 55544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2586, 55544 Classifications: {'RNA': 2586} Modifications used: {'rna2p_pur': 251, 'rna2p_pyr': 131, 'rna3p_pur': 1252, 'rna3p_pyr': 952} Link IDs: {'rna2p': 382, 'rna3p': 2203} Chain breaks: 6 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: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 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: "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: "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: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "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: "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: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} 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: "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: "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 Time building chain proxies: 30.99, per 1000 atoms: 0.39 Number of scatterers: 80165 At special positions: 0 Unit cell: (220.72, 207.08, 219.48, 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 62 16.00 P 2705 15.00 O 22707 8.00 N 14967 7.00 C 39724 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: 32.21 Conformation dependent library (CDL) restraints added in 3.5 seconds 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5164 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 40 sheets defined 27.5% alpha, 18.7% beta 816 base pairs and 1437 stacking pairs defined. Time for finding SS restraints: 25.07 Creating SS restraints... Processing helix chain 'V' and resid 13 through 22 removed outlier: 3.829A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 51 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 196 through 202 removed outlier: 4.348A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.935A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.837A pdb=" N LYS D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY D 72 " --> pdb=" O PHE D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.500A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 36 removed outlier: 3.590A pdb=" N ALA E 36 " --> pdb=" O VAL E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 40 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.556A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 removed outlier: 3.622A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.586A pdb=" N LEU E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 201 Processing helix chain 'G' and resid 60 through 78 removed outlier: 3.789A pdb=" N ALA G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY G 65 " --> pdb=" O TRP G 61 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G 78 " --> pdb=" O MET G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.203A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.549A pdb=" N LYS J 61 " --> pdb=" O ASN J 58 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL J 62 " --> pdb=" O ALA J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 58 through 62' Processing helix chain 'J' and resid 89 through 96 removed outlier: 3.832A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 107 removed outlier: 4.352A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 120 Processing helix chain 'K' and resid 113 through 118 Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.802A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 137 removed outlier: 4.390A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.772A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET N 20 " --> pdb=" O HIS N 16 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER N 27 " --> pdb=" O ASN N 23 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS N 31 " --> pdb=" O SER N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 55 removed outlier: 3.977A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 removed outlier: 3.605A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 79 removed outlier: 3.892A pdb=" N LYS N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 removed outlier: 3.626A pdb=" N ARG N 86 " --> pdb=" O GLU N 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 10 removed outlier: 3.973A pdb=" N GLN P 6 " --> pdb=" O ASN P 2 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 3.754A 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 100 removed outlier: 3.731A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 107 Processing helix chain 'Q' and resid 5 through 18 removed outlier: 3.519A pdb=" N ARG Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS Q 14 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 28 removed outlier: 4.084A pdb=" N ARG Q 27 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.295A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN Q 58 " --> pdb=" O ARG Q 54 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 84 removed outlier: 3.615A pdb=" N ASN Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.670A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 117 Processing helix chain 'S' and resid 14 through 22 removed outlier: 3.868A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP S 22 " --> pdb=" O ARG S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 25 No H-bonds generated for 'chain 'S' and resid 23 through 25' Processing helix chain 'S' and resid 28 through 38 removed outlier: 4.064A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 60 removed outlier: 4.093A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS S 49 " --> pdb=" O VAL S 45 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 removed outlier: 3.762A pdb=" N ASP S 68 " --> pdb=" O ASP S 65 " (cutoff:3.500A) 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 Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.837A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'X' and resid 52 through 61 Processing helix chain 'X' and resid 62 through 71 removed outlier: 3.666A pdb=" N VAL X 66 " --> pdb=" O GLY X 62 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU X 69 " --> pdb=" O THR X 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 34 removed outlier: 4.558A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET Y 30 " --> pdb=" O PHE Y 26 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA Y 32 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 45 removed outlier: 4.121A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN Y 45 " --> pdb=" O HIS Y 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 40 through 45' Processing helix chain 'Y' and resid 46 through 56 removed outlier: 3.655A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 16 Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 23 removed outlier: 3.509A pdb=" N ARG 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 Processing helix chain 'O' and resid 3 through 18 removed outlier: 4.854A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 62 removed outlier: 3.819A pdb=" N GLN O 61 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU O 62 " --> pdb=" O ALA O 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 58 through 62' Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 113 removed outlier: 3.695A pdb=" N ALA O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 11 through 19 removed outlier: 4.105A pdb=" N LEU F 15 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 removed outlier: 3.847A pdb=" N VAL F 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 60 removed outlier: 4.073A pdb=" N LEU F 49 " --> pdb=" O ASP F 45 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 removed outlier: 4.317A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE F 98 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 137 removed outlier: 3.831A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE F 137 " --> pdb=" O GLN F 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 133 through 137' Processing helix chain 'F' and resid 141 through 145 removed outlier: 3.839A pdb=" N VAL F 145 " --> pdb=" O TYR F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 172 removed outlier: 4.014A pdb=" N GLY F 165 " --> pdb=" O SER F 161 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.567A pdb=" N ALA Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 30 removed outlier: 3.639A pdb=" N ALA H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 50 Processing sheet with id=AA1, first strand: chain 'V' and resid 2 through 5 removed outlier: 5.576A pdb=" N PHE V 2 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL V 64 " --> pdb=" O PHE V 2 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ALA V 74 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL V 92 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 7 through 8 removed outlier: 3.603A pdb=" N PHE V 26 " --> pdb=" O LEU V 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.602A pdb=" N GLU C 34 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR C 61 " --> pdb=" O GLU C 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 104 removed outlier: 3.782A pdb=" N ARG C 101 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 128 through 130 removed outlier: 7.223A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET C 180 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AA8, first strand: chain 'D' and resid 169 through 175 removed outlier: 5.920A pdb=" N VAL D 107 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR D 25 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.253A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE D 82 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG D 33 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 32 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 3 Processing sheet with id=AB2, first strand: chain 'E' and resid 118 through 121 removed outlier: 5.977A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU E 147 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N THR E 189 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ILE E 149 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 8 through 9 removed outlier: 4.213A pdb=" N VAL G 8 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR G 50 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS G 43 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY G 52 " --> pdb=" O GLU G 41 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU G 41 " --> pdb=" O GLY G 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 17 through 18 removed outlier: 3.853A pdb=" N ILE G 23 " --> pdb=" O ARG G 34 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG G 34 " --> pdb=" O ILE G 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 121 through 123 removed outlier: 3.867A pdb=" N THR G 121 " --> pdb=" O LYS G 133 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS G 133 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU G 123 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL G 131 " --> pdb=" O GLU G 123 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY G 134 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN G 87 " --> pdb=" O ARG G 162 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG G 162 " --> pdb=" O GLN G 87 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL G 89 " --> pdb=" O GLY G 160 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY G 160 " --> pdb=" O VAL G 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 94 through 96 removed outlier: 3.565A pdb=" N ARG G 94 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA G 96 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE G 102 " --> pdb=" O HIS G 114 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS G 114 " --> pdb=" O ILE G 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.750A 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: 3.586A pdb=" N ALA J 87 " --> pdb=" O TYR J 74 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS J 76 " --> pdb=" O LYS J 85 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS J 85 " --> pdb=" O HIS J 76 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 6 through 10 removed outlier: 3.950A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU K 58 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL K 63 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.269A 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: 4.169A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE P 58 " --> pdb=" O PHE P 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS P 36 " --> pdb=" O GLU P 33 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 121 through 123 Processing sheet with id=AC3, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.872A pdb=" N ILE N 34 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE N 113 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR N 36 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.915A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N TYR R 2 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE R 41 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 19 through 22 removed outlier: 3.632A pdb=" N VAL R 20 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL R 96 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE R 101 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL R 58 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 72 through 78 removed outlier: 3.521A pdb=" N VAL R 72 " --> pdb=" O HIS R 89 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS R 89 " --> pdb=" O VAL R 72 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'S' and resid 3 through 7 removed outlier: 6.677A pdb=" N ASP S 94 " --> pdb=" O ILE S 85 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE S 85 " --> pdb=" O ASP S 94 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE S 96 " --> pdb=" O LYS S 83 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS S 83 " --> pdb=" O ILE S 96 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LYS S 98 " --> pdb=" O SER S 81 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER S 81 " --> pdb=" O LYS S 98 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR S 104 " --> pdb=" O PHE S 75 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE S 75 " --> pdb=" O THR S 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 11 through 14 removed outlier: 3.854A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP T 80 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.761A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY U 22 " --> pdb=" O VAL U 10 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'U' and resid 40 through 45 removed outlier: 3.888A pdb=" N VAL U 41 " --> pdb=" O LYS U 60 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS U 43 " --> pdb=" O VAL U 58 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL U 58 " --> pdb=" O LYS U 43 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN U 45 " --> pdb=" O GLY U 56 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY U 56 " --> pdb=" O GLN U 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'U' and resid 82 through 85 removed outlier: 3.895A pdb=" N ARG U 85 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 12 through 15 removed outlier: 3.982A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.740A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AD6, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AD7, first strand: chain 'O' and resid 47 through 50 removed outlier: 7.223A pdb=" N VAL O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA O 50 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA O 37 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 65 through 66 removed outlier: 4.173A pdb=" N CYS F 86 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 90 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE F 33 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR F 156 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE F 33 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR F 154 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU F 35 " --> pdb=" O ASP F 152 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP F 152 " --> pdb=" O LEU F 35 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR F 127 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.706A pdb=" N ARG Z 37 " --> pdb=" O ILE Z 4 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.974A pdb=" N ILE H 4 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL H 37 " --> pdb=" O ILE H 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'W' and resid 18 through 19 removed outlier: 4.013A pdb=" N GLY W 18 " --> pdb=" O ARG W 35 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 42 through 43 removed outlier: 6.511A pdb=" N HIS W 42 " --> pdb=" O ILE W 76 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ILE W 78 " --> pdb=" O HIS W 42 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 47 through 49 removed outlier: 3.857A pdb=" N GLY W 48 " --> pdb=" O PHE W 56 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 620 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2073 hydrogen bonds 3286 hydrogen bond angles 0 basepair planarities 816 basepair parallelities 1437 stacking parallelities Total time for adding SS restraints: 114.75 Time building geometry restraints manager: 35.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12151 1.33 - 1.45: 37454 1.45 - 1.57: 32306 1.57 - 1.69: 5403 1.69 - 1.82: 115 Bond restraints: 87429 Sorted by residual: bond pdb=" C LEU N 38 " pdb=" N PRO N 39 " ideal model delta sigma weight residual 1.336 1.385 -0.050 1.23e-02 6.61e+03 1.63e+01 bond pdb=" CA GLN Y 39 " pdb=" CB GLN Y 39 " ideal model delta sigma weight residual 1.527 1.580 -0.052 1.30e-02 5.92e+03 1.62e+01 bond pdb=" C GLU N 49 " pdb=" N PRO N 50 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.19e-02 7.06e+03 1.27e+01 bond pdb=" C LYS C 124 " pdb=" N PRO C 125 " ideal model delta sigma weight residual 1.333 1.359 -0.025 1.01e-02 9.80e+03 6.34e+00 bond pdb=" C ARG K 71 " pdb=" N PRO K 72 " ideal model delta sigma weight residual 1.337 1.361 -0.024 9.80e-03 1.04e+04 6.16e+00 ... (remaining 87424 not shown) Histogram of bond angle deviations from ideal: 71.38 - 84.97: 3 84.97 - 98.56: 2 98.56 - 112.16: 60543 112.16 - 125.75: 60837 125.75 - 139.35: 10097 Bond angle restraints: 131482 Sorted by residual: angle pdb=" OP1 A A2439 " pdb=" P A A2439 " pdb=" OP2 A A2439 " ideal model delta sigma weight residual 119.60 79.12 40.48 3.00e+00 1.11e-01 1.82e+02 angle pdb=" O3' U A2438 " pdb=" P A A2439 " pdb=" OP2 A A2439 " ideal model delta sigma weight residual 108.00 71.38 36.62 3.00e+00 1.11e-01 1.49e+02 angle pdb=" OP1 A A2439 " pdb=" P A A2439 " pdb=" O5' A A2439 " ideal model delta sigma weight residual 108.00 78.20 29.80 3.00e+00 1.11e-01 9.87e+01 angle pdb=" C ARG H 27 " pdb=" N ASN H 28 " pdb=" CA ASN H 28 " ideal model delta sigma weight residual 121.54 139.35 -17.81 1.91e+00 2.74e-01 8.69e+01 angle pdb=" O3' U A2438 " pdb=" P A A2439 " pdb=" OP1 A A2439 " ideal model delta sigma weight residual 108.00 135.86 -27.86 3.00e+00 1.11e-01 8.62e+01 ... (remaining 131477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 44632 35.58 - 71.16: 1504 71.16 - 106.75: 110 106.75 - 142.33: 9 142.33 - 177.91: 8 Dihedral angle restraints: 46263 sinusoidal: 38235 harmonic: 8028 Sorted by residual: dihedral pdb=" CA VAL H 31 " pdb=" C VAL H 31 " pdb=" N PRO H 32 " pdb=" CA PRO H 32 " ideal model delta harmonic sigma weight residual -180.00 -113.04 -66.96 0 5.00e+00 4.00e-02 1.79e+02 dihedral pdb=" CA THR D 151 " pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta harmonic sigma weight residual -180.00 -121.58 -58.42 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA PHE F 174 " pdb=" C PHE F 174 " pdb=" N PRO F 175 " pdb=" CA PRO F 175 " ideal model delta harmonic sigma weight residual -180.00 -127.54 -52.46 0 5.00e+00 4.00e-02 1.10e+02 ... (remaining 46260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 16204 0.080 - 0.161: 635 0.161 - 0.241: 40 0.241 - 0.322: 6 0.322 - 0.402: 2 Chirality restraints: 16887 Sorted by residual: chirality pdb=" CB ILE J 84 " pdb=" CA ILE J 84 " pdb=" CG1 ILE J 84 " pdb=" CG2 ILE J 84 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" C3' U A2092 " pdb=" C4' U A2092 " pdb=" O3' U A2092 " pdb=" C2' U A2092 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C1' C A2196 " pdb=" O4' C A2196 " pdb=" C2' C A2196 " pdb=" N1 C A2196 " both_signs ideal model delta sigma weight residual False 2.47 2.15 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 16884 not shown) Planarity restraints: 6592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 151 " 0.063 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO D 152 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 152 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 152 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS Y 44 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C LYS Y 44 " -0.052 2.00e-02 2.50e+03 pdb=" O LYS Y 44 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN Y 45 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A2196 " -0.035 2.00e-02 2.50e+03 1.89e-02 8.04e+00 pdb=" N1 C A2196 " 0.043 2.00e-02 2.50e+03 pdb=" C2 C A2196 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C A2196 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C A2196 " 0.000 2.00e-02 2.50e+03 pdb=" C4 C A2196 " -0.006 2.00e-02 2.50e+03 pdb=" N4 C A2196 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C A2196 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C A2196 " 0.006 2.00e-02 2.50e+03 ... (remaining 6589 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 15711 2.78 - 3.31: 63623 3.31 - 3.84: 168464 3.84 - 4.37: 194003 4.37 - 4.90: 259856 Nonbonded interactions: 701657 Sorted by model distance: nonbonded pdb=" O6 G A1168 " pdb=" O2 U A1181 " model vdw 2.252 2.432 nonbonded pdb=" O2' G A 561 " pdb=" OH TYR Q 44 " model vdw 2.265 2.440 nonbonded pdb=" O2' A A1794 " pdb=" O2' A A1900 " model vdw 2.276 2.440 nonbonded pdb=" OP2 G A 411 " pdb=" O2' A A2406 " model vdw 2.278 2.440 nonbonded pdb=" O2 C A1999 " pdb=" O2' U A2687 " model vdw 2.283 2.440 ... (remaining 701652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 9.760 Check model and map are aligned: 0.890 Set scattering table: 0.540 Process input model: 258.930 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 275.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 87429 Z= 0.180 Angle : 0.766 40.479 131482 Z= 0.402 Chirality : 0.034 0.402 16887 Planarity : 0.005 0.095 6592 Dihedral : 13.726 177.910 41099 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.89 % Favored : 92.90 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 4.65 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.13), residues: 2788 helix: -3.23 (0.13), residues: 695 sheet: -1.29 (0.22), residues: 491 loop : -2.63 (0.12), residues: 1602 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 985 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 992 average time/residue: 0.8836 time to fit residues: 1411.1240 Evaluate side-chains 525 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 524 time to evaluate : 3.230 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5564 time to fit residues: 4.4686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 458 optimal weight: 5.9990 chunk 411 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 chunk 219 optimal weight: 30.0000 chunk 425 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 316 optimal weight: 20.0000 chunk 493 optimal weight: 9.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 87 GLN C 85 ASN C 259 ASN D 140 HIS E 97 ASN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN L 35 HIS L 54 GLN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN Q 71 ASN R 12 HIS R 43 ASN ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS S 7 HIS ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN U 39 ASN ** X 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 HIS O 100 HIS ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.086 87429 Z= 0.387 Angle : 0.892 41.967 131482 Z= 0.443 Chirality : 0.043 0.316 16887 Planarity : 0.007 0.103 6592 Dihedral : 15.131 178.233 35588 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 26.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.86 % Favored : 90.93 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.14), residues: 2788 helix: -1.93 (0.17), residues: 732 sheet: -1.26 (0.24), residues: 440 loop : -2.28 (0.13), residues: 1616 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 663 time to evaluate : 3.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 673 average time/residue: 0.8256 time to fit residues: 928.9743 Evaluate side-chains 502 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 497 time to evaluate : 3.203 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6094 time to fit residues: 9.2348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 274 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 chunk 410 optimal weight: 1.9990 chunk 335 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 493 optimal weight: 8.9990 chunk 533 optimal weight: 5.9990 chunk 439 optimal weight: 8.9990 chunk 489 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 396 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN D 150 GLN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN J 76 HIS J 136 GLN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN ** X 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 HIS O 98 GLN ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 HIS Z 48 ASN ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 42 HIS W 53 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.103 87429 Z= 0.239 Angle : 0.650 28.357 131482 Z= 0.333 Chirality : 0.036 0.257 16887 Planarity : 0.005 0.097 6592 Dihedral : 14.836 179.790 35588 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.32 % Favored : 91.46 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.14), residues: 2788 helix: -1.21 (0.18), residues: 726 sheet: -1.06 (0.23), residues: 475 loop : -2.25 (0.14), residues: 1587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 639 time to evaluate : 3.325 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: 1 outliers final: 0 residues processed: 640 average time/residue: 0.8195 time to fit residues: 877.8655 Evaluate side-chains 485 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 3.305 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 488 optimal weight: 8.9990 chunk 371 optimal weight: 8.9990 chunk 256 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 235 optimal weight: 30.0000 chunk 331 optimal weight: 0.0570 chunk 495 optimal weight: 9.9990 chunk 524 optimal weight: 20.0000 chunk 259 optimal weight: 10.0000 chunk 469 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 overall best weight: 7.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS E 46 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN Q 80 ASN R 12 HIS ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN U 65 GLN ** X 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 87429 Z= 0.325 Angle : 0.748 13.291 131482 Z= 0.384 Chirality : 0.040 0.272 16887 Planarity : 0.006 0.092 6592 Dihedral : 15.352 178.789 35588 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.01 % Favored : 89.78 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.14), residues: 2788 helix: -1.31 (0.18), residues: 741 sheet: -1.06 (0.23), residues: 509 loop : -2.33 (0.14), residues: 1538 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 604 time to evaluate : 3.256 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 outliers start: 3 outliers final: 2 residues processed: 607 average time/residue: 0.7887 time to fit residues: 809.0508 Evaluate side-chains 479 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 477 time to evaluate : 3.235 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5692 time to fit residues: 5.6261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 437 optimal weight: 8.9990 chunk 297 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 390 optimal weight: 8.9990 chunk 216 optimal weight: 20.0000 chunk 447 optimal weight: 5.9990 chunk 362 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 268 optimal weight: 6.9990 chunk 471 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN C 152 GLN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 4 GLN ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN Z 33 HIS Z 48 ASN ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.6537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 87429 Z= 0.311 Angle : 0.738 12.691 131482 Z= 0.380 Chirality : 0.041 0.302 16887 Planarity : 0.006 0.107 6592 Dihedral : 15.600 179.904 35588 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 25.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.58 % Favored : 89.20 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.14), residues: 2788 helix: -1.28 (0.18), residues: 726 sheet: -1.18 (0.22), residues: 507 loop : -2.36 (0.14), residues: 1555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 593 time to evaluate : 3.271 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: 1 outliers final: 0 residues processed: 593 average time/residue: 0.7967 time to fit residues: 798.6686 Evaluate side-chains 474 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 474 time to evaluate : 3.238 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 176 optimal weight: 20.0000 chunk 472 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 525 optimal weight: 30.0000 chunk 436 optimal weight: 0.7980 chunk 243 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 275 optimal weight: 0.8980 overall best weight: 4.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 HIS ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN E 46 GLN G 72 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 HIS ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 36 GLN ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN Z 48 ASN ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 87429 Z= 0.229 Angle : 0.642 12.253 131482 Z= 0.335 Chirality : 0.037 0.285 16887 Planarity : 0.005 0.100 6592 Dihedral : 15.351 179.412 35588 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.97 % Favored : 89.81 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % 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: -2.52 (0.15), residues: 2788 helix: -1.05 (0.18), residues: 722 sheet: -1.13 (0.23), residues: 480 loop : -2.22 (0.14), residues: 1586 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 604 time to evaluate : 3.271 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: 2 outliers final: 0 residues processed: 605 average time/residue: 0.8006 time to fit residues: 822.3939 Evaluate side-chains 466 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 3.285 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 506 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 299 optimal weight: 9.9990 chunk 383 optimal weight: 7.9990 chunk 297 optimal weight: 5.9990 chunk 442 optimal weight: 0.9980 chunk 293 optimal weight: 10.0000 chunk 523 optimal weight: 20.0000 chunk 327 optimal weight: 6.9990 chunk 319 optimal weight: 10.0000 chunk 241 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 HIS ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN D 167 ASN E 46 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 HIS ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.7036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 87429 Z= 0.250 Angle : 0.667 12.063 131482 Z= 0.345 Chirality : 0.038 0.433 16887 Planarity : 0.005 0.097 6592 Dihedral : 15.434 179.610 35588 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.29 % Favored : 89.53 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 4.65 % 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: -2.44 (0.15), residues: 2788 helix: -0.96 (0.19), residues: 708 sheet: -1.17 (0.22), residues: 519 loop : -2.15 (0.14), residues: 1561 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 572 time to evaluate : 3.272 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: 2 outliers final: 0 residues processed: 574 average time/residue: 0.8150 time to fit residues: 803.7112 Evaluate side-chains 462 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 462 time to evaluate : 3.232 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 323 optimal weight: 4.9990 chunk 209 optimal weight: 50.0000 chunk 312 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 332 optimal weight: 1.9990 chunk 356 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 411 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN E 46 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN N 107 ASN ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN R 12 HIS ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.7280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 87429 Z= 0.238 Angle : 0.652 12.128 131482 Z= 0.338 Chirality : 0.037 0.265 16887 Planarity : 0.005 0.092 6592 Dihedral : 15.420 179.423 35588 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.62 % Favored : 89.24 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % 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: -2.36 (0.15), residues: 2788 helix: -0.88 (0.19), residues: 699 sheet: -1.16 (0.23), residues: 500 loop : -2.07 (0.15), residues: 1589 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 568 time to evaluate : 3.365 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 outliers start: 3 outliers final: 1 residues processed: 571 average time/residue: 0.7960 time to fit residues: 774.0580 Evaluate side-chains 453 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 452 time to evaluate : 3.265 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5651 time to fit residues: 4.5228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 476 optimal weight: 1.9990 chunk 501 optimal weight: 20.0000 chunk 457 optimal weight: 5.9990 chunk 487 optimal weight: 10.0000 chunk 293 optimal weight: 6.9990 chunk 212 optimal weight: 30.0000 chunk 382 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 440 optimal weight: 2.9990 chunk 461 optimal weight: 9.9990 chunk 486 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN E 46 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN ** Z 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.7373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 87429 Z= 0.198 Angle : 0.612 11.943 131482 Z= 0.318 Chirality : 0.035 0.259 16887 Planarity : 0.005 0.088 6592 Dihedral : 15.277 179.785 35588 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.83 % Favored : 90.03 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % 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: -2.32 (0.15), residues: 2788 helix: -0.89 (0.19), residues: 713 sheet: -1.08 (0.23), residues: 509 loop : -2.06 (0.15), residues: 1566 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 575 time to evaluate : 3.298 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 outliers start: 1 outliers final: 1 residues processed: 576 average time/residue: 0.7902 time to fit residues: 779.3883 Evaluate side-chains 467 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 466 time to evaluate : 3.198 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5799 time to fit residues: 4.5998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 320 optimal weight: 8.9990 chunk 515 optimal weight: 30.0000 chunk 314 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 358 optimal weight: 8.9990 chunk 540 optimal weight: 20.0000 chunk 497 optimal weight: 8.9990 chunk 430 optimal weight: 7.9990 chunk 44 optimal weight: 30.0000 chunk 332 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 HIS C 114 GLN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN G 127 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS U 53 GLN X 16 ASN ** X 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 42 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.7848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 87429 Z= 0.310 Angle : 0.742 11.963 131482 Z= 0.379 Chirality : 0.040 0.263 16887 Planarity : 0.006 0.083 6592 Dihedral : 15.780 179.549 35588 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 27.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.05 % Favored : 87.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % 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: -2.62 (0.15), residues: 2788 helix: -1.19 (0.19), residues: 710 sheet: -1.39 (0.22), residues: 513 loop : -2.18 (0.15), residues: 1565 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 550 time to evaluate : 3.332 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: 0 outliers final: 0 residues processed: 550 average time/residue: 0.8028 time to fit residues: 755.7838 Evaluate side-chains 442 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 3.208 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 342 optimal weight: 30.0000 chunk 458 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 397 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 431 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 443 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN E 46 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN ** X 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 36 GLN ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.107300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.079710 restraints weight = 260585.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.082372 restraints weight = 111686.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.083084 restraints weight = 63104.482| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.8500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.118 87429 Z= 0.380 Angle : 0.837 11.829 131482 Z= 0.425 Chirality : 0.045 0.295 16887 Planarity : 0.006 0.071 6592 Dihedral : 16.419 178.829 35588 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 31.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.20 % Favored : 86.62 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % 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: -3.03 (0.14), residues: 2788 helix: -1.58 (0.18), residues: 711 sheet: -1.61 (0.22), residues: 521 loop : -2.42 (0.14), residues: 1556 =============================================================================== Job complete usr+sys time: 13172.39 seconds wall clock time: 238 minutes 44.05 seconds (14324.05 seconds total)