Starting phenix.real_space_refine on Mon Mar 18 20:58:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spd_10282/03_2024/6spd_10282.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spd_10282/03_2024/6spd_10282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spd_10282/03_2024/6spd_10282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spd_10282/03_2024/6spd_10282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spd_10282/03_2024/6spd_10282.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spd_10282/03_2024/6spd_10282.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 2958 5.49 5 S 71 5.16 5 C 45126 2.51 5 N 16826 2.21 5 O 25371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 45": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 52": "NH1" <-> "NH2" Residue "M ARG 56": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 52": "NH1" <-> "NH2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 110": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "T ARG 76": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "V ARG 11": "NH1" <-> "NH2" Residue "V ARG 21": "NH1" <-> "NH2" Residue "V ARG 23": "NH1" <-> "NH2" Residue "V PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W ARG 14": "NH1" <-> "NH2" Residue "W ARG 20": "NH1" <-> "NH2" Residue "W ARG 41": "NH1" <-> "NH2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X ARG 48": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "2 ARG 10": "NH1" <-> "NH2" Residue "2 ARG 16": "NH1" <-> "NH2" Residue "2 ARG 39": "NH1" <-> "NH2" Residue "2 ARG 51": "NH1" <-> "NH2" Residue "3 PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 3": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 14": "NH1" <-> "NH2" Residue "4 ARG 19": "NH1" <-> "NH2" Residue "4 ARG 21": "NH1" <-> "NH2" Residue "4 ARG 33": "NH1" <-> "NH2" Residue "4 ARG 41": "NH1" <-> "NH2" Residue "5 ARG 39": "NH1" <-> "NH2" Residue "5 ARG 41": "NH1" <-> "NH2" Residue "6 ARG 19": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 90352 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 61164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2851, 61164 Inner-chain residues flagged as termini: ['pdbres=" A A 283 "', 'pdbres=" A A 923 "', 'pdbres=" A A1134 "', 'pdbres=" G A1173 "', 'pdbres=" U A1525 "', 'pdbres=" G A1707 "', 'pdbres=" A A1725 "'] Classifications: {'RNA': 2851} Modifications used: {'5*END': 8, 'rna2p_pur': 276, 'rna2p_pyr': 163, 'rna3p_pur': 1364, 'rna3p_pyr': 1048} Link IDs: {'rna2p': 439, 'rna3p': 2411} Chain breaks: 4 Chain: "B" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2469 Classifications: {'RNA': 116} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 50} Link IDs: {'rna2p': 11, 'rna3p': 104} Chain: "C" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2067 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 255} Chain: "D" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1557 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain: "E" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1516 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "F" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1402 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 7, 'TRANS': 167} Chain: "G" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1308 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain: "H" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1086 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "I" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1026 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain: "J" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1122 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "K" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1058 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "M" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1069 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "N" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "O" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 881 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'TRANS': 114} Chain: "P" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 894 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "Q" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "T" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 701 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "U" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 801 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "V" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1405 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 180} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "W" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 574 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'TRANS': 75} Chain: "X" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 630 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 476 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "Z" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 445 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "1" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 232 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "2" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 423 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "3" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 418 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "4" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 365 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "5" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 506 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "6" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Time building chain proxies: 35.59, per 1000 atoms: 0.39 Number of scatterers: 90352 At special positions: 0 Unit cell: (220, 226.6, 201.3, 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 71 16.00 P 2958 15.00 O 25371 8.00 N 16826 7.00 C 45126 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: 39.45 Conformation dependent library (CDL) restraints added in 4.3 seconds 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6278 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 52 sheets defined 24.3% alpha, 16.5% beta 791 base pairs and 1570 stacking pairs defined. Time for finding SS restraints: 32.39 Creating SS restraints... Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 207 through 213 removed outlier: 4.200A pdb=" N THR C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 213' Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.676A pdb=" N ASP D 44 " --> pdb=" O THR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 97 through 101 removed outlier: 4.088A pdb=" N LEU D 100 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 23 through 36 removed outlier: 3.741A pdb=" N VAL E 27 " --> pdb=" O ASN E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 108 removed outlier: 3.544A pdb=" N TYR E 100 " --> pdb=" O ASN E 96 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 114 Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.726A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 159 removed outlier: 3.588A pdb=" N LEU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.533A pdb=" N PHE E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU E 196 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU E 197 " --> pdb=" O LYS E 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 11 Processing helix chain 'F' and resid 11 through 20 removed outlier: 4.160A pdb=" N LYS F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU F 19 " --> pdb=" O LYS F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 62 removed outlier: 3.557A pdb=" N LEU F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 95 Processing helix chain 'F' and resid 96 through 101 removed outlier: 3.562A pdb=" N ASP F 101 " --> pdb=" O TYR F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 168 removed outlier: 3.546A pdb=" N GLY F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 81 removed outlier: 3.653A pdb=" N VAL G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.507A pdb=" N VAL G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 3.881A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 48 Processing helix chain 'H' and resid 50 through 58 Processing helix chain 'H' and resid 60 through 67 removed outlier: 3.730A pdb=" N ALA H 65 " --> pdb=" O LYS H 61 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU H 66 " --> pdb=" O LYS H 62 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 102 removed outlier: 4.010A pdb=" N GLU H 100 " --> pdb=" O ARG H 96 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA H 101 " --> pdb=" O ASP H 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 37 No H-bonds generated for 'chain 'I' and resid 35 through 37' Processing helix chain 'I' and resid 38 through 43 Processing helix chain 'I' and resid 78 through 85 Processing helix chain 'I' and resid 105 through 110 removed outlier: 4.568A pdb=" N ILE I 109 " --> pdb=" O GLN I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 113 No H-bonds generated for 'chain 'I' and resid 111 through 113' Processing helix chain 'I' and resid 122 through 132 removed outlier: 3.504A pdb=" N VAL I 126 " --> pdb=" O LEU I 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.681A pdb=" N THR J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 71 removed outlier: 3.591A pdb=" N THR J 70 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP J 71 " --> pdb=" O LYS J 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 67 through 71' Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.999A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS J 95 " --> pdb=" O LYS J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 107 removed outlier: 3.725A pdb=" N THR J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL J 105 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'L' and resid 37 through 41 removed outlier: 3.936A pdb=" N SER L 40 " --> pdb=" O GLY L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 Processing helix chain 'L' and resid 69 through 72 Processing helix chain 'L' and resid 80 through 85 removed outlier: 3.801A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL L 85 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 98 removed outlier: 3.760A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 136 removed outlier: 3.543A pdb=" N ARG L 132 " --> pdb=" O THR L 128 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 59 removed outlier: 4.120A pdb=" N ARG M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL M 58 " --> pdb=" O LEU M 54 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 116 removed outlier: 3.619A pdb=" N GLU M 116 " --> pdb=" O GLU M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 123 removed outlier: 3.515A pdb=" N ALA M 123 " --> pdb=" O ALA M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.563A pdb=" N PHE N 21 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL N 26 " --> pdb=" O GLN N 22 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER N 27 " --> pdb=" O ASN N 23 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU N 30 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS N 31 " --> pdb=" O SER N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 42 Processing helix chain 'N' and resid 43 through 47 removed outlier: 3.758A pdb=" N ARG N 46 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 53 Processing helix chain 'N' and resid 54 through 57 Processing helix chain 'N' and resid 59 through 68 Processing helix chain 'N' and resid 72 through 79 removed outlier: 3.554A pdb=" N VAL N 76 " --> pdb=" O SER N 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 22 removed outlier: 3.871A pdb=" N THR O 7 " --> pdb=" O VAL O 3 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LYS O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA O 15 " --> pdb=" O ARG O 11 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU O 21 " --> pdb=" O LEU O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 84 removed outlier: 4.295A pdb=" N LYS O 72 " --> pdb=" O ASP O 68 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL O 73 " --> pdb=" O ALA O 69 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA O 78 " --> pdb=" O GLY O 74 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU O 79 " --> pdb=" O GLN O 75 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG O 80 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA O 81 " --> pdb=" O VAL O 77 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS O 82 " --> pdb=" O ALA O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 112 removed outlier: 3.517A pdb=" N LEU O 105 " --> pdb=" O ARG O 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG O 110 " --> pdb=" O ALA O 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 10 Processing helix chain 'P' and resid 98 through 102 removed outlier: 3.859A pdb=" N LEU P 101 " --> pdb=" O LEU P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 21 removed outlier: 3.798A pdb=" N ARG Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG Q 13 " --> pdb=" O ILE Q 9 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 Processing helix chain 'Q' and resid 36 through 71 removed outlier: 3.646A pdb=" N ALA Q 42 " --> pdb=" O ALA Q 38 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG Q 50 " --> pdb=" O ALA Q 46 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE Q 57 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU Q 60 " --> pdb=" O GLN Q 56 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA Q 63 " --> pdb=" O ALA Q 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA Q 67 " --> pdb=" O ALA Q 63 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 84 removed outlier: 3.512A pdb=" N ALA Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 99 removed outlier: 3.535A pdb=" N ASP Q 97 " --> pdb=" O LYS Q 93 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU Q 98 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 117 removed outlier: 4.174A pdb=" N LYS Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.577A pdb=" N ALA S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA S 21 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLN S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.902A pdb=" N ASN S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE S 38 " --> pdb=" O ASN S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 60 removed outlier: 3.964A pdb=" N GLU S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS S 49 " --> pdb=" O GLU S 45 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER S 53 " --> pdb=" O LYS S 49 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA S 58 " --> pdb=" O ALA S 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 26 removed outlier: 3.657A pdb=" N GLY T 21 " --> pdb=" O GLU T 17 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU T 22 " --> pdb=" O LYS T 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP T 24 " --> pdb=" O THR T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 48 removed outlier: 3.647A pdb=" N GLU T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 16 through 25 removed outlier: 3.636A pdb=" N LEU V 22 " --> pdb=" O ALA V 18 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG V 23 " --> pdb=" O SER V 19 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG V 24 " --> pdb=" O ARG V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 56 Processing helix chain 'V' and resid 57 through 62 removed outlier: 4.419A pdb=" N PHE V 60 " --> pdb=" O GLU V 57 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS V 62 " --> pdb=" O ALA V 59 " (cutoff:3.500A) Processing helix chain 'V' and resid 117 through 122 Processing helix chain 'V' and resid 173 through 178 Processing helix chain 'W' and resid 73 through 76 removed outlier: 3.529A pdb=" N GLY W 76 " --> pdb=" O GLY W 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 73 through 76' Processing helix chain 'X' and resid 53 through 63 removed outlier: 3.715A pdb=" N ARG X 57 " --> pdb=" O ALA X 53 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE X 58 " --> pdb=" O LYS X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 73 removed outlier: 3.765A pdb=" N ASP X 70 " --> pdb=" O ALA X 66 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU X 71 " --> pdb=" O VAL X 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 7 removed outlier: 3.734A pdb=" N GLU Y 7 " --> pdb=" O ASN Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 34 removed outlier: 3.600A pdb=" N THR Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER Y 19 " --> pdb=" O GLY Y 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS Y 20 " --> pdb=" O ASN Y 16 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU Y 21 " --> pdb=" O ASN Y 17 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG Y 23 " --> pdb=" O SER Y 19 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP Y 24 " --> pdb=" O HIS Y 20 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU Y 28 " --> pdb=" O ASP Y 24 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS Y 32 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 44 removed outlier: 4.081A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 39 through 44' Processing helix chain 'Y' and resid 46 through 59 removed outlier: 3.561A pdb=" N ALA Y 51 " --> pdb=" O LYS Y 47 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG Y 52 " --> pdb=" O ARG Y 48 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL Y 53 " --> pdb=" O ASP Y 49 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU Y 57 " --> pdb=" O VAL Y 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 27 removed outlier: 3.853A pdb=" N LYS Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 50 removed outlier: 3.699A pdb=" N MET Z 46 " --> pdb=" O GLU Z 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE Z 47 " --> pdb=" O ASN Z 43 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN Z 48 " --> pdb=" O ARG Z 44 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 50' Processing helix chain '1' and resid 8 through 13 Processing helix chain '2' and resid 9 through 15 Processing helix chain '2' and resid 16 through 19 removed outlier: 4.133A pdb=" N HIS 2 19 " --> pdb=" O ARG 2 16 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 16 through 19' Processing helix chain '4' and resid 9 through 17 removed outlier: 3.584A pdb=" N ARG 4 14 " --> pdb=" O LEU 4 10 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL 4 15 " --> pdb=" O LYS 4 11 " (cutoff:3.500A) Processing helix chain '4' and resid 17 through 22 Processing helix chain '4' and resid 25 through 38 removed outlier: 3.511A pdb=" N GLN 4 29 " --> pdb=" O LYS 4 25 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY 4 38 " --> pdb=" O ARG 4 34 " (cutoff:3.500A) Processing helix chain '5' and resid 9 through 14 Processing helix chain '5' and resid 36 through 41 Processing helix chain '5' and resid 50 through 61 removed outlier: 4.661A pdb=" N ALA 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG 5 56 " --> pdb=" O SER 5 52 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG 5 59 " --> pdb=" O ALA 5 55 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER 5 60 " --> pdb=" O ARG 5 56 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 34 removed outlier: 3.518A pdb=" N HIS 6 33 " --> pdb=" O GLU 6 30 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA3, first strand: chain 'C' and resid 74 through 75 removed outlier: 4.640A pdb=" N ILE C 74 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE C 117 " --> pdb=" O ILE C 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.726A pdb=" N ARG C 102 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR C 96 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.564A pdb=" N VAL C 184 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET C 181 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.590A pdb=" N VAL D 201 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLN D 105 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE D 177 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU D 29 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LYS D 9 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 34 through 39 removed outlier: 6.578A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N PHE D 38 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA D 48 " --> pdb=" O PHE D 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 117 through 120 removed outlier: 6.742A pdb=" N LEU E 146 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N THR E 188 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL E 148 " --> pdb=" O THR E 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 31 through 36 removed outlier: 6.014A pdb=" N ILE F 34 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR F 157 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 36 " --> pdb=" O THR F 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AB2, first strand: chain 'G' and resid 16 through 17 Processing sheet with id=AB3, first strand: chain 'G' and resid 42 through 45 removed outlier: 3.962A pdb=" N ARG G 51 " --> pdb=" O ILE G 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 122 through 124 Processing sheet with id=AB5, first strand: chain 'G' and resid 95 through 99 Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB7, first strand: chain 'H' and resid 79 through 80 removed outlier: 3.647A pdb=" N VAL H 146 " --> pdb=" O LEU H 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'H' and resid 127 through 130 removed outlier: 3.545A pdb=" N PHE H 127 " --> pdb=" O LEU H 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 12 through 14 removed outlier: 3.777A pdb=" N VAL I 13 " --> pdb=" O THR I 55 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.743A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 76 through 77 Processing sheet with id=AC3, first strand: chain 'K' and resid 7 through 10 removed outlier: 6.726A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N ALA K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP K 9 " --> pdb=" O ALA K 84 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU K 86 " --> pdb=" O ASP K 9 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.617A pdb=" N ILE K 76 " --> pdb=" O THR P 74 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR P 61 " --> pdb=" O ILE P 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 74 through 78 removed outlier: 3.502A pdb=" N ALA L 75 " --> pdb=" O ARG L 107 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL L 108 " --> pdb=" O ALA L 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 89 through 90 removed outlier: 6.536A pdb=" N LYS L 141 " --> pdb=" O LEU L 122 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 63 through 66 removed outlier: 3.548A pdb=" N GLU M 107 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU M 34 " --> pdb=" O LEU M 103 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU M 105 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR M 32 " --> pdb=" O GLU M 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 40 through 42 removed outlier: 3.775A pdb=" N TYR M 92 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.288A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 48 through 53 removed outlier: 3.633A pdb=" N ALA O 50 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR O 30 " --> pdb=" O TYR O 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 39 through 45 removed outlier: 6.706A pdb=" N THR P 26 " --> pdb=" O LYS P 88 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN P 30 " --> pdb=" O SER P 84 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER P 84 " --> pdb=" O GLN P 30 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LYS P 32 " --> pdb=" O VAL P 82 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL P 82 " --> pdb=" O LYS P 32 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 2 through 5 removed outlier: 6.904A pdb=" N TYR R 2 " --> pdb=" O VAL R 41 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL R 41 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 19 through 22 removed outlier: 4.648A pdb=" N HIS R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLN R 91 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASP R 70 " --> pdb=" O GLN R 91 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE R 93 " --> pdb=" O ARG R 68 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ARG R 68 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU R 95 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS R 66 " --> pdb=" O GLU R 95 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LYS R 97 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL R 64 " --> pdb=" O LYS R 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 3 through 8 removed outlier: 6.433A pdb=" N ALA S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL S 71 " --> pdb=" O ALA S 108 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 82 through 87 Processing sheet with id=AD7, first strand: chain 'T' and resid 10 through 13 removed outlier: 4.307A pdb=" N GLY T 12 " --> pdb=" O LYS T 32 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL T 33 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG T 56 " --> pdb=" O ALA T 85 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'T' and resid 66 through 69 removed outlier: 3.670A pdb=" N GLY T 72 " --> pdb=" O THR T 69 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 10 through 12 removed outlier: 4.030A pdb=" N ILE U 71 " --> pdb=" O ASP U 80 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 24 through 27 removed outlier: 3.557A pdb=" N LYS U 26 " --> pdb=" O VAL U 34 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 40 through 44 removed outlier: 3.661A pdb=" N VAL U 58 " --> pdb=" O ARG U 43 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 82 through 87 removed outlier: 4.580A pdb=" N LYS U 85 " --> pdb=" O ILE U 92 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE U 92 " --> pdb=" O LYS U 85 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 5 through 7 removed outlier: 8.005A pdb=" N PHE V 94 " --> pdb=" O PRO V 30 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL V 32 " --> pdb=" O PHE V 94 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG V 96 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N TYR V 34 " --> pdb=" O ARG V 96 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 105 through 107 removed outlier: 3.897A pdb=" N ALA V 105 " --> pdb=" O VAL V 136 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 125 through 129 removed outlier: 6.507A pdb=" N VAL V 160 " --> pdb=" O VAL V 184 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 46 through 47 removed outlier: 3.579A pdb=" N ARG W 77 " --> pdb=" O LYS W 72 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'W' and resid 66 through 67 Processing sheet with id=AE9, first strand: chain 'X' and resid 13 through 16 removed outlier: 3.533A pdb=" N GLY X 15 " --> pdb=" O ARG X 27 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 33 through 34 Processing sheet with id=AF2, first strand: chain 'X' and resid 37 through 39 Processing sheet with id=AF3, first strand: chain 'Z' and resid 3 through 7 removed outlier: 3.515A pdb=" N VAL Z 4 " --> pdb=" O VAL Z 37 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL Z 6 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL Z 35 " --> pdb=" O VAL Z 6 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '2' and resid 27 through 29 Processing sheet with id=AF5, first strand: chain '3' and resid 16 through 21 removed outlier: 3.662A pdb=" N GLN 3 41 " --> pdb=" O ASP 3 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '5' and resid 15 through 17 removed outlier: 3.585A pdb=" N LYS 5 15 " --> pdb=" O LYS 5 22 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY 5 20 " --> pdb=" O THR 5 17 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '6' and resid 14 through 19 removed outlier: 3.508A pdb=" N ILE 6 26 " --> pdb=" O LYS 6 15 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1722 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1957 hydrogen bonds 3164 hydrogen bond angles 0 basepair planarities 791 basepair parallelities 1570 stacking parallelities Total time for adding SS restraints: 155.01 Time building geometry restraints manager: 42.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 9601 1.31 - 1.44: 42898 1.44 - 1.56: 39794 1.56 - 1.69: 5916 1.69 - 1.82: 124 Bond restraints: 98333 Sorted by residual: bond pdb=" O5' C A2606 " pdb=" C5' C A2606 " ideal model delta sigma weight residual 1.420 1.492 -0.072 1.50e-02 4.44e+03 2.28e+01 bond pdb=" CA ALA D 76 " pdb=" CB ALA D 76 " ideal model delta sigma weight residual 1.529 1.459 0.070 1.65e-02 3.67e+03 1.81e+01 bond pdb=" C LYS L 29 " pdb=" O LYS L 29 " ideal model delta sigma weight residual 1.235 1.187 0.049 1.26e-02 6.30e+03 1.50e+01 bond pdb=" C HIS C 90 " pdb=" N ILE C 91 " ideal model delta sigma weight residual 1.329 1.282 0.047 1.38e-02 5.25e+03 1.16e+01 bond pdb=" C3' U A2604 " pdb=" O3' U A2604 " ideal model delta sigma weight residual 1.417 1.467 -0.050 1.50e-02 4.44e+03 1.09e+01 ... (remaining 98328 not shown) Histogram of bond angle deviations from ideal: 91.66 - 100.72: 465 100.72 - 109.77: 44484 109.77 - 118.82: 53201 118.82 - 127.87: 43793 127.87 - 136.92: 5509 Bond angle restraints: 147452 Sorted by residual: angle pdb=" O3' C A2606 " pdb=" C3' C A2606 " pdb=" C2' C A2606 " ideal model delta sigma weight residual 113.70 95.12 18.58 1.50e+00 4.44e-01 1.53e+02 angle pdb=" O3' A A 974 " pdb=" C3' A A 974 " pdb=" C2' A A 974 " ideal model delta sigma weight residual 109.50 124.43 -14.93 1.50e+00 4.44e-01 9.90e+01 angle pdb=" N ARG W 39 " pdb=" CA ARG W 39 " pdb=" C ARG W 39 " ideal model delta sigma weight residual 110.80 91.66 19.14 2.13e+00 2.20e-01 8.07e+01 angle pdb=" N LEU R 51 " pdb=" CA LEU R 51 " pdb=" C LEU R 51 " ideal model delta sigma weight residual 109.64 99.46 10.18 1.27e+00 6.20e-01 6.43e+01 angle pdb=" O4' C A2130 " pdb=" C1' C A2130 " pdb=" C2' C A2130 " ideal model delta sigma weight residual 107.60 99.71 7.89 1.00e+00 1.00e+00 6.22e+01 ... (remaining 147447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 54641 35.63 - 71.26: 7301 71.26 - 106.89: 808 106.89 - 142.52: 41 142.52 - 178.16: 67 Dihedral angle restraints: 62858 sinusoidal: 53090 harmonic: 9768 Sorted by residual: dihedral pdb=" CA VAL V 154 " pdb=" C VAL V 154 " pdb=" N GLU V 155 " pdb=" CA GLU V 155 " ideal model delta harmonic sigma weight residual 180.00 109.47 70.53 0 5.00e+00 4.00e-02 1.99e+02 dihedral pdb=" CA ALA K 118 " pdb=" C ALA K 118 " pdb=" N PRO K 119 " pdb=" CA PRO K 119 " ideal model delta harmonic sigma weight residual 180.00 -113.69 -66.31 0 5.00e+00 4.00e-02 1.76e+02 dihedral pdb=" CA LEU R 51 " pdb=" C LEU R 51 " pdb=" N PRO R 52 " pdb=" CA PRO R 52 " ideal model delta harmonic sigma weight residual -180.00 -119.76 -60.24 0 5.00e+00 4.00e-02 1.45e+02 ... (remaining 62855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 18056 0.138 - 0.276: 804 0.276 - 0.414: 48 0.414 - 0.552: 10 0.552 - 0.690: 1 Chirality restraints: 18919 Sorted by residual: chirality pdb=" C1' A A1262 " pdb=" O4' A A1262 " pdb=" C2' A A1262 " pdb=" N9 A A1262 " both_signs ideal model delta sigma weight residual False 2.46 1.77 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" C1' G A 774 " pdb=" O4' G A 774 " pdb=" C2' G A 774 " pdb=" N9 G A 774 " both_signs ideal model delta sigma weight residual False 2.46 1.98 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" C3' C A2130 " pdb=" C4' C A2130 " pdb=" O3' C A2130 " pdb=" C2' C A2130 " both_signs ideal model delta sigma weight residual False -2.48 -2.00 -0.48 2.00e-01 2.50e+01 5.70e+00 ... (remaining 18916 not shown) Planarity restraints: 7667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 127 " -0.058 2.00e-02 2.50e+03 3.97e-02 2.76e+01 pdb=" CG PHE D 127 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 PHE D 127 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE D 127 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 127 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE D 127 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE D 127 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP 3 36 " -0.082 5.00e-02 4.00e+02 1.26e-01 2.53e+01 pdb=" N PRO 3 37 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO 3 37 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO 3 37 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A2017 " 0.063 2.00e-02 2.50e+03 2.92e-02 2.35e+01 pdb=" N9 A A2017 " -0.052 2.00e-02 2.50e+03 pdb=" C8 A A2017 " -0.018 2.00e-02 2.50e+03 pdb=" N7 A A2017 " -0.006 2.00e-02 2.50e+03 pdb=" C5 A A2017 " 0.007 2.00e-02 2.50e+03 pdb=" C6 A A2017 " -0.008 2.00e-02 2.50e+03 pdb=" N6 A A2017 " 0.043 2.00e-02 2.50e+03 pdb=" N1 A A2017 " -0.017 2.00e-02 2.50e+03 pdb=" C2 A A2017 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A A2017 " 0.000 2.00e-02 2.50e+03 pdb=" C4 A A2017 " -0.011 2.00e-02 2.50e+03 ... (remaining 7664 not shown) Histogram of nonbonded interaction distances: 0.40 - 1.30: 11 1.30 - 2.20: 174 2.20 - 3.10: 58375 3.10 - 4.00: 263091 4.00 - 4.90: 471200 Warning: very small nonbonded interaction distances. Nonbonded interactions: 792851 Sorted by model distance: nonbonded pdb=" N2 G A2131 " pdb=" O6 G A2135 " model vdw 0.400 2.520 nonbonded pdb=" OP1 A A1165 " pdb=" O6 G A1166 " model vdw 0.475 3.040 nonbonded pdb=" O2 C A2094 " pdb=" O4 U A2095 " model vdw 0.589 3.040 nonbonded pdb=" C6 A A1169 " pdb=" N4 C A1170 " model vdw 0.840 3.340 nonbonded pdb=" C5' A A2134 " pdb=" C8 G A2135 " model vdw 0.999 3.660 ... (remaining 792846 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 individual isotropic 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: 4.270 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: 16.320 Check model and map are aligned: 1.030 Set scattering table: 0.650 Process input model: 329.440 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.250 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: 0.030 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 357.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4943 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 : 0.010 0.100 98333 Z= 0.624 Angle : 1.156 19.135 147452 Z= 0.614 Chirality : 0.065 0.690 18919 Planarity : 0.007 0.126 7667 Dihedral : 24.534 178.156 56580 Min Nonbonded Distance : 0.400 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.71 % Allowed : 12.15 % Favored : 87.14 % Rotamer: Outliers : 1.26 % Allowed : 5.12 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 1.15 % 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: -5.12 (0.11), residues: 3398 helix: -4.69 (0.07), residues: 753 sheet: -2.52 (0.19), residues: 574 loop : -3.29 (0.10), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.006 TRP C 213 HIS 0.025 0.004 HIS N 16 PHE 0.083 0.005 PHE D 127 TYR 0.030 0.004 TYR H 25 ARG 0.021 0.002 ARG V 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 724 time to evaluate : 3.807 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: C 130 MET cc_start: 0.0377 (ptm) cc_final: -0.0084 (tmm) REVERT: D 12 MET cc_start: 0.7683 (mtp) cc_final: 0.7421 (mtt) REVERT: E 137 LEU cc_start: 0.5871 (mt) cc_final: 0.4982 (tp) REVERT: F 4 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7599 (tm) REVERT: F 38 MET cc_start: 0.4460 (tmt) cc_final: 0.3128 (tmt) REVERT: F 130 MET cc_start: 0.6733 (tmm) cc_final: 0.6435 (tmm) REVERT: G 33 LEU cc_start: 0.7334 (pp) cc_final: 0.6766 (pp) REVERT: G 38 HIS cc_start: 0.6209 (p90) cc_final: 0.5707 (p90) REVERT: G 130 ASP cc_start: 0.7016 (t0) cc_final: 0.6278 (p0) REVERT: J 100 VAL cc_start: 0.7825 (t) cc_final: 0.7557 (m) REVERT: J 133 THR cc_start: 0.8304 (m) cc_final: 0.7998 (t) REVERT: K 14 SER cc_start: 0.7898 (p) cc_final: 0.7624 (t) REVERT: M 81 VAL cc_start: 0.7105 (t) cc_final: 0.6574 (m) REVERT: N 110 MET cc_start: 0.7239 (mmt) cc_final: 0.6852 (mmt) REVERT: O 64 THR cc_start: 0.7588 (p) cc_final: 0.7173 (m) REVERT: O 68 ASP cc_start: 0.7931 (m-30) cc_final: 0.7562 (t0) REVERT: P 8 GLN cc_start: 0.8215 (tt0) cc_final: 0.8008 (tp40) REVERT: P 72 GLU cc_start: 0.7670 (pt0) cc_final: 0.6573 (pt0) REVERT: P 107 LYS cc_start: 0.6619 (ttmm) cc_final: 0.6359 (mppt) REVERT: R 99 THR cc_start: 0.6311 (p) cc_final: 0.5508 (p) REVERT: V 131 ILE cc_start: 0.6456 (tt) cc_final: 0.6244 (tt) REVERT: W 38 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7268 (t) REVERT: Y 30 MET cc_start: 0.5542 (mmm) cc_final: 0.5247 (mmp) REVERT: 3 29 LYS cc_start: 0.5924 (mtpt) cc_final: 0.5580 (tttp) REVERT: 3 35 TYR cc_start: 0.6621 (t80) cc_final: 0.5980 (t80) REVERT: 6 8 LYS cc_start: 0.7923 (pmtt) cc_final: 0.7659 (pttt) REVERT: 6 34 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7844 (ttpt) outliers start: 35 outliers final: 4 residues processed: 746 average time/residue: 0.9980 time to fit residues: 1211.3699 Evaluate side-chains 404 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 398 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain 5 residue 37 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 531 optimal weight: 1.9990 chunk 476 optimal weight: 1.9990 chunk 264 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 chunk 321 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 493 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 299 optimal weight: 0.9980 chunk 366 optimal weight: 5.9990 chunk 571 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 HIS D 33 ASN D 68 HIS D 126 ASN E 61 GLN E 93 GLN F 37 ASN F 52 ASN F 63 GLN F 135 GLN G 23 GLN G 73 ASN ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 GLN I 19 ASN J 58 ASN J 77 HIS K 3 GLN K 89 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 HIS M 96 GLN N 62 ASN N 107 ASN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 GLN ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN ** R 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS S 61 ASN T 77 ASN T 90 GLN V 83 HIS V 110 HIS V 113 ASN V 158 GLN ** V 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 186 ASN W 35 ASN Y 20 HIS Y 58 ASN Z 33 HIS ** 1 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 5 GLN 4 26 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 98333 Z= 0.242 Angle : 0.881 19.396 147452 Z= 0.430 Chirality : 0.044 0.323 18919 Planarity : 0.006 0.068 7667 Dihedral : 24.832 179.549 49961 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.33 % Favored : 90.23 % Rotamer: Outliers : 3.32 % Allowed : 12.09 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.12), residues: 3398 helix: -3.28 (0.14), residues: 768 sheet: -2.07 (0.19), residues: 616 loop : -2.98 (0.11), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 213 HIS 0.013 0.002 HIS 5 30 PHE 0.035 0.002 PHE D 127 TYR 0.025 0.002 TYR G 164 ARG 0.016 0.001 ARG L 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 548 time to evaluate : 3.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 181 MET cc_start: 0.3115 (mpp) cc_final: 0.2649 (mpp) REVERT: C 225 MET cc_start: 0.7555 (mtt) cc_final: 0.7325 (mtt) REVERT: D 127 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.7767 (t80) REVERT: F 173 PHE cc_start: 0.6589 (t80) cc_final: 0.6079 (t80) REVERT: G 49 GLU cc_start: 0.6675 (pp20) cc_final: 0.6133 (pp20) REVERT: G 73 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7713 (m-40) REVERT: G 124 GLU cc_start: 0.7927 (mp0) cc_final: 0.7373 (mp0) REVERT: G 130 ASP cc_start: 0.6876 (t0) cc_final: 0.5966 (p0) REVERT: J 100 VAL cc_start: 0.8413 (t) cc_final: 0.8133 (m) REVERT: J 133 THR cc_start: 0.8584 (m) cc_final: 0.8217 (t) REVERT: K 29 HIS cc_start: 0.7706 (p-80) cc_final: 0.7133 (p90) REVERT: K 38 ILE cc_start: 0.8791 (mm) cc_final: 0.8472 (mm) REVERT: K 88 ASN cc_start: 0.7341 (m110) cc_final: 0.6982 (m-40) REVERT: K 91 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.5790 (pp30) REVERT: M 17 ASN cc_start: 0.8300 (m-40) cc_final: 0.7954 (m-40) REVERT: M 81 VAL cc_start: 0.7659 (t) cc_final: 0.7163 (m) REVERT: M 96 GLN cc_start: 0.8246 (mt0) cc_final: 0.7867 (mm-40) REVERT: M 111 GLU cc_start: 0.6625 (pm20) cc_final: 0.6418 (pm20) REVERT: N 27 SER cc_start: 0.8102 (m) cc_final: 0.7781 (m) REVERT: N 110 MET cc_start: 0.7525 (mmt) cc_final: 0.6912 (mmt) REVERT: O 64 THR cc_start: 0.7698 (p) cc_final: 0.7414 (m) REVERT: O 68 ASP cc_start: 0.7743 (m-30) cc_final: 0.7366 (t0) REVERT: P 15 ASN cc_start: 0.6829 (m-40) cc_final: 0.6479 (m-40) REVERT: P 107 LYS cc_start: 0.6712 (ttmm) cc_final: 0.6112 (mtmm) REVERT: Q 78 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.6965 (mtp-110) REVERT: Q 97 ASP cc_start: 0.7036 (m-30) cc_final: 0.6533 (t0) REVERT: S 47 MET cc_start: 0.7625 (mmm) cc_final: 0.7251 (mmm) REVERT: S 78 GLU cc_start: 0.6828 (pt0) cc_final: 0.6383 (pm20) REVERT: S 86 MET cc_start: 0.5255 (tmm) cc_final: 0.4793 (tpt) REVERT: U 50 MET cc_start: 0.3884 (ppp) cc_final: 0.3390 (pmm) REVERT: V 77 ILE cc_start: 0.6892 (mp) cc_final: 0.6667 (mp) REVERT: V 159 ILE cc_start: 0.4689 (OUTLIER) cc_final: 0.4400 (pt) REVERT: V 161 HIS cc_start: 0.4633 (m90) cc_final: 0.4360 (m-70) REVERT: W 38 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7152 (t) REVERT: Y 30 MET cc_start: 0.5606 (mmm) cc_final: 0.5396 (mmp) REVERT: Z 37 VAL cc_start: 0.5845 (OUTLIER) cc_final: 0.5473 (p) REVERT: 2 15 MET cc_start: 0.7531 (mtt) cc_final: 0.7219 (mtt) REVERT: 4 22 MET cc_start: 0.5915 (tpp) cc_final: 0.5636 (tpt) REVERT: 4 41 ARG cc_start: 0.6985 (mtm-85) cc_final: 0.6677 (mtm110) REVERT: 6 8 LYS cc_start: 0.8006 (pmtt) cc_final: 0.7700 (pttt) REVERT: 6 18 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7539 (tpp80) REVERT: 6 34 LYS cc_start: 0.8353 (ttmt) cc_final: 0.7918 (ttpt) REVERT: 6 37 GLN cc_start: 0.7244 (tt0) cc_final: 0.7016 (tt0) outliers start: 92 outliers final: 48 residues processed: 601 average time/residue: 0.9380 time to fit residues: 934.4462 Evaluate side-chains 477 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 423 time to evaluate : 3.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain O residue 25 VAL Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 54 ARG Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain Q residue 101 ASN Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain T residue 61 ASN Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain V residue 60 PHE Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 159 ILE Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 55 LYS Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 3 residue 44 ILE Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 5 residue 37 THR Chi-restraints excluded: chain 6 residue 12 ARG Chi-restraints excluded: chain 6 residue 16 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 317 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 475 optimal weight: 4.9990 chunk 388 optimal weight: 0.0170 chunk 157 optimal weight: 7.9990 chunk 572 optimal weight: 10.0000 chunk 618 optimal weight: 7.9990 chunk 509 optimal weight: 0.0870 chunk 567 optimal weight: 0.0040 chunk 195 optimal weight: 6.9990 chunk 459 optimal weight: 3.9990 overall best weight: 1.8212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS G 23 GLN G 38 HIS G 73 ASN H 82 HIS P 13 GLN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 GLN ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 HIS U 73 ASN V 158 GLN ** V 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 186 ASN Z 43 ASN ** 1 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 41 HIS 4 6 GLN ** 6 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 33 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.7461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 98333 Z= 0.253 Angle : 0.745 14.067 147452 Z= 0.380 Chirality : 0.040 0.565 18919 Planarity : 0.006 0.112 7667 Dihedral : 24.588 179.944 49959 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.95 % Favored : 88.79 % Rotamer: Outliers : 4.51 % Allowed : 14.80 % Favored : 80.69 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.30 % 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: -3.78 (0.12), residues: 3398 helix: -2.53 (0.16), residues: 763 sheet: -1.78 (0.20), residues: 619 loop : -2.85 (0.11), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 213 HIS 0.088 0.003 HIS R 82 PHE 0.040 0.002 PHE D 127 TYR 0.025 0.002 TYR G 164 ARG 0.025 0.001 ARG G 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 614 time to evaluate : 3.876 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: C 6 CYS cc_start: 0.6475 (t) cc_final: 0.5874 (t) REVERT: C 36 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.6453 (tptt) REVERT: C 130 MET cc_start: 0.2993 (ptp) cc_final: 0.2791 (mtm) REVERT: C 181 MET cc_start: 0.5090 (mpp) cc_final: 0.4699 (mpp) REVERT: C 203 ARG cc_start: 0.7313 (ttp-170) cc_final: 0.7099 (ttp-170) REVERT: D 8 ARG cc_start: 0.7456 (ttt-90) cc_final: 0.7034 (ttt180) REVERT: D 85 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6878 (pp) REVERT: D 127 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8137 (t80) REVERT: D 160 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8716 (mtmt) REVERT: E 43 LYS cc_start: 0.5947 (ttmp) cc_final: 0.5718 (tttm) REVERT: E 95 LEU cc_start: 0.5217 (mp) cc_final: 0.4565 (mt) REVERT: E 147 ILE cc_start: 0.4932 (mt) cc_final: 0.4706 (mt) REVERT: F 149 LEU cc_start: 0.2148 (OUTLIER) cc_final: 0.1894 (pt) REVERT: F 173 PHE cc_start: 0.6367 (t80) cc_final: 0.6092 (t80) REVERT: G 49 GLU cc_start: 0.7368 (pp20) cc_final: 0.6348 (mp0) REVERT: G 106 SER cc_start: 0.7744 (t) cc_final: 0.7493 (m) REVERT: G 130 ASP cc_start: 0.7074 (t0) cc_final: 0.6476 (m-30) REVERT: G 155 GLU cc_start: 0.6826 (tt0) cc_final: 0.6471 (tt0) REVERT: J 4 TYR cc_start: 0.7345 (t80) cc_final: 0.6577 (t80) REVERT: K 29 HIS cc_start: 0.7922 (p-80) cc_final: 0.7338 (p90) REVERT: K 38 ILE cc_start: 0.8870 (mm) cc_final: 0.8520 (mm) REVERT: K 88 ASN cc_start: 0.7413 (m110) cc_final: 0.7100 (m-40) REVERT: K 91 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.5965 (pp30) REVERT: L 45 LYS cc_start: 0.7559 (pttt) cc_final: 0.6837 (mtmt) REVERT: L 111 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6241 (mmp) REVERT: M 81 VAL cc_start: 0.8349 (t) cc_final: 0.7936 (m) REVERT: M 98 GLN cc_start: 0.8330 (mt0) cc_final: 0.8123 (mt0) REVERT: M 107 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7696 (pp20) REVERT: M 130 SER cc_start: 0.8194 (m) cc_final: 0.7991 (m) REVERT: N 27 SER cc_start: 0.8579 (m) cc_final: 0.7900 (p) REVERT: N 99 LYS cc_start: 0.8461 (mtpt) cc_final: 0.8227 (mttp) REVERT: O 28 CYS cc_start: 0.7669 (m) cc_final: 0.7066 (m) REVERT: O 68 ASP cc_start: 0.7920 (m-30) cc_final: 0.7541 (t0) REVERT: P 15 ASN cc_start: 0.6477 (m-40) cc_final: 0.6167 (m-40) REVERT: P 28 ILE cc_start: 0.7925 (tt) cc_final: 0.7676 (mt) REVERT: P 64 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7876 (ttmt) REVERT: P 88 LYS cc_start: 0.8385 (mtpt) cc_final: 0.8179 (mtpp) REVERT: P 107 LYS cc_start: 0.6829 (ttmm) cc_final: 0.6181 (mtmm) REVERT: R 27 VAL cc_start: 0.6545 (p) cc_final: 0.6330 (m) REVERT: R 86 ARG cc_start: 0.7792 (ptt-90) cc_final: 0.7466 (ptp-170) REVERT: R 97 LYS cc_start: 0.7885 (mtpp) cc_final: 0.7592 (mtmt) REVERT: S 34 ASN cc_start: 0.6898 (m-40) cc_final: 0.6672 (m-40) REVERT: S 47 MET cc_start: 0.8216 (mmm) cc_final: 0.7114 (mmm) REVERT: S 86 MET cc_start: 0.6380 (OUTLIER) cc_final: 0.5841 (tpp) REVERT: T 15 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7766 (tp) REVERT: T 55 GLN cc_start: 0.6694 (tp-100) cc_final: 0.6211 (tt0) REVERT: U 50 MET cc_start: 0.4045 (ppp) cc_final: 0.3484 (pmm) REVERT: W 19 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7207 (mmtm) REVERT: W 38 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8268 (t) REVERT: W 55 LYS cc_start: 0.7750 (tptp) cc_final: 0.6712 (ttmm) REVERT: W 82 ILE cc_start: 0.6814 (OUTLIER) cc_final: 0.6450 (mt) REVERT: Z 12 LEU cc_start: 0.8536 (tt) cc_final: 0.8284 (tt) REVERT: Z 44 ARG cc_start: 0.8272 (mtp85) cc_final: 0.7987 (mtp85) REVERT: Z 48 ASN cc_start: 0.7869 (m-40) cc_final: 0.7531 (m110) REVERT: 3 44 ILE cc_start: 0.5716 (OUTLIER) cc_final: 0.5003 (mt) REVERT: 6 18 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7697 (tpp80) REVERT: 6 34 LYS cc_start: 0.8450 (ttmt) cc_final: 0.7980 (ttpt) outliers start: 125 outliers final: 59 residues processed: 690 average time/residue: 0.9577 time to fit residues: 1114.5624 Evaluate side-chains 554 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 481 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain N residue 8 ARG Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain O residue 25 VAL Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 54 ARG Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 15 ILE Chi-restraints excluded: chain V residue 60 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 23 ASN Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain 3 residue 44 ILE Chi-restraints excluded: chain 5 residue 30 HIS Chi-restraints excluded: chain 6 residue 12 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 565 optimal weight: 7.9990 chunk 430 optimal weight: 6.9990 chunk 296 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 273 optimal weight: 8.9990 chunk 384 optimal weight: 1.9990 chunk 574 optimal weight: 7.9990 chunk 607 optimal weight: 7.9990 chunk 300 optimal weight: 0.0980 chunk 544 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN J 132 HIS K 56 GLN P 42 GLN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS R 83 HIS S 15 GLN U 2 GLN U 68 ASN U 99 GLN V 81 GLN ** V 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 46 HIS Z 43 ASN Z 48 ASN 2 6 ASN 3 22 ASN ** 6 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.9980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 98333 Z= 0.303 Angle : 0.790 14.817 147452 Z= 0.398 Chirality : 0.042 0.407 18919 Planarity : 0.007 0.093 7667 Dihedral : 24.516 179.193 49958 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.54 % Favored : 89.14 % Rotamer: Outliers : 5.85 % Allowed : 17.11 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.12), residues: 3398 helix: -2.41 (0.16), residues: 762 sheet: -1.60 (0.21), residues: 538 loop : -2.74 (0.12), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP F 83 HIS 0.103 0.003 HIS R 82 PHE 0.042 0.003 PHE D 127 TYR 0.042 0.003 TYR T 83 ARG 0.014 0.001 ARG H 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 599 time to evaluate : 3.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7776 (mmm160) REVERT: C 22 GLN cc_start: 0.6923 (mp-120) cc_final: 0.6710 (mp10) REVERT: C 200 HIS cc_start: 0.7491 (t-90) cc_final: 0.6940 (t-170) REVERT: C 211 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8870 (t) REVERT: C 257 LYS cc_start: 0.8670 (mmtp) cc_final: 0.8332 (mmtp) REVERT: C 258 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8199 (p) REVERT: D 8 ARG cc_start: 0.7585 (ttt-90) cc_final: 0.7277 (ttt180) REVERT: D 85 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7218 (pp) REVERT: D 127 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.7859 (t80) REVERT: D 187 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8600 (mp) REVERT: E 47 THR cc_start: 0.7901 (p) cc_final: 0.7165 (p) REVERT: E 50 GLU cc_start: 0.7191 (mp0) cc_final: 0.6142 (mp0) REVERT: E 60 ARG cc_start: 0.7402 (tmm160) cc_final: 0.7099 (ttt180) REVERT: F 61 THR cc_start: 0.7233 (p) cc_final: 0.6987 (p) REVERT: F 173 PHE cc_start: 0.5989 (t80) cc_final: 0.5692 (t80) REVERT: G 38 HIS cc_start: 0.6313 (p90) cc_final: 0.5883 (p90) REVERT: G 49 GLU cc_start: 0.6806 (pp20) cc_final: 0.6391 (mp0) REVERT: G 124 GLU cc_start: 0.7855 (mp0) cc_final: 0.7410 (mp0) REVERT: G 130 ASP cc_start: 0.7366 (t0) cc_final: 0.6825 (m-30) REVERT: G 155 GLU cc_start: 0.6995 (tt0) cc_final: 0.6718 (tt0) REVERT: J 4 TYR cc_start: 0.7436 (t80) cc_final: 0.7005 (t80) REVERT: J 23 GLN cc_start: 0.7744 (tp40) cc_final: 0.7505 (mm110) REVERT: J 103 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8614 (p) REVERT: J 116 ARG cc_start: 0.8359 (mpp80) cc_final: 0.7995 (mtt90) REVERT: J 138 GLN cc_start: 0.7894 (pm20) cc_final: 0.7135 (mt0) REVERT: K 38 ILE cc_start: 0.8940 (mm) cc_final: 0.8652 (mm) REVERT: K 91 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6148 (pp30) REVERT: L 45 LYS cc_start: 0.8358 (pttt) cc_final: 0.7693 (mmtp) REVERT: L 125 ILE cc_start: 0.6466 (pt) cc_final: 0.6128 (pt) REVERT: M 81 VAL cc_start: 0.8553 (t) cc_final: 0.8236 (m) REVERT: M 130 SER cc_start: 0.8099 (m) cc_final: 0.7874 (m) REVERT: N 27 SER cc_start: 0.8638 (m) cc_final: 0.8043 (p) REVERT: N 73 LYS cc_start: 0.8289 (mmtp) cc_final: 0.7918 (mmtt) REVERT: O 28 CYS cc_start: 0.7730 (m) cc_final: 0.7459 (m) REVERT: O 68 ASP cc_start: 0.8179 (m-30) cc_final: 0.7901 (t0) REVERT: P 15 ASN cc_start: 0.6641 (m-40) cc_final: 0.6386 (m-40) REVERT: P 28 ILE cc_start: 0.7976 (tt) cc_final: 0.7752 (mt) REVERT: P 107 LYS cc_start: 0.7023 (ttmm) cc_final: 0.6411 (mtmm) REVERT: Q 11 ARG cc_start: 0.6662 (mtp85) cc_final: 0.6365 (mtt-85) REVERT: Q 49 ASP cc_start: 0.7908 (m-30) cc_final: 0.7605 (m-30) REVERT: Q 52 GLN cc_start: 0.8778 (mt0) cc_final: 0.8511 (mt0) REVERT: Q 71 GLN cc_start: 0.8542 (mt0) cc_final: 0.8272 (mt0) REVERT: R 20 LEU cc_start: 0.8242 (tp) cc_final: 0.7938 (tt) REVERT: R 37 ARG cc_start: 0.6127 (ttp-110) cc_final: 0.5560 (ptp90) REVERT: S 36 LEU cc_start: 0.8395 (tp) cc_final: 0.7953 (tp) REVERT: S 60 HIS cc_start: 0.5541 (OUTLIER) cc_final: 0.4514 (t-90) REVERT: T 77 ASN cc_start: 0.8389 (t0) cc_final: 0.8105 (t0) REVERT: U 50 MET cc_start: 0.4490 (ppp) cc_final: 0.3979 (pmm) REVERT: W 19 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7225 (mmtm) REVERT: W 55 LYS cc_start: 0.7681 (tptp) cc_final: 0.7008 (ttmm) REVERT: Y 16 ASN cc_start: 0.6076 (m-40) cc_final: 0.5707 (m110) REVERT: Z 20 LYS cc_start: 0.9182 (mtpp) cc_final: 0.8932 (mtpt) REVERT: Z 42 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6719 (mt-10) REVERT: Z 48 ASN cc_start: 0.8350 (m110) cc_final: 0.8117 (m110) REVERT: 4 25 LYS cc_start: 0.8496 (tptm) cc_final: 0.8084 (tmmt) REVERT: 5 53 ASP cc_start: 0.8405 (t0) cc_final: 0.7422 (m-30) REVERT: 6 18 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7811 (ttm-80) REVERT: 6 34 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8037 (ttpt) outliers start: 162 outliers final: 93 residues processed: 710 average time/residue: 0.8877 time to fit residues: 1064.0146 Evaluate side-chains 623 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 521 time to evaluate : 3.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 102 ASN Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 54 ARG Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain Q residue 101 ASN Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 60 HIS Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 7 ASN Chi-restraints excluded: chain V residue 60 PHE Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 142 ASP Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 23 ASN Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 2 residue 6 ASN Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 3 residue 30 ILE Chi-restraints excluded: chain 3 residue 38 VAL Chi-restraints excluded: chain 3 residue 44 ILE Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 30 HIS Chi-restraints excluded: chain 5 residue 33 THR Chi-restraints excluded: chain 5 residue 37 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 506 optimal weight: 5.9990 chunk 345 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 452 optimal weight: 1.9990 chunk 250 optimal weight: 7.9990 chunk 518 optimal weight: 0.0670 chunk 420 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 310 optimal weight: 0.5980 chunk 545 optimal weight: 0.5980 chunk 153 optimal weight: 7.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 29 GLN G 73 ASN J 76 HIS J 132 HIS L 2 GLN N 107 ASN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 GLN U 73 ASN ** V 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 161 HIS ** V 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 46 HIS X 35 HIS 2 6 ASN 4 29 GLN ** 6 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 37 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 1.0388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.096 98333 Z= 0.141 Angle : 0.612 12.538 147452 Z= 0.309 Chirality : 0.034 0.320 18919 Planarity : 0.005 0.100 7667 Dihedral : 24.285 179.777 49957 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.27 % Favored : 90.64 % Rotamer: Outliers : 3.64 % Allowed : 20.35 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.13), residues: 3398 helix: -1.85 (0.17), residues: 781 sheet: -1.38 (0.21), residues: 565 loop : -2.60 (0.12), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 83 HIS 0.008 0.001 HIS J 47 PHE 0.028 0.001 PHE D 127 TYR 0.016 0.001 TYR G 164 ARG 0.008 0.000 ARG 4 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 560 time to evaluate : 3.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ARG cc_start: 0.7944 (mmm-85) cc_final: 0.7514 (mmm-85) REVERT: C 83 TYR cc_start: 0.8337 (t80) cc_final: 0.8062 (t80) REVERT: C 100 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6379 (tm-30) REVERT: C 102 ARG cc_start: 0.7431 (mtp85) cc_final: 0.7140 (mtp180) REVERT: C 130 MET cc_start: 0.5690 (ptp) cc_final: 0.5302 (mtm) REVERT: C 200 HIS cc_start: 0.7551 (t-90) cc_final: 0.7102 (t-170) REVERT: C 258 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8318 (p) REVERT: D 8 ARG cc_start: 0.7517 (ttt-90) cc_final: 0.7290 (ttt180) REVERT: D 85 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7431 (pp) REVERT: E 47 THR cc_start: 0.7740 (p) cc_final: 0.7098 (p) REVERT: E 50 GLU cc_start: 0.7074 (mp0) cc_final: 0.6326 (mp0) REVERT: E 57 LYS cc_start: 0.7733 (ptpp) cc_final: 0.7191 (mtpp) REVERT: E 60 ARG cc_start: 0.7291 (ttm170) cc_final: 0.7053 (ttp-110) REVERT: E 154 GLU cc_start: 0.5878 (mp0) cc_final: 0.5531 (pp20) REVERT: F 4 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7605 (tm) REVERT: F 130 MET cc_start: 0.7289 (ppp) cc_final: 0.7033 (tmm) REVERT: F 173 PHE cc_start: 0.6223 (t80) cc_final: 0.5986 (t80) REVERT: G 38 HIS cc_start: 0.6342 (p90) cc_final: 0.5901 (p90) REVERT: G 49 GLU cc_start: 0.7030 (pp20) cc_final: 0.6359 (mp0) REVERT: G 73 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8289 (t0) REVERT: G 124 GLU cc_start: 0.7941 (mp0) cc_final: 0.7469 (mp0) REVERT: G 130 ASP cc_start: 0.7161 (t0) cc_final: 0.6562 (m-30) REVERT: J 116 ARG cc_start: 0.8307 (mpp80) cc_final: 0.7938 (mtt90) REVERT: J 138 GLN cc_start: 0.7861 (pm20) cc_final: 0.7175 (mt0) REVERT: K 29 HIS cc_start: 0.7937 (p-80) cc_final: 0.7508 (p90) REVERT: K 38 ILE cc_start: 0.8968 (mm) cc_final: 0.8696 (mm) REVERT: L 45 LYS cc_start: 0.8318 (pttt) cc_final: 0.7712 (mmtp) REVERT: M 81 VAL cc_start: 0.8507 (t) cc_final: 0.8185 (m) REVERT: M 130 SER cc_start: 0.8109 (m) cc_final: 0.7866 (m) REVERT: N 27 SER cc_start: 0.8625 (m) cc_final: 0.8031 (p) REVERT: N 49 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7841 (mm-30) REVERT: N 73 LYS cc_start: 0.8169 (mmtp) cc_final: 0.7864 (mmmt) REVERT: O 68 ASP cc_start: 0.8194 (m-30) cc_final: 0.7912 (t0) REVERT: P 28 ILE cc_start: 0.7962 (tt) cc_final: 0.7704 (mt) REVERT: P 54 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5605 (tpt170) REVERT: P 90 ARG cc_start: 0.6794 (ptm-80) cc_final: 0.6474 (ptm-80) REVERT: P 107 LYS cc_start: 0.6967 (ttmm) cc_final: 0.6362 (mtmm) REVERT: Q 11 ARG cc_start: 0.6658 (mtp85) cc_final: 0.6387 (mtt-85) REVERT: Q 49 ASP cc_start: 0.7820 (m-30) cc_final: 0.7460 (m-30) REVERT: Q 52 GLN cc_start: 0.8774 (mt0) cc_final: 0.8553 (mt0) REVERT: Q 85 LYS cc_start: 0.6892 (tmtp) cc_final: 0.6681 (mptt) REVERT: R 20 LEU cc_start: 0.8316 (tp) cc_final: 0.8073 (tt) REVERT: R 79 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8750 (ptp-170) REVERT: S 36 LEU cc_start: 0.8392 (tp) cc_final: 0.7856 (tp) REVERT: S 86 MET cc_start: 0.7227 (tpp) cc_final: 0.6976 (ttm) REVERT: S 104 THR cc_start: 0.8126 (m) cc_final: 0.7897 (m) REVERT: T 10 LEU cc_start: 0.7712 (mt) cc_final: 0.7264 (mp) REVERT: U 50 MET cc_start: 0.4623 (ppp) cc_final: 0.4125 (pmm) REVERT: W 12 ASN cc_start: 0.6959 (OUTLIER) cc_final: 0.6361 (p0) REVERT: W 55 LYS cc_start: 0.7530 (tptp) cc_final: 0.7251 (ttmm) REVERT: X 49 LEU cc_start: 0.7690 (pt) cc_final: 0.7363 (mp) REVERT: Y 56 VAL cc_start: 0.8466 (p) cc_final: 0.8260 (m) REVERT: Z 42 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6617 (mt-10) REVERT: Z 48 ASN cc_start: 0.8528 (m110) cc_final: 0.8257 (m110) REVERT: 3 6 ARG cc_start: 0.6599 (ptm160) cc_final: 0.6021 (ptm160) REVERT: 4 25 LYS cc_start: 0.8478 (tptm) cc_final: 0.8062 (tmmt) REVERT: 5 22 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7539 (ptpt) REVERT: 5 53 ASP cc_start: 0.8250 (t0) cc_final: 0.7561 (m-30) REVERT: 6 18 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7694 (tpp80) REVERT: 6 34 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8012 (ttpt) outliers start: 101 outliers final: 57 residues processed: 630 average time/residue: 0.9048 time to fit residues: 962.8915 Evaluate side-chains 583 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 518 time to evaluate : 3.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain P residue 54 ARG Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 60 HIS Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 58 VAL Chi-restraints excluded: chain V residue 60 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 90 MET Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 142 ASP Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 23 ASN Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain 5 residue 22 LYS Chi-restraints excluded: chain 5 residue 27 PHE Chi-restraints excluded: chain 5 residue 30 HIS Chi-restraints excluded: chain 6 residue 12 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 204 optimal weight: 8.9990 chunk 547 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 356 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 608 optimal weight: 7.9990 chunk 505 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 319 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN J 132 HIS L 54 GLN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** R 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN X 36 HIS 2 37 HIS 3 22 ASN 3 42 HIS ** 6 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 33 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 1.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.113 98333 Z= 0.629 Angle : 1.108 14.278 147452 Z= 0.546 Chirality : 0.058 0.477 18919 Planarity : 0.009 0.103 7667 Dihedral : 24.979 180.000 49956 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.71 % Favored : 85.96 % Rotamer: Outliers : 6.82 % Allowed : 19.78 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.48 % 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 (0.12), residues: 3398 helix: -2.38 (0.16), residues: 755 sheet: -1.76 (0.20), residues: 574 loop : -2.90 (0.12), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 125 HIS 0.020 0.003 HIS R 82 PHE 0.084 0.004 PHE D 127 TYR 0.035 0.004 TYR H 25 ARG 0.017 0.002 ARG C 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 610 time to evaluate : 3.897 Fit side-chains revert: symmetry clash REVERT: C 83 TYR cc_start: 0.8566 (t80) cc_final: 0.8067 (t80) REVERT: C 192 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7912 (mp) REVERT: C 197 ASN cc_start: 0.8331 (t0) cc_final: 0.7944 (t0) REVERT: C 199 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7288 (mm-30) REVERT: C 200 HIS cc_start: 0.7955 (t-90) cc_final: 0.7618 (t-170) REVERT: D 8 ARG cc_start: 0.7797 (ttt-90) cc_final: 0.7487 (ttm170) REVERT: D 12 MET cc_start: 0.8218 (mtp) cc_final: 0.8007 (mtt) REVERT: D 59 SER cc_start: 0.8607 (t) cc_final: 0.8373 (p) REVERT: D 71 LYS cc_start: 0.8406 (mmpt) cc_final: 0.8051 (mtmt) REVERT: D 85 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7674 (pp) REVERT: D 127 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.7727 (t80) REVERT: D 128 ARG cc_start: 0.8003 (ptp90) cc_final: 0.7701 (ptp90) REVERT: E 50 GLU cc_start: 0.7343 (mp0) cc_final: 0.6284 (mp0) REVERT: E 60 ARG cc_start: 0.7888 (tmm160) cc_final: 0.7558 (ttt180) REVERT: E 95 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6723 (mp) REVERT: E 154 GLU cc_start: 0.6414 (mp0) cc_final: 0.6163 (pp20) REVERT: E 167 ASP cc_start: 0.8400 (t70) cc_final: 0.8046 (t0) REVERT: F 4 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7810 (tm) REVERT: F 173 PHE cc_start: 0.6361 (t80) cc_final: 0.5955 (t80) REVERT: G 10 LYS cc_start: 0.7767 (mmtt) cc_final: 0.7134 (mmmt) REVERT: G 38 HIS cc_start: 0.6390 (p90) cc_final: 0.6034 (p90) REVERT: G 130 ASP cc_start: 0.7483 (t0) cc_final: 0.7054 (m-30) REVERT: G 166 ASP cc_start: 0.5807 (OUTLIER) cc_final: 0.5555 (t0) REVERT: I 35 ILE cc_start: -0.0004 (OUTLIER) cc_final: -0.0269 (mt) REVERT: J 31 GLU cc_start: 0.7272 (mp0) cc_final: 0.7009 (mp0) REVERT: J 35 ARG cc_start: 0.8222 (ttm110) cc_final: 0.7840 (mtp-110) REVERT: J 116 ARG cc_start: 0.8146 (mpp80) cc_final: 0.7838 (mtt90) REVERT: K 38 ILE cc_start: 0.8893 (mm) cc_final: 0.8602 (mm) REVERT: K 45 GLU cc_start: 0.7888 (tt0) cc_final: 0.7144 (tt0) REVERT: K 71 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6174 (ptp90) REVERT: K 91 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6085 (pp30) REVERT: L 73 ASP cc_start: 0.7656 (m-30) cc_final: 0.7366 (m-30) REVERT: L 107 ARG cc_start: 0.7719 (mpp80) cc_final: 0.7479 (mpp-170) REVERT: M 48 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7979 (mm-30) REVERT: N 27 SER cc_start: 0.8648 (m) cc_final: 0.8093 (p) REVERT: N 34 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8023 (pt) REVERT: N 73 LYS cc_start: 0.8582 (mmtp) cc_final: 0.8241 (mmmt) REVERT: P 54 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6386 (tpm170) REVERT: P 107 LYS cc_start: 0.7349 (ttmm) cc_final: 0.6726 (mtmm) REVERT: Q 19 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8322 (tppt) REVERT: Q 45 TYR cc_start: 0.8855 (m-10) cc_final: 0.8210 (m-10) REVERT: Q 49 ASP cc_start: 0.7706 (m-30) cc_final: 0.7230 (m-30) REVERT: Q 52 GLN cc_start: 0.8900 (mt0) cc_final: 0.8612 (mt0) REVERT: Q 84 LYS cc_start: 0.7877 (mttt) cc_final: 0.7557 (ttpt) REVERT: Q 85 LYS cc_start: 0.7432 (tmtp) cc_final: 0.7165 (mmtt) REVERT: R 18 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7489 (mm-30) REVERT: R 34 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7297 (p0) REVERT: R 79 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8711 (ttm170) REVERT: S 36 LEU cc_start: 0.8693 (tp) cc_final: 0.8362 (mt) REVERT: S 61 ASN cc_start: 0.6935 (OUTLIER) cc_final: 0.6573 (m110) REVERT: S 92 ARG cc_start: 0.6682 (ttp-170) cc_final: 0.6473 (mtm110) REVERT: T 5 ARG cc_start: 0.7805 (tpm-80) cc_final: 0.7450 (tpp-160) REVERT: U 50 MET cc_start: 0.5051 (ppp) cc_final: 0.4029 (ptp) REVERT: U 57 ILE cc_start: 0.7951 (mt) cc_final: 0.7597 (tt) REVERT: V 44 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8366 (p) REVERT: W 12 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6771 (p0) REVERT: W 55 LYS cc_start: 0.7996 (tptp) cc_final: 0.6951 (ttmm) REVERT: X 41 GLU cc_start: 0.7635 (tp30) cc_final: 0.6772 (mp0) REVERT: X 58 ILE cc_start: 0.8368 (mt) cc_final: 0.7992 (mt) REVERT: Z 7 THR cc_start: 0.7780 (m) cc_final: 0.7323 (p) REVERT: Z 44 ARG cc_start: 0.8550 (mtp85) cc_final: 0.8050 (mtp85) REVERT: Z 48 ASN cc_start: 0.8539 (m110) cc_final: 0.8215 (m110) REVERT: 3 6 ARG cc_start: 0.7428 (ptm160) cc_final: 0.7140 (ptm160) REVERT: 3 23 LYS cc_start: 0.7860 (tppt) cc_final: 0.7626 (mmtt) REVERT: 4 25 LYS cc_start: 0.8722 (tptm) cc_final: 0.8071 (tmmt) REVERT: 5 22 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8062 (pttt) REVERT: 5 35 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8126 (mtp) REVERT: 5 51 LYS cc_start: 0.7724 (tmtt) cc_final: 0.7262 (pptt) REVERT: 5 53 ASP cc_start: 0.8451 (t0) cc_final: 0.7582 (m-30) REVERT: 6 34 LYS cc_start: 0.8704 (ttmt) cc_final: 0.7984 (ttpt) outliers start: 189 outliers final: 114 residues processed: 732 average time/residue: 0.9024 time to fit residues: 1125.2934 Evaluate side-chains 675 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 543 time to evaluate : 3.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain J residue 4 TYR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 25 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 54 ARG Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 58 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 7 ASN Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 142 ASP Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain X residue 10 LYS Chi-restraints excluded: chain X residue 23 ASN Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 12 LEU Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 2 residue 22 LEU Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 22 LYS Chi-restraints excluded: chain 5 residue 27 PHE Chi-restraints excluded: chain 5 residue 30 HIS Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 37 THR Chi-restraints excluded: chain 5 residue 52 SER Chi-restraints excluded: chain 6 residue 23 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 586 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 346 optimal weight: 6.9990 chunk 444 optimal weight: 1.9990 chunk 344 optimal weight: 1.9990 chunk 512 optimal weight: 1.9990 chunk 339 optimal weight: 7.9990 chunk 606 optimal weight: 2.9990 chunk 379 optimal weight: 7.9990 chunk 369 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN I 12 GLN L 2 GLN L 4 ASN P 42 GLN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN Z 43 ASN ** 6 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 1.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 98333 Z= 0.244 Angle : 0.707 13.534 147452 Z= 0.358 Chirality : 0.040 0.311 18919 Planarity : 0.005 0.093 7667 Dihedral : 24.426 179.695 49956 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.77 % Favored : 89.08 % Rotamer: Outliers : 4.37 % Allowed : 23.10 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.13), residues: 3398 helix: -1.84 (0.18), residues: 760 sheet: -1.56 (0.21), residues: 554 loop : -2.75 (0.12), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 213 HIS 0.008 0.001 HIS R 82 PHE 0.045 0.002 PHE D 127 TYR 0.020 0.002 TYR G 164 ARG 0.007 0.001 ARG V 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 565 time to evaluate : 3.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8135 (pm20) REVERT: C 200 HIS cc_start: 0.7988 (t-90) cc_final: 0.7619 (t-170) REVERT: D 8 ARG cc_start: 0.7691 (ttt-90) cc_final: 0.7454 (ttm170) REVERT: D 59 SER cc_start: 0.8533 (t) cc_final: 0.8186 (p) REVERT: D 71 LYS cc_start: 0.8331 (mmpt) cc_final: 0.8049 (mtmt) REVERT: D 85 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7685 (pp) REVERT: D 127 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8090 (t80) REVERT: E 47 THR cc_start: 0.8139 (p) cc_final: 0.7439 (p) REVERT: E 50 GLU cc_start: 0.7265 (mp0) cc_final: 0.6433 (mp0) REVERT: E 60 ARG cc_start: 0.7666 (tmm160) cc_final: 0.7404 (ttp-110) REVERT: E 167 ASP cc_start: 0.8485 (t70) cc_final: 0.8174 (t0) REVERT: E 197 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7900 (tm-30) REVERT: F 4 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7589 (tm) REVERT: F 173 PHE cc_start: 0.6453 (t80) cc_final: 0.6095 (t80) REVERT: G 38 HIS cc_start: 0.6141 (p90) cc_final: 0.5729 (p90) REVERT: G 49 GLU cc_start: 0.7632 (pt0) cc_final: 0.7269 (mp0) REVERT: G 73 ASN cc_start: 0.8788 (t0) cc_final: 0.8195 (t0) REVERT: G 92 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8114 (t) REVERT: G 124 GLU cc_start: 0.7965 (mp0) cc_final: 0.7687 (mp0) REVERT: G 130 ASP cc_start: 0.7430 (t0) cc_final: 0.6793 (m-30) REVERT: G 166 ASP cc_start: 0.5648 (OUTLIER) cc_final: 0.5439 (t0) REVERT: J 31 GLU cc_start: 0.7247 (mp0) cc_final: 0.6938 (mp0) REVERT: J 116 ARG cc_start: 0.8207 (mpp80) cc_final: 0.7801 (mtt90) REVERT: K 38 ILE cc_start: 0.8929 (mm) cc_final: 0.8650 (mm) REVERT: K 45 GLU cc_start: 0.7733 (tt0) cc_final: 0.7054 (tt0) REVERT: K 71 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.5938 (ptp90) REVERT: K 91 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.6915 (mp10) REVERT: K 92 GLU cc_start: 0.6739 (pm20) cc_final: 0.6494 (pm20) REVERT: L 73 ASP cc_start: 0.7322 (m-30) cc_final: 0.6189 (t0) REVERT: L 107 ARG cc_start: 0.7707 (mpp80) cc_final: 0.7363 (mpp-170) REVERT: M 81 VAL cc_start: 0.8511 (t) cc_final: 0.8158 (m) REVERT: N 27 SER cc_start: 0.8588 (m) cc_final: 0.8009 (p) REVERT: N 34 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.7875 (pt) REVERT: P 28 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7438 (mt) REVERT: P 90 ARG cc_start: 0.6645 (ptm-80) cc_final: 0.6382 (ptm-80) REVERT: P 107 LYS cc_start: 0.7139 (ttmm) cc_final: 0.6621 (mtmm) REVERT: Q 45 TYR cc_start: 0.8970 (m-10) cc_final: 0.8728 (m-10) REVERT: Q 49 ASP cc_start: 0.7921 (m-30) cc_final: 0.7503 (m-30) REVERT: Q 52 GLN cc_start: 0.8838 (mt0) cc_final: 0.8519 (mt0) REVERT: Q 85 LYS cc_start: 0.7832 (tmtp) cc_final: 0.7541 (mmtm) REVERT: Q 116 SER cc_start: 0.7247 (t) cc_final: 0.7012 (m) REVERT: R 58 LYS cc_start: 0.8044 (tptp) cc_final: 0.7798 (tptm) REVERT: S 86 MET cc_start: 0.7258 (tpp) cc_final: 0.6555 (ptm) REVERT: S 92 ARG cc_start: 0.6793 (ttp-170) cc_final: 0.6484 (mtm110) REVERT: T 10 LEU cc_start: 0.8633 (mt) cc_final: 0.8354 (mp) REVERT: U 32 ARG cc_start: 0.7940 (mtp85) cc_final: 0.7555 (mtp180) REVERT: U 50 MET cc_start: 0.5199 (ppp) cc_final: 0.4296 (ptp) REVERT: U 99 GLN cc_start: 0.6489 (tp-100) cc_final: 0.6283 (tp-100) REVERT: W 12 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6855 (p0) REVERT: W 55 LYS cc_start: 0.7838 (tptp) cc_final: 0.7316 (ttmm) REVERT: X 23 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7510 (p0) REVERT: X 41 GLU cc_start: 0.7643 (tp30) cc_final: 0.6781 (mp0) REVERT: X 58 ILE cc_start: 0.8397 (mt) cc_final: 0.7970 (mt) REVERT: Y 45 GLN cc_start: 0.8231 (tm-30) cc_final: 0.8008 (pp30) REVERT: Z 44 ARG cc_start: 0.8321 (mtp85) cc_final: 0.7885 (mtp85) REVERT: Z 48 ASN cc_start: 0.8472 (m110) cc_final: 0.8253 (m110) REVERT: 3 6 ARG cc_start: 0.7178 (ptm160) cc_final: 0.6883 (ptm160) REVERT: 4 1 MET cc_start: 0.6768 (ptp) cc_final: 0.6521 (ptt) REVERT: 4 25 LYS cc_start: 0.8667 (tptm) cc_final: 0.8067 (tmmt) REVERT: 5 22 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7485 (ptpt) REVERT: 5 51 LYS cc_start: 0.7661 (tttt) cc_final: 0.7196 (pttp) REVERT: 5 53 ASP cc_start: 0.8155 (t0) cc_final: 0.7909 (m-30) REVERT: 6 18 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7883 (ttm-80) REVERT: 6 34 LYS cc_start: 0.8587 (ttmt) cc_final: 0.8041 (ttpt) outliers start: 121 outliers final: 78 residues processed: 645 average time/residue: 0.8815 time to fit residues: 967.5165 Evaluate side-chains 635 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 544 time to evaluate : 3.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 54 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 7 ASN Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 142 ASP Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 23 ASN Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 22 LYS Chi-restraints excluded: chain 5 residue 27 PHE Chi-restraints excluded: chain 5 residue 30 HIS Chi-restraints excluded: chain 5 residue 43 LEU Chi-restraints excluded: chain 5 residue 52 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 375 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 362 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 385 optimal weight: 1.9990 chunk 413 optimal weight: 10.0000 chunk 299 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 476 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 GLN ** V 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN Y 58 ASN ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** 6 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 1.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 98333 Z= 0.263 Angle : 0.699 20.766 147452 Z= 0.354 Chirality : 0.039 0.302 18919 Planarity : 0.005 0.091 7667 Dihedral : 24.316 179.571 49956 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.54 % Favored : 88.35 % Rotamer: Outliers : 4.69 % Allowed : 23.13 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.30 % 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: -3.21 (0.13), residues: 3398 helix: -1.59 (0.18), residues: 769 sheet: -1.50 (0.21), residues: 565 loop : -2.65 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 125 HIS 0.010 0.001 HIS L 104 PHE 0.045 0.002 PHE D 127 TYR 0.020 0.002 TYR C 83 ARG 0.008 0.001 ARG V 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 544 time to evaluate : 4.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 180 GLU cc_start: 0.6964 (tt0) cc_final: 0.6630 (tt0) REVERT: C 199 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: C 200 HIS cc_start: 0.8068 (t-90) cc_final: 0.7745 (t-170) REVERT: D 8 ARG cc_start: 0.7721 (ttt-90) cc_final: 0.7484 (ttm170) REVERT: D 59 SER cc_start: 0.8418 (t) cc_final: 0.8028 (p) REVERT: D 71 LYS cc_start: 0.8366 (mmpt) cc_final: 0.8078 (mtmt) REVERT: D 85 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7949 (pp) REVERT: D 160 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8397 (mtmt) REVERT: E 47 THR cc_start: 0.8203 (p) cc_final: 0.7553 (p) REVERT: E 50 GLU cc_start: 0.7255 (mp0) cc_final: 0.6423 (mp0) REVERT: E 167 ASP cc_start: 0.8557 (t70) cc_final: 0.8281 (t0) REVERT: E 197 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7775 (tm-30) REVERT: F 4 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7621 (tm) REVERT: F 173 PHE cc_start: 0.6457 (t80) cc_final: 0.6122 (t80) REVERT: G 38 HIS cc_start: 0.6105 (p90) cc_final: 0.5704 (p90) REVERT: G 49 GLU cc_start: 0.7683 (pt0) cc_final: 0.7304 (mp0) REVERT: G 124 GLU cc_start: 0.7930 (mp0) cc_final: 0.7609 (mp0) REVERT: G 130 ASP cc_start: 0.7561 (t0) cc_final: 0.6919 (m-30) REVERT: J 31 GLU cc_start: 0.7237 (mp0) cc_final: 0.6951 (mp0) REVERT: J 116 ARG cc_start: 0.8254 (mpp80) cc_final: 0.7891 (mtt90) REVERT: J 142 ILE cc_start: 0.4931 (OUTLIER) cc_final: 0.4722 (pp) REVERT: K 38 ILE cc_start: 0.8950 (mm) cc_final: 0.8679 (mm) REVERT: K 45 GLU cc_start: 0.7728 (tt0) cc_final: 0.7075 (tt0) REVERT: K 71 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6031 (ptp90) REVERT: K 91 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6954 (mp10) REVERT: L 55 GLN cc_start: 0.9186 (tp-100) cc_final: 0.8937 (mm110) REVERT: L 72 MET cc_start: 0.6184 (pmm) cc_final: 0.5925 (pmm) REVERT: L 107 ARG cc_start: 0.7539 (mpp80) cc_final: 0.7249 (mpp-170) REVERT: L 129 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7770 (mmmt) REVERT: M 26 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8148 (ttpp) REVERT: M 81 VAL cc_start: 0.8508 (t) cc_final: 0.8179 (m) REVERT: N 27 SER cc_start: 0.8557 (m) cc_final: 0.8020 (p) REVERT: N 34 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.7847 (pt) REVERT: P 28 ILE cc_start: 0.7804 (tt) cc_final: 0.7541 (mt) REVERT: P 54 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.6020 (tpm170) REVERT: P 107 LYS cc_start: 0.7129 (ttmm) cc_final: 0.6556 (mtmm) REVERT: Q 49 ASP cc_start: 0.7770 (m-30) cc_final: 0.7341 (m-30) REVERT: Q 52 GLN cc_start: 0.8818 (mt0) cc_final: 0.8493 (mt0) REVERT: Q 85 LYS cc_start: 0.7862 (tmtp) cc_final: 0.7557 (mptt) REVERT: S 86 MET cc_start: 0.7245 (tpp) cc_final: 0.6547 (ptm) REVERT: S 92 ARG cc_start: 0.6606 (ttp-170) cc_final: 0.6269 (mtm110) REVERT: U 50 MET cc_start: 0.4816 (ppp) cc_final: 0.3899 (ptp) REVERT: U 92 ILE cc_start: 0.7304 (mm) cc_final: 0.7019 (mm) REVERT: U 95 PHE cc_start: 0.6771 (m-80) cc_final: 0.5557 (m-80) REVERT: V 165 LEU cc_start: 0.4502 (OUTLIER) cc_final: 0.4150 (pt) REVERT: W 12 ASN cc_start: 0.7223 (OUTLIER) cc_final: 0.6775 (p0) REVERT: W 36 ILE cc_start: 0.7990 (mm) cc_final: 0.7767 (mm) REVERT: W 55 LYS cc_start: 0.7801 (tptp) cc_final: 0.7425 (ttmm) REVERT: W 72 LYS cc_start: 0.8077 (pttm) cc_final: 0.7869 (ptpt) REVERT: X 5 CYS cc_start: 0.7958 (t) cc_final: 0.7474 (t) REVERT: X 23 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.7620 (p0) REVERT: X 41 GLU cc_start: 0.8025 (tp30) cc_final: 0.7175 (mp0) REVERT: X 58 ILE cc_start: 0.8387 (mt) cc_final: 0.8177 (mt) REVERT: Y 45 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7843 (pt0) REVERT: Z 44 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7753 (mtp85) REVERT: Z 46 MET cc_start: 0.9067 (mtt) cc_final: 0.8659 (mtm) REVERT: 3 6 ARG cc_start: 0.7325 (ptm160) cc_final: 0.6980 (ptm160) REVERT: 4 25 LYS cc_start: 0.8599 (tptm) cc_final: 0.8038 (tmmt) REVERT: 5 22 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7490 (ptpt) REVERT: 6 18 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7862 (ttm-80) REVERT: 6 34 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8089 (ttpt) outliers start: 130 outliers final: 97 residues processed: 630 average time/residue: 0.8751 time to fit residues: 938.3877 Evaluate side-chains 636 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 525 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 26 LYS Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 54 ARG Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 7 ASN Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 94 PHE Chi-restraints excluded: chain V residue 142 ASP Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain V residue 165 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 16 ASN Chi-restraints excluded: chain X residue 23 ASN Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 3 residue 30 ILE Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 22 LYS Chi-restraints excluded: chain 5 residue 27 PHE Chi-restraints excluded: chain 5 residue 30 HIS Chi-restraints excluded: chain 5 residue 33 THR Chi-restraints excluded: chain 5 residue 43 LEU Chi-restraints excluded: chain 5 residue 46 THR Chi-restraints excluded: chain 5 residue 52 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 551 optimal weight: 0.6980 chunk 580 optimal weight: 8.9990 chunk 529 optimal weight: 6.9990 chunk 564 optimal weight: 1.9990 chunk 340 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 443 optimal weight: 8.9990 chunk 173 optimal weight: 6.9990 chunk 510 optimal weight: 3.9990 chunk 534 optimal weight: 0.7980 chunk 562 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN L 99 ASN N 107 ASN P 42 GLN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 GLN ** V 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** 6 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 1.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 98333 Z= 0.180 Angle : 0.635 13.956 147452 Z= 0.322 Chirality : 0.036 0.291 18919 Planarity : 0.005 0.088 7667 Dihedral : 24.248 179.859 49956 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.30 % Favored : 89.64 % Rotamer: Outliers : 4.01 % Allowed : 23.93 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.13), residues: 3398 helix: -1.42 (0.18), residues: 780 sheet: -1.35 (0.21), residues: 609 loop : -2.59 (0.12), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 83 HIS 0.009 0.001 HIS L 104 PHE 0.030 0.002 PHE D 127 TYR 0.020 0.001 TYR C 83 ARG 0.007 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 537 time to evaluate : 3.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 96 TYR cc_start: 0.8034 (m-80) cc_final: 0.7760 (m-80) REVERT: C 180 GLU cc_start: 0.6983 (tt0) cc_final: 0.6602 (tt0) REVERT: C 199 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: C 200 HIS cc_start: 0.8079 (t-90) cc_final: 0.7761 (t-170) REVERT: C 240 SER cc_start: 0.7601 (m) cc_final: 0.7086 (p) REVERT: D 8 ARG cc_start: 0.7618 (ttt-90) cc_final: 0.7395 (ttm170) REVERT: D 59 SER cc_start: 0.8355 (t) cc_final: 0.7946 (p) REVERT: D 71 LYS cc_start: 0.8356 (mmpt) cc_final: 0.8092 (mtmt) REVERT: D 85 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7923 (pp) REVERT: D 160 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8436 (mtmt) REVERT: E 50 GLU cc_start: 0.7242 (mp0) cc_final: 0.6537 (mp0) REVERT: E 167 ASP cc_start: 0.8504 (t70) cc_final: 0.8110 (t0) REVERT: E 197 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7706 (tm-30) REVERT: F 4 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7587 (tm) REVERT: F 173 PHE cc_start: 0.6483 (t80) cc_final: 0.6169 (t80) REVERT: G 38 HIS cc_start: 0.6180 (p90) cc_final: 0.5815 (p90) REVERT: G 49 GLU cc_start: 0.7599 (pt0) cc_final: 0.7302 (mp0) REVERT: G 124 GLU cc_start: 0.7929 (mp0) cc_final: 0.7630 (mp0) REVERT: G 130 ASP cc_start: 0.7530 (t0) cc_final: 0.6884 (m-30) REVERT: J 31 GLU cc_start: 0.7236 (mp0) cc_final: 0.6915 (mp0) REVERT: J 116 ARG cc_start: 0.8338 (mpp80) cc_final: 0.7962 (mtt90) REVERT: J 142 ILE cc_start: 0.4857 (OUTLIER) cc_final: 0.4631 (pp) REVERT: K 38 ILE cc_start: 0.8946 (mm) cc_final: 0.8669 (mm) REVERT: K 45 GLU cc_start: 0.7639 (tt0) cc_final: 0.7013 (tt0) REVERT: K 71 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6059 (ptp90) REVERT: K 91 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6945 (mp10) REVERT: K 92 GLU cc_start: 0.6976 (pm20) cc_final: 0.6728 (pm20) REVERT: L 55 GLN cc_start: 0.9191 (tp-100) cc_final: 0.8971 (mm110) REVERT: L 107 ARG cc_start: 0.7531 (mpp80) cc_final: 0.7249 (mpp-170) REVERT: L 129 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7708 (mmmt) REVERT: M 26 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8116 (ttpp) REVERT: M 81 VAL cc_start: 0.8497 (t) cc_final: 0.8177 (m) REVERT: N 27 SER cc_start: 0.8573 (m) cc_final: 0.8018 (p) REVERT: N 34 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7840 (pt) REVERT: P 28 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7354 (mt) REVERT: P 54 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.5893 (tpm170) REVERT: P 107 LYS cc_start: 0.7099 (ttmm) cc_final: 0.6566 (mtmm) REVERT: Q 49 ASP cc_start: 0.7851 (m-30) cc_final: 0.7389 (m-30) REVERT: Q 52 GLN cc_start: 0.8803 (mt0) cc_final: 0.8517 (mt0) REVERT: Q 85 LYS cc_start: 0.7823 (tmtp) cc_final: 0.7539 (mmtm) REVERT: R 1 MET cc_start: 0.5051 (tmm) cc_final: 0.4573 (tpp) REVERT: S 86 MET cc_start: 0.7218 (tpp) cc_final: 0.6508 (ptm) REVERT: S 92 ARG cc_start: 0.6642 (ttp-170) cc_final: 0.6289 (mtm110) REVERT: U 7 ASP cc_start: 0.6181 (p0) cc_final: 0.5924 (p0) REVERT: U 50 MET cc_start: 0.4832 (ppp) cc_final: 0.3920 (ptp) REVERT: U 95 PHE cc_start: 0.6839 (m-80) cc_final: 0.5838 (m-10) REVERT: V 165 LEU cc_start: 0.4508 (OUTLIER) cc_final: 0.4151 (pt) REVERT: W 12 ASN cc_start: 0.7167 (OUTLIER) cc_final: 0.6701 (p0) REVERT: W 36 ILE cc_start: 0.7839 (mm) cc_final: 0.7595 (mm) REVERT: W 55 LYS cc_start: 0.7686 (tptp) cc_final: 0.7430 (ttmm) REVERT: W 72 LYS cc_start: 0.8056 (pttm) cc_final: 0.7825 (ptpt) REVERT: X 5 CYS cc_start: 0.7864 (t) cc_final: 0.7536 (t) REVERT: X 23 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7429 (p0) REVERT: X 41 GLU cc_start: 0.7940 (tp30) cc_final: 0.7264 (mp0) REVERT: X 58 ILE cc_start: 0.8386 (mt) cc_final: 0.8161 (mt) REVERT: Y 45 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7856 (pt0) REVERT: Z 46 MET cc_start: 0.9050 (mtt) cc_final: 0.8627 (mtm) REVERT: 2 31 LYS cc_start: 0.7280 (mmtp) cc_final: 0.7059 (mmtm) REVERT: 3 6 ARG cc_start: 0.7268 (ptm160) cc_final: 0.6928 (ptm160) REVERT: 4 25 LYS cc_start: 0.8576 (tptm) cc_final: 0.8033 (tmmt) REVERT: 5 22 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7752 (ptpt) REVERT: 5 56 ARG cc_start: 0.7653 (ttm170) cc_final: 0.7395 (ttm170) REVERT: 5 58 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7503 (mt-10) REVERT: 6 18 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7860 (ttm-80) REVERT: 6 34 LYS cc_start: 0.8514 (ttmt) cc_final: 0.8007 (ttpt) outliers start: 111 outliers final: 78 residues processed: 613 average time/residue: 0.8807 time to fit residues: 917.0376 Evaluate side-chains 616 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 523 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 26 LYS Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 54 ARG Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 142 ASP Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain V residue 165 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 23 ASN Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 5 residue 22 LYS Chi-restraints excluded: chain 5 residue 27 PHE Chi-restraints excluded: chain 5 residue 30 HIS Chi-restraints excluded: chain 5 residue 43 LEU Chi-restraints excluded: chain 5 residue 46 THR Chi-restraints excluded: chain 5 residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 370 optimal weight: 1.9990 chunk 597 optimal weight: 0.9980 chunk 364 optimal weight: 8.9990 chunk 283 optimal weight: 10.0000 chunk 415 optimal weight: 0.0970 chunk 626 optimal weight: 6.9990 chunk 576 optimal weight: 20.0000 chunk 499 optimal weight: 0.0470 chunk 51 optimal weight: 7.9990 chunk 385 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 overall best weight: 1.2280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** 6 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 1.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.209 98333 Z= 0.181 Angle : 0.665 59.165 147452 Z= 0.345 Chirality : 0.036 0.291 18919 Planarity : 0.005 0.087 7667 Dihedral : 24.248 179.852 49956 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.39 % Favored : 89.55 % Rotamer: Outliers : 3.61 % Allowed : 24.43 % Favored : 71.96 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.13), residues: 3398 helix: -1.40 (0.19), residues: 780 sheet: -1.32 (0.21), residues: 603 loop : -2.58 (0.12), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 83 HIS 0.007 0.001 HIS R 82 PHE 0.030 0.001 PHE D 127 TYR 0.018 0.001 TYR C 83 ARG 0.006 0.000 ARG C 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 523 time to evaluate : 3.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 96 TYR cc_start: 0.8032 (m-80) cc_final: 0.7768 (m-80) REVERT: C 180 GLU cc_start: 0.6979 (tt0) cc_final: 0.6603 (tt0) REVERT: C 199 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7389 (mm-30) REVERT: C 200 HIS cc_start: 0.8077 (t-90) cc_final: 0.7762 (t-170) REVERT: D 8 ARG cc_start: 0.7618 (ttt-90) cc_final: 0.7393 (ttm170) REVERT: D 59 SER cc_start: 0.8352 (t) cc_final: 0.7944 (p) REVERT: D 71 LYS cc_start: 0.8355 (mmpt) cc_final: 0.8091 (mtmt) REVERT: D 85 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7922 (pp) REVERT: D 160 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8436 (mtmt) REVERT: E 50 GLU cc_start: 0.7238 (mp0) cc_final: 0.6534 (mp0) REVERT: E 167 ASP cc_start: 0.8503 (t70) cc_final: 0.8108 (t0) REVERT: E 197 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7700 (tm-30) REVERT: F 4 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7585 (tm) REVERT: F 173 PHE cc_start: 0.6497 (t80) cc_final: 0.6179 (t80) REVERT: G 38 HIS cc_start: 0.6178 (p90) cc_final: 0.5812 (p90) REVERT: G 49 GLU cc_start: 0.7642 (pt0) cc_final: 0.7409 (mp0) REVERT: G 124 GLU cc_start: 0.7927 (mp0) cc_final: 0.7626 (mp0) REVERT: G 130 ASP cc_start: 0.7529 (t0) cc_final: 0.6883 (m-30) REVERT: J 31 GLU cc_start: 0.7234 (mp0) cc_final: 0.6910 (mp0) REVERT: J 116 ARG cc_start: 0.8336 (mpp80) cc_final: 0.7959 (mtt90) REVERT: J 142 ILE cc_start: 0.4853 (OUTLIER) cc_final: 0.4649 (pp) REVERT: K 38 ILE cc_start: 0.8945 (mm) cc_final: 0.8668 (mm) REVERT: K 45 GLU cc_start: 0.7638 (tt0) cc_final: 0.6994 (tt0) REVERT: K 71 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6057 (ptp90) REVERT: K 91 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6945 (mp10) REVERT: K 92 GLU cc_start: 0.6979 (pm20) cc_final: 0.6723 (pm20) REVERT: L 55 GLN cc_start: 0.9190 (tp-100) cc_final: 0.8973 (mm110) REVERT: L 72 MET cc_start: 0.6480 (pmm) cc_final: 0.5951 (pmm) REVERT: L 107 ARG cc_start: 0.7527 (mpp80) cc_final: 0.7240 (mpp-170) REVERT: L 129 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7690 (mmmt) REVERT: M 26 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8116 (ttpp) REVERT: M 81 VAL cc_start: 0.8496 (t) cc_final: 0.8176 (m) REVERT: N 27 SER cc_start: 0.8573 (m) cc_final: 0.8017 (p) REVERT: N 34 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7837 (pt) REVERT: P 28 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7352 (mt) REVERT: P 54 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.5888 (tpm170) REVERT: P 107 LYS cc_start: 0.7099 (ttmm) cc_final: 0.6564 (mtmm) REVERT: Q 49 ASP cc_start: 0.7850 (m-30) cc_final: 0.7384 (m-30) REVERT: Q 52 GLN cc_start: 0.8801 (mt0) cc_final: 0.8516 (mt0) REVERT: Q 85 LYS cc_start: 0.7821 (tmtp) cc_final: 0.7538 (mmtm) REVERT: Q 111 GLU cc_start: 0.7857 (pp20) cc_final: 0.7615 (pp20) REVERT: R 1 MET cc_start: 0.5059 (tmm) cc_final: 0.4569 (tpp) REVERT: S 86 MET cc_start: 0.7214 (tpp) cc_final: 0.6505 (ptm) REVERT: S 92 ARG cc_start: 0.6643 (ttp-170) cc_final: 0.6287 (mtm110) REVERT: U 7 ASP cc_start: 0.6186 (p0) cc_final: 0.5922 (p0) REVERT: U 50 MET cc_start: 0.4827 (ppp) cc_final: 0.3917 (ptp) REVERT: U 95 PHE cc_start: 0.6829 (m-80) cc_final: 0.5835 (m-10) REVERT: V 165 LEU cc_start: 0.4507 (OUTLIER) cc_final: 0.4150 (pt) REVERT: W 12 ASN cc_start: 0.7164 (OUTLIER) cc_final: 0.6698 (p0) REVERT: W 36 ILE cc_start: 0.7825 (mm) cc_final: 0.7589 (mm) REVERT: W 55 LYS cc_start: 0.7683 (tptp) cc_final: 0.7431 (ttmm) REVERT: W 72 LYS cc_start: 0.8059 (pttm) cc_final: 0.7824 (ptpt) REVERT: X 5 CYS cc_start: 0.7862 (t) cc_final: 0.7533 (t) REVERT: X 23 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7433 (p0) REVERT: X 41 GLU cc_start: 0.7953 (tp30) cc_final: 0.7275 (mp0) REVERT: X 58 ILE cc_start: 0.8391 (mt) cc_final: 0.8163 (mt) REVERT: Y 45 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7860 (pt0) REVERT: Z 46 MET cc_start: 0.9051 (mtt) cc_final: 0.8626 (mtm) REVERT: 2 31 LYS cc_start: 0.7278 (mmtp) cc_final: 0.7056 (mmtm) REVERT: 3 6 ARG cc_start: 0.7258 (ptm160) cc_final: 0.6924 (ptm160) REVERT: 4 25 LYS cc_start: 0.8575 (tptm) cc_final: 0.8034 (tmmt) REVERT: 5 22 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7749 (ptpt) REVERT: 5 56 ARG cc_start: 0.7672 (ttm170) cc_final: 0.7451 (ttm170) REVERT: 5 58 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7500 (mt-10) REVERT: 6 18 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7857 (ttm-80) REVERT: 6 34 LYS cc_start: 0.8514 (ttmt) cc_final: 0.8003 (ttpt) outliers start: 100 outliers final: 81 residues processed: 586 average time/residue: 0.8813 time to fit residues: 875.4804 Evaluate side-chains 618 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 522 time to evaluate : 3.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 164 TYR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 26 LYS Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 54 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 91 HIS Chi-restraints excluded: chain V residue 103 LEU Chi-restraints excluded: chain V residue 142 ASP Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain V residue 165 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 23 ASN Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 5 residue 22 LYS Chi-restraints excluded: chain 5 residue 27 PHE Chi-restraints excluded: chain 5 residue 30 HIS Chi-restraints excluded: chain 5 residue 43 LEU Chi-restraints excluded: chain 5 residue 46 THR Chi-restraints excluded: chain 5 residue 48 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 396 optimal weight: 5.9990 chunk 531 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 460 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 499 optimal weight: 0.5980 chunk 209 optimal weight: 30.0000 chunk 513 optimal weight: 0.0170 chunk 63 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 overall best weight: 3.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** 6 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.125647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.108110 restraints weight = 172942.267| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 0.56 r_work: 0.3169 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 1.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.209 98333 Z= 0.181 Angle : 0.665 59.164 147452 Z= 0.345 Chirality : 0.036 0.291 18919 Planarity : 0.005 0.087 7667 Dihedral : 24.248 179.852 49956 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.39 % Favored : 89.55 % Rotamer: Outliers : 3.46 % Allowed : 24.47 % Favored : 72.07 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.13), residues: 3398 helix: -1.40 (0.19), residues: 780 sheet: -1.32 (0.21), residues: 603 loop : -2.58 (0.12), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 83 HIS 0.007 0.001 HIS R 82 PHE 0.030 0.001 PHE D 127 TYR 0.018 0.001 TYR C 83 ARG 0.006 0.000 ARG C 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17606.56 seconds wall clock time: 313 minutes 41.44 seconds (18821.44 seconds total)