Starting phenix.real_space_refine on Sat Apr 13 12:11:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8why_37552/04_2024/8why_37552.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8why_37552/04_2024/8why_37552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8why_37552/04_2024/8why_37552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8why_37552/04_2024/8why_37552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8why_37552/04_2024/8why_37552.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8why_37552/04_2024/8why_37552.pdb" } resolution = 2.7 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= 0.002 sd= 0.011 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 3134 5.49 5 S 47 5.16 5 C 43907 2.51 5 N 16766 2.21 5 O 25818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 19": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G GLU 23": "OE1" <-> "OE2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G GLU 163": "OE1" <-> "OE2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "M PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 102": "OE1" <-> "OE2" Residue "O GLU 15": "OE1" <-> "OE2" Residue "O GLU 135": "OE1" <-> "OE2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 101": "OE1" <-> "OE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "T GLU 97": "OE1" <-> "OE2" Residue "U GLU 30": "OE1" <-> "OE2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W GLU 25": "OE1" <-> "OE2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "Z PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 9": "OE1" <-> "OE2" Residue "2 GLU 12": "OE1" <-> "OE2" Residue "2 GLU 17": "OE1" <-> "OE2" Residue "2 GLU 24": "OE1" <-> "OE2" Residue "2 GLU 28": "OE1" <-> "OE2" Residue "3 GLU 3": "OE1" <-> "OE2" Residue "3 GLU 55": "OE1" <-> "OE2" Residue "5 GLU 23": "OE1" <-> "OE2" Residue "6 ASP 6": "OD1" <-> "OD2" Residue "6 GLU 53": "OE1" <-> "OE2" Residue "4 GLU 36": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 89672 Number of models: 1 Model: "" Number of chains: 28 Chain: "E" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2110 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 19, 'TRANS': 255} Chain: "F" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "G" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1569 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "H" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1436 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain: "I" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1260 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 11, 'TRANS': 153} Chain: "J" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 308 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "M" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "N" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "O" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "Q" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 941 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "S" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 907 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "T" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "U" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "V" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "W" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 756 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "X" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 710 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain breaks: 1 Chain: "Z" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 574 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "1" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "2" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 527 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "3" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 470 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "5" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "6" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "7" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 372 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "8" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 502 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "4" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 364 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "A" Number of atoms: 64799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3017, 64799 Classifications: {'RNA': 3017} Modifications used: {'rna2p_pur': 292, 'rna2p_pyr': 148, 'rna3p_pur': 1436, 'rna3p_pyr': 1141} Link IDs: {'rna2p': 440, 'rna3p': 2576} Chain breaks: 3 Chain: "B" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2502 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 46} Link IDs: {'rna2p': 14, 'rna3p': 102} Time building chain proxies: 34.39, per 1000 atoms: 0.38 Number of scatterers: 89672 At special positions: 0 Unit cell: (222.56, 202.23, 243.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 3134 15.00 O 25818 8.00 N 16766 7.00 C 43907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 37.40 Conformation dependent library (CDL) restraints added in 4.2 seconds 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5236 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 44 sheets defined 31.5% alpha, 21.8% beta 1079 base pairs and 1578 stacking pairs defined. Time for finding SS restraints: 34.47 Creating SS restraints... Processing helix chain 'E' and resid 10 through 14 removed outlier: 3.648A pdb=" N ARG E 14 " --> pdb=" O PRO E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 198 through 204 removed outlier: 4.315A pdb=" N SER E 202 " --> pdb=" O ALA E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 removed outlier: 3.836A pdb=" N MET E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 226 Processing helix chain 'E' and resid 262 through 266 removed outlier: 3.967A pdb=" N LYS E 266 " --> pdb=" O PRO E 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 58 through 62 Processing helix chain 'F' and resid 63 through 74 Processing helix chain 'F' and resid 88 through 93 Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 125 through 131 Processing helix chain 'G' and resid 21 through 26 Processing helix chain 'G' and resid 30 through 46 Processing helix chain 'G' and resid 103 through 121 removed outlier: 3.600A pdb=" N ASN G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 149 Processing helix chain 'G' and resid 162 through 169 Processing helix chain 'G' and resid 179 through 183 removed outlier: 3.691A pdb=" N LEU G 183 " --> pdb=" O PRO G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 190 Processing helix chain 'G' and resid 198 through 210 removed outlier: 3.628A pdb=" N LYS G 210 " --> pdb=" O SER G 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 28 removed outlier: 3.845A pdb=" N ILE H 19 " --> pdb=" O TYR H 15 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG H 20 " --> pdb=" O ARG H 16 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.714A pdb=" N ILE H 35 " --> pdb=" O VAL H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 53 Processing helix chain 'H' and resid 54 through 69 removed outlier: 3.693A pdb=" N ASN H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 113 Processing helix chain 'H' and resid 114 through 118 Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'I' and resid 3 through 7 removed outlier: 3.703A pdb=" N GLN I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3 through 7' Processing helix chain 'I' and resid 59 through 82 removed outlier: 4.517A pdb=" N GLY I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU I 68 " --> pdb=" O SER I 64 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU I 82 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 151 Processing helix chain 'J' and resid 22 through 29 Processing helix chain 'M' and resid 24 through 38 Processing helix chain 'M' and resid 58 through 62 removed outlier: 3.656A pdb=" N ILE M 62 " --> pdb=" O ALA M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 72 Processing helix chain 'M' and resid 89 through 96 Processing helix chain 'M' and resid 96 through 107 removed outlier: 3.982A pdb=" N VAL M 100 " --> pdb=" O HIS M 96 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL M 101 " --> pdb=" O PRO M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 120 removed outlier: 3.862A pdb=" N LYS M 120 " --> pdb=" O ARG M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 136 Processing helix chain 'N' and resid 104 through 109 removed outlier: 4.167A pdb=" N GLU N 108 " --> pdb=" O ARG N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 118 Processing helix chain 'O' and resid 80 through 87 Processing helix chain 'O' and resid 94 through 101 Processing helix chain 'O' and resid 130 through 140 Processing helix chain 'Q' and resid 13 through 32 Processing helix chain 'Q' and resid 38 through 57 Proline residue: Q 46 - end of helix removed outlier: 3.599A pdb=" N LYS Q 57 " --> pdb=" O THR Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 71 removed outlier: 4.089A pdb=" N LYS Q 69 " --> pdb=" O GLU Q 65 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG Q 71 " --> pdb=" O MET Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 72 through 82 Processing helix chain 'Q' and resid 82 through 87 Processing helix chain 'R' and resid 9 through 27 removed outlier: 3.566A pdb=" N LEU R 25 " --> pdb=" O ARG R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 72 Processing helix chain 'R' and resid 76 through 95 Processing helix chain 'R' and resid 111 through 123 Processing helix chain 'S' and resid 4 through 12 removed outlier: 4.020A pdb=" N ALA S 10 " --> pdb=" O PHE S 6 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER S 11 " --> pdb=" O VAL S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 55 removed outlier: 3.611A pdb=" N SER S 55 " --> pdb=" O GLY S 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 52 through 55' Processing helix chain 'S' and resid 96 through 102 Processing helix chain 'S' and resid 103 through 108 removed outlier: 3.588A pdb=" N LYS S 106 " --> pdb=" O ARG S 103 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS S 108 " --> pdb=" O LYS S 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 21 removed outlier: 3.954A pdb=" N LYS T 13 " --> pdb=" O ASN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.695A pdb=" N ARG T 28 " --> pdb=" O ARG T 25 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER T 29 " --> pdb=" O GLY T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 71 removed outlier: 3.563A pdb=" N ARG T 51 " --> pdb=" O TYR T 47 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS T 54 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY T 55 " --> pdb=" O ARG T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 87 Processing helix chain 'T' and resid 91 through 102 Processing helix chain 'T' and resid 102 through 117 Processing helix chain 'U' and resid 51 through 57 Processing helix chain 'V' and resid 20 through 29 removed outlier: 3.636A pdb=" N VAL V 27 " --> pdb=" O LYS V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 46 Processing helix chain 'V' and resid 50 through 68 Processing helix chain 'V' and resid 72 through 74 No H-bonds generated for 'chain 'V' and resid 72 through 74' Processing helix chain 'V' and resid 96 through 98 No H-bonds generated for 'chain 'V' and resid 96 through 98' Processing helix chain 'W' and resid 17 through 25 Processing helix chain 'W' and resid 38 through 51 Processing helix chain 'W' and resid 93 through 97 Processing helix chain '1' and resid 53 through 58 Processing helix chain '2' and resid 6 through 11 Processing helix chain '2' and resid 14 through 39 Processing helix chain '2' and resid 44 through 67 removed outlier: 4.276A pdb=" N ARG 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) Processing helix chain '3' and resid 16 through 27 Processing helix chain '3' and resid 40 through 50 Processing helix chain '5' and resid 9 through 18 Processing helix chain '5' and resid 43 through 49 Processing helix chain '7' and resid 11 through 20 Processing helix chain '7' and resid 20 through 27 removed outlier: 3.973A pdb=" N THR 7 27 " --> pdb=" O LEU 7 23 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 41 Processing helix chain '8' and resid 7 through 14 Processing helix chain '8' and resid 37 through 44 Processing helix chain '8' and resid 51 through 64 removed outlier: 4.584A pdb=" N SER 8 56 " --> pdb=" O ALA 8 52 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ARG 8 57 " --> pdb=" O ALA 8 53 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 6 removed outlier: 3.860A pdb=" N ILE 4 5 " --> pdb=" O LYS 4 2 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS 4 6 " --> pdb=" O THR 4 3 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 2 through 6' Processing helix chain '4' and resid 42 through 47 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'E' and resid 102 through 106 removed outlier: 6.634A pdb=" N ILE E 92 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE E 82 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU E 94 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 130 through 132 removed outlier: 5.925A pdb=" N LEU E 165 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG E 176 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY E 167 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG E 184 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE E 268 " --> pdb=" O ARG E 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 145 through 146 removed outlier: 6.093A pdb=" N VAL E 145 " --> pdb=" O LYS E 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 17 removed outlier: 6.099A pdb=" N LYS F 10 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LYS F 30 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY F 12 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS F 195 " --> pdb=" O VAL F 182 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL F 182 " --> pdb=" O LYS F 195 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL F 112 " --> pdb=" O ASN F 179 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR F 117 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU F 205 " --> pdb=" O THR F 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 80 through 85 removed outlier: 3.574A pdb=" N ARG F 38 " --> pdb=" O GLN F 51 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA F 53 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL F 36 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 120 through 124 removed outlier: 3.616A pdb=" N GLY F 122 " --> pdb=" O MET F 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 14 through 20 removed outlier: 4.006A pdb=" N GLY G 16 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU G 3 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ILE G 124 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP G 6 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA G 126 " --> pdb=" O ASP G 6 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N HIS G 125 " --> pdb=" O PHE G 196 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU G 155 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N SER G 197 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL G 157 " --> pdb=" O SER G 197 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL G 154 " --> pdb=" O HIS G 176 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE G 178 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL G 156 " --> pdb=" O ILE G 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 47 through 48 removed outlier: 3.675A pdb=" N GLY G 48 " --> pdb=" O ARG G 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 73 through 76 removed outlier: 3.707A pdb=" N GLY H 93 " --> pdb=" O ARG H 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 16 through 20 Processing sheet with id=AB4, first strand: chain 'I' and resid 42 through 44 Processing sheet with id=AB5, first strand: chain 'I' and resid 122 through 126 Processing sheet with id=AB6, first strand: chain 'I' and resid 96 through 100 removed outlier: 3.550A pdb=" N GLN I 98 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 18 through 20 removed outlier: 3.877A pdb=" N LEU J 3 " --> pdb=" O VAL J 19 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 122 through 124 removed outlier: 6.640A pdb=" N TRP M 15 " --> pdb=" O ILE M 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 73 through 77 Processing sheet with id=AC1, first strand: chain 'N' and resid 7 through 10 removed outlier: 5.989A pdb=" N LYS N 17 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA N 16 " --> pdb=" O ALA N 46 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA N 46 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU N 18 " --> pdb=" O LYS N 44 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL N 40 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N VAL N 24 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL N 38 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS N 59 " --> pdb=" O ILE N 87 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA N 83 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ALA N 84 " --> pdb=" O ARG N 7 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS N 9 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE N 86 " --> pdb=" O LYS N 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 69 through 70 removed outlier: 6.632A pdb=" N THR S 57 " --> pdb=" O ARG S 49 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG S 49 " --> pdb=" O THR S 57 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR S 59 " --> pdb=" O ILE S 47 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLU S 63 " --> pdb=" O LYS S 43 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N LYS S 43 " --> pdb=" O GLU S 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG S 38 " --> pdb=" O VAL S 31 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR S 24 " --> pdb=" O LEU S 86 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS S 82 " --> pdb=" O HIS S 28 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS S 30 " --> pdb=" O ILE S 80 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE S 80 " --> pdb=" O LYS S 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 76 through 79 removed outlier: 6.023A pdb=" N GLN O 76 " --> pdb=" O LYS O 111 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU O 113 " --> pdb=" O GLN O 76 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL O 78 " --> pdb=" O LEU O 113 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 91 through 93 removed outlier: 7.659A pdb=" N THR O 145 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL O 124 " --> pdb=" O THR O 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Q' and resid 33 through 37 removed outlier: 4.233A pdb=" N MET Q 110 " --> pdb=" O VAL Q 100 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 58 through 64 removed outlier: 5.983A pdb=" N THR R 59 " --> pdb=" O ASN R 53 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASN R 53 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA R 61 " --> pdb=" O LEU R 51 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU R 38 " --> pdb=" O ASP R 103 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'S' and resid 89 through 90 removed outlier: 4.379A pdb=" N LYS S 110 " --> pdb=" O ASP S 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 12 through 16 removed outlier: 6.926A pdb=" N TYR U 4 " --> pdb=" O VAL U 42 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL U 42 " --> pdb=" O TYR U 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE U 6 " --> pdb=" O ALA U 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 21 through 25 removed outlier: 6.489A pdb=" N LEU U 94 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N HIS U 67 " --> pdb=" O LEU U 94 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL U 96 " --> pdb=" O LEU U 65 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR U 61 " --> pdb=" O THR U 100 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'U' and resid 73 through 79 removed outlier: 4.261A pdb=" N TYR U 84 " --> pdb=" O LYS U 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 9 through 17 removed outlier: 5.538A pdb=" N SER V 108 " --> pdb=" O TYR V 16 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLU V 115 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL V 78 " --> pdb=" O GLU V 115 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'V' and resid 89 through 94 Processing sheet with id=AD4, first strand: chain 'W' and resid 11 through 14 removed outlier: 4.388A pdb=" N LYS W 80 " --> pdb=" O VAL W 33 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'W' and resid 66 through 69 Processing sheet with id=AD6, first strand: chain 'X' and resid 66 through 67 removed outlier: 7.010A pdb=" N LYS X 32 " --> pdb=" O ALA X 26 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA X 26 " --> pdb=" O LYS X 32 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU X 34 " --> pdb=" O LEU X 24 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR X 8 " --> pdb=" O VAL X 74 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL X 73 " --> pdb=" O THR X 81 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 40 through 43 Processing sheet with id=AD8, first strand: chain 'X' and resid 83 through 87 Processing sheet with id=AD9, first strand: chain 'Z' and resid 22 through 23 removed outlier: 6.865A pdb=" N LEU Z 59 " --> pdb=" O LEU Z 37 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 30 through 31 Processing sheet with id=AE2, first strand: chain '1' and resid 13 through 18 Processing sheet with id=AE3, first strand: chain '1' and resid 33 through 39 Processing sheet with id=AE4, first strand: chain '3' and resid 34 through 38 Processing sheet with id=AE5, first strand: chain '5' and resid 27 through 32 Processing sheet with id=AE6, first strand: chain '6' and resid 22 through 26 removed outlier: 3.505A pdb=" N THR 6 47 " --> pdb=" O CYS 6 42 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '8' and resid 15 through 16 Processing sheet with id=AE8, first strand: chain '4' and resid 21 through 26 removed outlier: 7.489A pdb=" N ILE 4 33 " --> pdb=" O ASP 4 11 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N THR 4 13 " --> pdb=" O ILE 4 33 " (cutoff:3.500A) 893 hydrogen bonds defined for protein. 2460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2760 hydrogen bonds 4380 hydrogen bond angles 0 basepair planarities 1079 basepair parallelities 1578 stacking parallelities Total time for adding SS restraints: 177.90 Time building geometry restraints manager: 40.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11528 1.33 - 1.45: 42762 1.45 - 1.57: 37420 1.57 - 1.69: 6263 1.69 - 1.81: 79 Bond restraints: 98052 Sorted by residual: bond pdb=" CA CYS 6 18 " pdb=" C CYS 6 18 " ideal model delta sigma weight residual 1.529 1.514 0.015 9.30e-03 1.16e+04 2.56e+00 bond pdb=" CA PRO V 47 " pdb=" CB PRO V 47 " ideal model delta sigma weight residual 1.531 1.522 0.009 6.20e-03 2.60e+04 2.02e+00 bond pdb=" CA ARG 6 21 " pdb=" C ARG 6 21 " ideal model delta sigma weight residual 1.524 1.508 0.016 1.22e-02 6.72e+03 1.79e+00 bond pdb=" CB LYS J 2 " pdb=" CG LYS J 2 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CB LYS R 4 " pdb=" CG LYS R 4 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.67e+00 ... (remaining 98047 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.08: 14465 105.08 - 112.30: 56482 112.30 - 119.52: 32256 119.52 - 126.74: 36293 126.74 - 133.97: 8585 Bond angle restraints: 148081 Sorted by residual: angle pdb=" C CYS 6 18 " pdb=" CA CYS 6 18 " pdb=" CB CYS 6 18 " ideal model delta sigma weight residual 116.54 110.41 6.13 1.15e+00 7.56e-01 2.84e+01 angle pdb=" C GLY H 89 " pdb=" N MET H 90 " pdb=" CA MET H 90 " ideal model delta sigma weight residual 121.98 109.00 12.98 3.11e+00 1.03e-01 1.74e+01 angle pdb=" C ALA R 89 " pdb=" N GLU R 90 " pdb=" CA GLU R 90 " ideal model delta sigma weight residual 121.14 114.23 6.91 1.75e+00 3.27e-01 1.56e+01 angle pdb=" CB LYS J 2 " pdb=" CG LYS J 2 " pdb=" CD LYS J 2 " ideal model delta sigma weight residual 111.30 119.97 -8.67 2.30e+00 1.89e-01 1.42e+01 angle pdb=" C3' G A2094 " pdb=" O3' G A2094 " pdb=" P G A2095 " ideal model delta sigma weight residual 120.20 125.67 -5.47 1.50e+00 4.44e-01 1.33e+01 ... (remaining 148076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 54362 35.91 - 71.81: 7914 71.81 - 107.72: 881 107.72 - 143.62: 21 143.62 - 179.53: 30 Dihedral angle restraints: 63208 sinusoidal: 55041 harmonic: 8167 Sorted by residual: dihedral pdb=" O4' C A1535 " pdb=" C1' C A1535 " pdb=" N1 C A1535 " pdb=" C2 C A1535 " ideal model delta sinusoidal sigma weight residual 200.00 20.47 179.53 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A2025 " pdb=" C1' C A2025 " pdb=" N1 C A2025 " pdb=" C2 C A2025 " ideal model delta sinusoidal sigma weight residual -160.00 12.47 -172.47 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C A3046 " pdb=" C1' C A3046 " pdb=" N1 C A3046 " pdb=" C2 C A3046 " ideal model delta sinusoidal sigma weight residual -160.00 11.23 -171.23 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 63205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 18001 0.073 - 0.145: 1010 0.145 - 0.218: 73 0.218 - 0.291: 10 0.291 - 0.364: 2 Chirality restraints: 19096 Sorted by residual: chirality pdb=" CG LEU R 87 " pdb=" CB LEU R 87 " pdb=" CD1 LEU R 87 " pdb=" CD2 LEU R 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" C1' G A 297 " pdb=" O4' G A 297 " pdb=" C2' G A 297 " pdb=" N9 G A 297 " both_signs ideal model delta sigma weight residual False 2.46 2.12 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C1' U A2804 " pdb=" O4' U A2804 " pdb=" C2' U A2804 " pdb=" N1 U A2804 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 19093 not shown) Planarity restraints: 7120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS 4 42 " -0.061 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO 4 43 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO 4 43 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO 4 43 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A1098 " 0.043 2.00e-02 2.50e+03 1.95e-02 1.05e+01 pdb=" N9 A A1098 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A A1098 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A A1098 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A A1098 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A A1098 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A A1098 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A A1098 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A A1098 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A A1098 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A A1098 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 24 " 0.032 2.00e-02 2.50e+03 1.68e-02 8.49e+00 pdb=" N9 G B 24 " -0.034 2.00e-02 2.50e+03 pdb=" C8 G B 24 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G B 24 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 24 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 24 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G B 24 " 0.016 2.00e-02 2.50e+03 pdb=" N1 G B 24 " 0.000 2.00e-02 2.50e+03 pdb=" C2 G B 24 " -0.027 2.00e-02 2.50e+03 pdb=" N2 G B 24 " 0.014 2.00e-02 2.50e+03 pdb=" N3 G B 24 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G B 24 " 0.002 2.00e-02 2.50e+03 ... (remaining 7117 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 2114 2.61 - 3.18: 68624 3.18 - 3.75: 186879 3.75 - 4.33: 253209 4.33 - 4.90: 328783 Nonbonded interactions: 839609 Sorted by model distance: nonbonded pdb=" O2' G A2333 " pdb=" OP2 G A2343 " model vdw 2.033 2.440 nonbonded pdb=" O2' G A 643 " pdb=" OP1 G A 644 " model vdw 2.044 2.440 nonbonded pdb=" O2 U A 329 " pdb=" O6 G A 446 " model vdw 2.048 2.432 nonbonded pdb=" OP1 U A2386 " pdb=" O2' A A2393 " model vdw 2.050 2.440 nonbonded pdb=" OG1 THR 8 19 " pdb=" OP1 G A 745 " model vdw 2.050 2.440 ... (remaining 839604 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: 4.740 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: 0.050 Extract box with map and model: 14.490 Check model and map are aligned: 1.010 Set scattering table: 0.630 Process input model: 353.640 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:9.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 385.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 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 : 0.004 0.068 98052 Z= 0.245 Angle : 0.581 12.979 148081 Z= 0.303 Chirality : 0.036 0.364 19096 Planarity : 0.005 0.092 7120 Dihedral : 24.511 179.530 57972 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 4.64 % Allowed : 28.68 % Favored : 66.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.15 (0.16), residues: 2846 helix: 0.98 (0.19), residues: 771 sheet: 0.05 (0.21), residues: 665 loop : -0.29 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP V 45 HIS 0.007 0.001 HIS J 11 PHE 0.027 0.001 PHE I 106 TYR 0.016 0.001 TYR Q 47 ARG 0.030 0.000 ARG R 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 284 time to evaluate : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 6 22 ASN cc_start: 0.8616 (m-40) cc_final: 0.8386 (m-40) outliers start: 109 outliers final: 103 residues processed: 385 average time/residue: 1.5552 time to fit residues: 831.8196 Evaluate side-chains 379 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 276 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 57 ASP Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 22 VAL Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 51 LYS Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 51 SER Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 12 ASN Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 5 residue 39 VAL Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 25 GLN Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 22 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 498 optimal weight: 10.0000 chunk 447 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 301 optimal weight: 10.0000 chunk 238 optimal weight: 20.0000 chunk 462 optimal weight: 20.0000 chunk 178 optimal weight: 6.9990 chunk 281 optimal weight: 10.0000 chunk 344 optimal weight: 10.0000 chunk 535 optimal weight: 20.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 42 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.0452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 98052 Z= 0.397 Angle : 0.623 8.921 148081 Z= 0.323 Chirality : 0.040 0.281 19096 Planarity : 0.005 0.077 7120 Dihedral : 24.450 179.856 52573 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 6.72 % Allowed : 25.53 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.12 (0.16), residues: 2846 helix: 1.07 (0.19), residues: 769 sheet: -0.09 (0.21), residues: 623 loop : -0.30 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP V 45 HIS 0.005 0.001 HIS U 90 PHE 0.012 0.002 PHE Q 80 TYR 0.016 0.002 TYR Q 47 ARG 0.009 0.001 ARG 6 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 285 time to evaluate : 3.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 160 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7513 (ttm110) REVERT: H 162 THR cc_start: 0.9110 (m) cc_final: 0.8889 (t) REVERT: I 91 PHE cc_start: 0.6058 (m-80) cc_final: 0.5019 (m-10) REVERT: I 98 GLN cc_start: 0.6518 (pp30) cc_final: 0.6315 (pp30) REVERT: O 15 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: O 65 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8736 (pttt) REVERT: Q 101 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: R 24 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.6459 (ptp90) REVERT: 3 28 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8757 (pp) REVERT: 5 23 GLU cc_start: 0.7782 (mp0) cc_final: 0.7475 (mp0) REVERT: 6 22 ASN cc_start: 0.8669 (m-40) cc_final: 0.8430 (m-40) REVERT: 6 35 ARG cc_start: 0.7752 (ptp-110) cc_final: 0.7549 (ptp-170) outliers start: 158 outliers final: 90 residues processed: 404 average time/residue: 1.6644 time to fit residues: 920.6594 Evaluate side-chains 373 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 277 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 57 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 65 LYS Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain O residue 146 GLU Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain V residue 38 GLU Chi-restraints excluded: chain V residue 51 SER Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain Z residue 83 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 1 residue 61 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 29 THR Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 27 LYS Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 5 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 297 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 445 optimal weight: 10.0000 chunk 364 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 536 optimal weight: 50.0000 chunk 579 optimal weight: 30.0000 chunk 478 optimal weight: 10.0000 chunk 532 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 430 optimal weight: 50.0000 overall best weight: 7.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 GLN H 62 ASN ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 98052 Z= 0.378 Angle : 0.612 8.889 148081 Z= 0.317 Chirality : 0.039 0.275 19096 Planarity : 0.005 0.075 7120 Dihedral : 24.357 179.433 52503 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 6.60 % Allowed : 25.40 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.15 (0.15), residues: 2846 helix: 1.12 (0.19), residues: 768 sheet: -0.09 (0.21), residues: 620 loop : -0.29 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP V 45 HIS 0.004 0.001 HIS Q 77 PHE 0.014 0.002 PHE R 127 TYR 0.015 0.002 TYR Q 47 ARG 0.005 0.001 ARG 4 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 288 time to evaluate : 3.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 273 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6754 (mtm-85) REVERT: F 186 ASP cc_start: 0.8490 (t0) cc_final: 0.8283 (t70) REVERT: G 6 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8347 (p0) REVERT: G 160 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7540 (ttm110) REVERT: I 91 PHE cc_start: 0.5807 (m-80) cc_final: 0.4932 (m-10) REVERT: O 15 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: O 65 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8733 (pttt) REVERT: Q 101 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: R 24 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.6597 (ptp90) REVERT: R 87 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8388 (mm) REVERT: S 101 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: 2 21 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9136 (ttmm) REVERT: 3 28 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8795 (pp) REVERT: 5 23 GLU cc_start: 0.7785 (mp0) cc_final: 0.7481 (mp0) outliers start: 155 outliers final: 93 residues processed: 401 average time/residue: 1.6647 time to fit residues: 914.7470 Evaluate side-chains 381 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 277 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 57 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 65 LYS Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain O residue 146 GLU Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 38 GLU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain Z residue 83 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 61 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 27 LYS Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 6 residue 54 SER Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 29 GLN Chi-restraints excluded: chain 4 residue 33 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 530 optimal weight: 10.0000 chunk 403 optimal weight: 8.9990 chunk 278 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 chunk 360 optimal weight: 10.0000 chunk 538 optimal weight: 50.0000 chunk 570 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 chunk 510 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 ASN ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 98052 Z= 0.438 Angle : 0.647 9.669 148081 Z= 0.334 Chirality : 0.041 0.284 19096 Planarity : 0.005 0.082 7120 Dihedral : 24.361 179.282 52492 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 6.68 % Allowed : 25.96 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.10 (0.15), residues: 2846 helix: 1.09 (0.18), residues: 768 sheet: -0.11 (0.21), residues: 620 loop : -0.32 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP V 45 HIS 0.005 0.001 HIS Q 77 PHE 0.019 0.002 PHE I 106 TYR 0.016 0.002 TYR Q 47 ARG 0.006 0.001 ARG 4 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 294 time to evaluate : 3.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 88 ASP cc_start: 0.8363 (p0) cc_final: 0.8129 (p0) REVERT: F 186 ASP cc_start: 0.8565 (t0) cc_final: 0.8341 (t70) REVERT: G 6 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8347 (p0) REVERT: G 160 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7563 (ttm110) REVERT: I 91 PHE cc_start: 0.5795 (m-80) cc_final: 0.4976 (m-10) REVERT: I 98 GLN cc_start: 0.6459 (pp30) cc_final: 0.6116 (pp30) REVERT: O 15 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: Q 101 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: R 24 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.6542 (ptp90) REVERT: R 116 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8618 (tp) REVERT: S 48 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8906 (ptt180) REVERT: S 101 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: W 96 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8287 (t80) REVERT: 3 28 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8749 (pp) REVERT: 5 23 GLU cc_start: 0.7797 (mp0) cc_final: 0.7495 (mp0) REVERT: 4 8 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6369 (tm-30) outliers start: 157 outliers final: 95 residues processed: 412 average time/residue: 1.6905 time to fit residues: 957.1403 Evaluate side-chains 386 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 280 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 57 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain O residue 146 GLU Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 38 GLU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain Z residue 83 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 61 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 8 GLU Chi-restraints excluded: chain 4 residue 33 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 474 optimal weight: 10.0000 chunk 323 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 424 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 486 optimal weight: 10.0000 chunk 394 optimal weight: 50.0000 chunk 0 optimal weight: 8.9990 chunk 291 optimal weight: 10.0000 chunk 511 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 overall best weight: 5.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 ASN ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 42 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 98052 Z= 0.312 Angle : 0.602 9.627 148081 Z= 0.315 Chirality : 0.038 0.345 19096 Planarity : 0.005 0.076 7120 Dihedral : 24.378 179.747 52484 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 6.04 % Allowed : 26.43 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.18 (0.15), residues: 2846 helix: 1.17 (0.19), residues: 769 sheet: -0.01 (0.21), residues: 607 loop : -0.32 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP V 45 HIS 0.014 0.001 HIS J 11 PHE 0.013 0.002 PHE Q 80 TYR 0.017 0.002 TYR Q 47 ARG 0.006 0.000 ARG 2 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 286 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 88 ASP cc_start: 0.8349 (p0) cc_final: 0.8081 (p0) REVERT: F 174 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8383 (ttt90) REVERT: F 186 ASP cc_start: 0.8539 (t0) cc_final: 0.8320 (t70) REVERT: G 6 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8347 (p0) REVERT: G 160 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7546 (ttm110) REVERT: I 91 PHE cc_start: 0.5826 (m-80) cc_final: 0.5134 (m-10) REVERT: I 98 GLN cc_start: 0.6539 (pp30) cc_final: 0.6027 (pp30) REVERT: O 15 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7569 (tt0) REVERT: Q 101 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: R 24 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.6536 (ptp90) REVERT: R 116 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8630 (tp) REVERT: S 48 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8876 (ptt180) REVERT: S 101 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: 2 21 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9152 (ttmm) REVERT: 3 28 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8689 (pp) REVERT: 5 23 GLU cc_start: 0.7788 (mp0) cc_final: 0.7487 (mp0) REVERT: 6 35 ARG cc_start: 0.7856 (ptp-110) cc_final: 0.7596 (ptp-110) outliers start: 142 outliers final: 102 residues processed: 394 average time/residue: 1.6713 time to fit residues: 906.3724 Evaluate side-chains 393 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 280 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 174 ARG Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain O residue 146 GLU Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 15 ASP Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Z residue 12 ASN Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain Z residue 83 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 61 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 27 LYS Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 33 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 191 optimal weight: 0.6980 chunk 513 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 334 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 570 optimal weight: 10.0000 chunk 473 optimal weight: 10.0000 chunk 264 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 299 optimal weight: 10.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 ASN M 147 GLN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 42 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 98052 Z= 0.275 Angle : 0.572 9.961 148081 Z= 0.298 Chirality : 0.036 0.290 19096 Planarity : 0.005 0.067 7120 Dihedral : 24.315 179.529 52482 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.32 % Allowed : 27.06 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.27 (0.16), residues: 2846 helix: 1.32 (0.19), residues: 763 sheet: -0.01 (0.21), residues: 617 loop : -0.27 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP V 45 HIS 0.004 0.001 HIS E 38 PHE 0.022 0.001 PHE I 106 TYR 0.016 0.001 TYR Q 47 ARG 0.007 0.000 ARG X 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 282 time to evaluate : 3.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 88 ASP cc_start: 0.8323 (p0) cc_final: 0.8066 (p0) REVERT: F 186 ASP cc_start: 0.8565 (t0) cc_final: 0.8350 (t70) REVERT: G 6 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8318 (p0) REVERT: G 160 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7531 (ttm110) REVERT: I 58 ASP cc_start: 0.6514 (m-30) cc_final: 0.6261 (m-30) REVERT: I 91 PHE cc_start: 0.5950 (m-80) cc_final: 0.5244 (m-10) REVERT: I 98 GLN cc_start: 0.6526 (pp30) cc_final: 0.6012 (pp30) REVERT: O 15 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: Q 101 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7948 (tt0) REVERT: R 24 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.6468 (ptp90) REVERT: R 116 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8642 (tt) REVERT: S 48 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8817 (ptt180) REVERT: S 101 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: T 28 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.7990 (mtt-85) REVERT: 2 21 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9116 (ttmm) REVERT: 3 28 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8628 (pp) REVERT: 5 23 GLU cc_start: 0.7778 (mp0) cc_final: 0.7476 (mp0) outliers start: 125 outliers final: 85 residues processed: 376 average time/residue: 1.6763 time to fit residues: 867.5396 Evaluate side-chains 370 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 274 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain O residue 146 GLU Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 28 ARG Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Z residue 12 ASN Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 1 residue 61 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 27 LYS Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 44 ASN Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 33 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 550 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 325 optimal weight: 10.0000 chunk 416 optimal weight: 10.0000 chunk 322 optimal weight: 30.0000 chunk 480 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 568 optimal weight: 10.0000 chunk 355 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 overall best weight: 9.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 ASN ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 GLN ** 6 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.112 98052 Z= 0.493 Angle : 0.675 8.938 148081 Z= 0.347 Chirality : 0.043 0.286 19096 Planarity : 0.005 0.086 7120 Dihedral : 24.340 179.791 52470 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 6.17 % Allowed : 26.68 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.08 (0.15), residues: 2846 helix: 1.08 (0.19), residues: 766 sheet: -0.11 (0.21), residues: 622 loop : -0.35 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP V 45 HIS 0.007 0.001 HIS J 11 PHE 0.016 0.002 PHE Q 80 TYR 0.014 0.002 TYR Q 47 ARG 0.006 0.001 ARG E 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 279 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 188 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8185 (mtp85) REVERT: F 88 ASP cc_start: 0.8331 (p0) cc_final: 0.8065 (p0) REVERT: F 174 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8403 (ttt90) REVERT: F 186 ASP cc_start: 0.8553 (t0) cc_final: 0.8331 (t70) REVERT: G 6 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8311 (p0) REVERT: G 160 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7570 (ttm110) REVERT: I 91 PHE cc_start: 0.5957 (m-80) cc_final: 0.5286 (m-10) REVERT: I 98 GLN cc_start: 0.6493 (pp30) cc_final: 0.5978 (pp30) REVERT: O 15 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: Q 101 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: R 24 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.6472 (ptp90) REVERT: R 116 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8644 (tp) REVERT: S 48 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8879 (ptt180) REVERT: S 101 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: T 28 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8035 (mtt-85) REVERT: T 59 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8829 (ttmm) REVERT: W 70 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6404 (ptt90) REVERT: 2 41 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8119 (pt) REVERT: 5 23 GLU cc_start: 0.7809 (mp0) cc_final: 0.7507 (mp0) REVERT: 5 36 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7790 (mm-40) REVERT: 7 28 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8492 (ttm170) outliers start: 145 outliers final: 109 residues processed: 389 average time/residue: 1.6654 time to fit residues: 887.8948 Evaluate side-chains 402 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 277 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 188 ARG Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 174 ARG Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain O residue 146 GLU Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 28 ARG Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 38 GLU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Z residue 12 ASN Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 83 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 1 residue 61 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 5 residue 36 GLN Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 27 LYS Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 44 ASN Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 28 ARG Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 33 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 351 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 chunk 339 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 361 optimal weight: 10.0000 chunk 387 optimal weight: 7.9990 chunk 281 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 446 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 47 GLN H 62 ASN M 147 GLN ** 6 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 11 ASN 8 25 GLN 4 42 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 98052 Z= 0.218 Angle : 0.565 10.865 148081 Z= 0.294 Chirality : 0.035 0.337 19096 Planarity : 0.004 0.061 7120 Dihedral : 24.314 178.790 52468 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.98 % Allowed : 28.13 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.30 (0.16), residues: 2846 helix: 1.34 (0.19), residues: 766 sheet: -0.06 (0.21), residues: 632 loop : -0.22 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP V 45 HIS 0.003 0.001 HIS E 38 PHE 0.024 0.001 PHE I 106 TYR 0.016 0.001 TYR Q 47 ARG 0.007 0.000 ARG X 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 280 time to evaluate : 3.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 188 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8183 (mtp85) REVERT: F 88 ASP cc_start: 0.8321 (p0) cc_final: 0.8058 (p0) REVERT: G 6 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8278 (p0) REVERT: G 160 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7572 (ttm110) REVERT: I 91 PHE cc_start: 0.5966 (m-80) cc_final: 0.5298 (m-10) REVERT: I 98 GLN cc_start: 0.6537 (pp30) cc_final: 0.6041 (pp30) REVERT: O 15 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: Q 101 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: R 12 GLU cc_start: 0.8244 (tp30) cc_final: 0.7555 (tp30) REVERT: R 24 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.6465 (ptp90) REVERT: R 116 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8690 (tt) REVERT: S 48 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8813 (ptt180) REVERT: S 101 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: T 28 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.7993 (mtt-85) REVERT: 5 23 GLU cc_start: 0.7807 (mp0) cc_final: 0.7510 (mp0) REVERT: 5 36 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7837 (mm-40) outliers start: 117 outliers final: 85 residues processed: 369 average time/residue: 1.6848 time to fit residues: 853.2801 Evaluate side-chains 370 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 274 time to evaluate : 3.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 188 ARG Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain O residue 146 GLU Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 28 ARG Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain V residue 38 GLU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Z residue 12 ASN Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 61 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 5 residue 36 GLN Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 27 LYS Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 517 optimal weight: 10.0000 chunk 544 optimal weight: 10.0000 chunk 497 optimal weight: 10.0000 chunk 529 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 416 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 478 optimal weight: 10.0000 chunk 501 optimal weight: 50.0000 chunk 528 optimal weight: 10.0000 overall best weight: 9.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 ASN M 147 GLN 2 40 GLN 7 11 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 98052 Z= 0.476 Angle : 0.665 10.290 148081 Z= 0.342 Chirality : 0.042 0.304 19096 Planarity : 0.005 0.084 7120 Dihedral : 24.312 179.973 52466 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.23 % Allowed : 27.91 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.12 (0.15), residues: 2846 helix: 1.15 (0.19), residues: 761 sheet: -0.11 (0.20), residues: 629 loop : -0.32 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP V 45 HIS 0.009 0.001 HIS J 11 PHE 0.015 0.002 PHE Q 80 TYR 0.015 0.002 TYR Q 47 ARG 0.007 0.001 ARG 6 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 276 time to evaluate : 3.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 188 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8189 (mtp85) REVERT: F 88 ASP cc_start: 0.8368 (p0) cc_final: 0.8116 (p0) REVERT: G 6 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8316 (p0) REVERT: G 160 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7559 (ttm110) REVERT: I 91 PHE cc_start: 0.5968 (m-80) cc_final: 0.5324 (m-10) REVERT: I 98 GLN cc_start: 0.6549 (pp30) cc_final: 0.6078 (pp30) REVERT: J 11 HIS cc_start: 0.7207 (m90) cc_final: 0.7005 (m90) REVERT: O 15 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: Q 101 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: R 24 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.6470 (ptp90) REVERT: R 116 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8728 (tp) REVERT: S 48 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8906 (ptt180) REVERT: S 101 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: T 28 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8030 (mtt-85) REVERT: W 70 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6389 (ptt90) REVERT: 5 23 GLU cc_start: 0.7804 (mp0) cc_final: 0.7505 (mp0) REVERT: 5 36 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7785 (mm-40) REVERT: 6 30 ARG cc_start: 0.8453 (ptp-110) cc_final: 0.8168 (ptp90) REVERT: 7 28 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8510 (ttm170) outliers start: 123 outliers final: 97 residues processed: 366 average time/residue: 1.7046 time to fit residues: 853.6227 Evaluate side-chains 382 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 272 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 188 ARG Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain O residue 146 GLU Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 28 ARG Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 38 GLU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 61 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 5 residue 36 GLN Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 27 LYS Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 44 ASN Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 28 ARG Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 347 optimal weight: 8.9990 chunk 560 optimal weight: 10.0000 chunk 342 optimal weight: 10.0000 chunk 265 optimal weight: 7.9990 chunk 389 optimal weight: 7.9990 chunk 587 optimal weight: 10.0000 chunk 540 optimal weight: 30.0000 chunk 468 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 361 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 ASN M 147 GLN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 40 GLN 7 11 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 98052 Z= 0.411 Angle : 0.641 11.345 148081 Z= 0.332 Chirality : 0.040 0.324 19096 Planarity : 0.005 0.081 7120 Dihedral : 24.326 179.776 52466 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.11 % Allowed : 28.26 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.10 (0.15), residues: 2846 helix: 1.13 (0.19), residues: 761 sheet: -0.13 (0.20), residues: 628 loop : -0.33 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP V 45 HIS 0.005 0.001 HIS 4 20 PHE 0.033 0.002 PHE I 106 TYR 0.016 0.002 TYR Q 47 ARG 0.007 0.001 ARG X 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 274 time to evaluate : 4.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 188 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8190 (mtp85) REVERT: E 273 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6742 (mtm-85) REVERT: F 88 ASP cc_start: 0.8359 (p0) cc_final: 0.8081 (p0) REVERT: F 174 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8398 (ttt90) REVERT: G 6 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8294 (p0) REVERT: G 160 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7556 (ttm110) REVERT: I 91 PHE cc_start: 0.5962 (m-80) cc_final: 0.5331 (m-10) REVERT: I 98 GLN cc_start: 0.6552 (pp30) cc_final: 0.6070 (pp30) REVERT: J 11 HIS cc_start: 0.7190 (m90) cc_final: 0.6971 (m90) REVERT: O 15 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: Q 101 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: R 24 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.6518 (ptp90) REVERT: R 116 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8639 (tp) REVERT: S 48 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8895 (ptt180) REVERT: S 101 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: T 28 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8033 (mtt-85) REVERT: W 70 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6577 (ptt90) REVERT: 5 23 GLU cc_start: 0.7802 (mp0) cc_final: 0.7499 (mp0) REVERT: 5 36 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7802 (mm-40) REVERT: 6 30 ARG cc_start: 0.8428 (ptp-110) cc_final: 0.8140 (ptp90) REVERT: 7 28 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8517 (ttm170) outliers start: 120 outliers final: 97 residues processed: 365 average time/residue: 1.7178 time to fit residues: 856.8350 Evaluate side-chains 386 residues out of total 2350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 274 time to evaluate : 3.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 188 ARG Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 174 ARG Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain O residue 146 GLU Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 28 ARG Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain U residue 73 ILE Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 38 GLU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Z residue 12 ASN Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 61 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 5 residue 36 GLN Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 27 LYS Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 44 ASN Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 28 ARG Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 371 optimal weight: 10.0000 chunk 498 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 431 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 468 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 481 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 ASN M 147 GLN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 40 GLN 7 11 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.057501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039991 restraints weight = 370063.238| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.16 r_work: 0.2716 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 98052 Z= 0.298 Angle : 0.601 12.548 148081 Z= 0.313 Chirality : 0.037 0.285 19096 Planarity : 0.005 0.075 7120 Dihedral : 24.348 179.423 52464 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.77 % Allowed : 28.60 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.16 (0.16), residues: 2846 helix: 1.20 (0.19), residues: 763 sheet: -0.10 (0.21), residues: 629 loop : -0.30 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP V 45 HIS 0.004 0.001 HIS J 11 PHE 0.016 0.002 PHE I 106 TYR 0.016 0.002 TYR Q 47 ARG 0.006 0.000 ARG 6 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17743.77 seconds wall clock time: 313 minutes 54.76 seconds (18834.76 seconds total)