Starting phenix.real_space_refine on Sat Apr 13 20:26:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wic_37563/04_2024/8wic_37563.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wic_37563/04_2024/8wic_37563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wic_37563/04_2024/8wic_37563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wic_37563/04_2024/8wic_37563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wic_37563/04_2024/8wic_37563.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wic_37563/04_2024/8wic_37563.pdb" } resolution = 3.5 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 3215 5.49 5 S 45 5.16 5 C 44640 2.51 5 N 17068 2.21 5 O 26364 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 96": "OE1" <-> "OE2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "M GLU 141": "OE1" <-> "OE2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "O GLU 15": "OE1" <-> "OE2" Residue "O GLU 97": "OE1" <-> "OE2" Residue "O GLU 146": "OE1" <-> "OE2" Residue "Q GLU 38": "OE1" <-> "OE2" Residue "Q GLU 82": "OE1" <-> "OE2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R GLU 67": "OE1" <-> "OE2" Residue "R GLU 98": "OE1" <-> "OE2" Residue "S GLU 63": "OE1" <-> "OE2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S GLU 111": "OE1" <-> "OE2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "T GLU 97": "OE1" <-> "OE2" Residue "U GLU 30": "OE1" <-> "OE2" Residue "U GLU 63": "OE1" <-> "OE2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "V GLU 85": "OE1" <-> "OE2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W GLU 47": "OE1" <-> "OE2" Residue "X GLU 36": "OE1" <-> "OE2" Residue "Z GLU 35": "OE1" <-> "OE2" Residue "2 GLU 63": "OE1" <-> "OE2" Residue "3 GLU 57": "OE1" <-> "OE2" Residue "5 GLU 23": "OE1" <-> "OE2" Residue "8 GLU 34": "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: 91332 Number of models: 1 Model: "" Number of chains: 29 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: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1563 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "G" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1562 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "H" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1428 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 8, 'TRANS': 171} 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: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "R" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 951 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "S" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 899 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "T" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} 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: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 751 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "X" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 706 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 88} 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: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 465 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} 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: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 397 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain: "7" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} 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: 64906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3022, 64906 Classifications: {'RNA': 3022} Modifications used: {'rna2p_pur': 292, 'rna2p_pyr': 147, 'rna3p_pur': 1439, 'rna3p_pyr': 1144} Link IDs: {'rna2p': 439, 'rna3p': 2582} 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} Chain: "C" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1622 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 29, 'rna3p_pyr': 30} Link IDs: {'rna2p': 16, 'rna3p': 59} Time building chain proxies: 36.31, per 1000 atoms: 0.40 Number of scatterers: 91332 At special positions: 0 Unit cell: (222.56, 201.16, 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 45 16.00 P 3215 15.00 O 26364 8.00 N 17068 7.00 C 44640 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: 41.18 Conformation dependent library (CDL) restraints added in 3.6 seconds 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5218 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 43 sheets defined 30.9% alpha, 21.8% beta 1102 base pairs and 1641 stacking pairs defined. Time for finding SS restraints: 35.43 Creating SS restraints... Processing helix chain 'E' and resid 10 through 14 removed outlier: 3.771A 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: 4.343A pdb=" N SER E 202 " --> pdb=" O ALA E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 removed outlier: 3.872A pdb=" N MET E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 226 removed outlier: 3.605A pdb=" N VAL E 225 " --> pdb=" O ARG E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 266 removed outlier: 3.960A 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 63 through 74 Processing helix chain 'F' and resid 88 through 93 Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.618A pdb=" N ILE F 105 " --> pdb=" O THR F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 130 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 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: 3.692A pdb=" N LEU G 183 " --> pdb=" O PRO G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 191 removed outlier: 3.522A pdb=" N ALA G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 210 Processing helix chain 'H' and resid 9 through 28 removed outlier: 3.757A pdb=" N ILE H 19 " --> pdb=" O TYR H 15 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG H 20 " --> pdb=" O ARG H 16 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.997A pdb=" N ILE H 35 " --> pdb=" O VAL H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 52 Processing helix chain 'H' and resid 54 through 69 removed outlier: 3.673A pdb=" N ASN H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 113 Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'I' and resid 59 through 82 removed outlier: 4.397A pdb=" N GLY I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU I 68 " --> pdb=" O SER I 64 " (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 67 through 72 Processing helix chain 'M' and resid 89 through 96 Processing helix chain 'M' and resid 96 through 108 removed outlier: 4.110A pdb=" N VAL M 100 " --> pdb=" O HIS M 96 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL M 101 " --> pdb=" O PRO M 97 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET M 108 " --> pdb=" O ALA M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 120 removed outlier: 3.803A 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: 4.245A 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 5 through 9 removed outlier: 3.894A pdb=" N LEU O 9 " --> pdb=" O LEU O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 61 removed outlier: 3.742A pdb=" N LEU O 61 " --> pdb=" O ILE O 57 " (cutoff:3.500A) 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 removed outlier: 3.551A pdb=" N ALA O 140 " --> pdb=" O ALA O 136 " (cutoff:3.500A) 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: 3.626A pdb=" N LYS Q 57 " --> pdb=" O THR Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 71 removed outlier: 4.080A pdb=" N LYS Q 69 " --> pdb=" O GLU Q 65 " (cutoff:3.500A) removed outlier: 3.628A 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 26 removed outlier: 3.761A 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 96 Processing helix chain 'R' and resid 111 through 123 Processing helix chain 'S' and resid 4 through 12 removed outlier: 4.183A pdb=" N ALA S 10 " --> pdb=" O PHE S 6 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER S 11 " --> pdb=" O VAL S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 55 removed outlier: 3.563A 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 'T' and resid 6 through 21 removed outlier: 4.059A pdb=" N LYS T 13 " --> pdb=" O ASN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.693A pdb=" N ARG T 28 " --> pdb=" O ARG T 25 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER T 29 " --> pdb=" O GLY T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 71 removed outlier: 3.541A pdb=" N ARG T 51 " --> pdb=" O TYR T 47 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS T 54 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 4.482A 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 removed outlier: 3.511A pdb=" N PHE T 106 " --> pdb=" O ASP T 102 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 58 Processing helix chain 'V' and resid 20 through 29 removed outlier: 3.589A 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 69 removed outlier: 3.518A pdb=" N VAL V 54 " --> pdb=" O ALA V 50 " (cutoff:3.500A) 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 6 through 9 removed outlier: 3.839A pdb=" N ASP W 9 " --> pdb=" O ASP W 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 6 through 9' 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: 4.235A 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: 4.069A 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 13 Processing helix chain '8' and resid 37 through 44 Processing helix chain '8' and resid 51 through 64 removed outlier: 4.609A pdb=" N SER 8 56 " --> pdb=" O ALA 8 52 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG 8 57 " --> pdb=" O ALA 8 53 " (cutoff:3.500A) 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: 6.547A pdb=" N ILE E 92 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE E 82 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 6.534A 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: 6.002A pdb=" N LEU E 165 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG E 176 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY E 167 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG E 184 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 5.804A 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: 6.063A 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: 6.640A pdb=" N VAL F 28 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N MET F 13 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL F 26 " --> pdb=" O MET F 13 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLN F 15 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL F 24 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL F 191 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL F 185 " --> pdb=" O VAL F 191 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU F 193 " --> pdb=" O HIS F 183 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS F 181 " --> pdb=" O LYS F 195 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL F 112 " --> pdb=" O ASN F 179 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR F 117 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 7.286A 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: 3.616A pdb=" N ARG F 38 " --> pdb=" O GLN F 51 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA F 53 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 5.806A 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: 3.567A 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 19 removed outlier: 4.089A pdb=" N GLY G 16 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ILE G 124 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP G 6 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA G 126 " --> pdb=" O ASP G 6 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N HIS G 125 " --> pdb=" O PHE G 196 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU G 155 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER G 197 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL G 157 " --> pdb=" O SER G 197 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 73 through 76 removed outlier: 3.625A pdb=" N GLY H 93 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS H 40 " --> pdb=" O VAL H 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 9 through 10 removed outlier: 3.859A pdb=" N VAL I 9 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE I 51 " --> pdb=" O VAL I 9 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER I 42 " --> pdb=" O THR I 54 " (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 122 through 125 Processing sheet with id=AB5, first strand: chain 'I' and resid 96 through 100 removed outlier: 3.531A pdb=" N ARG I 96 " --> pdb=" O ALA I 107 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN I 98 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 18 through 20 removed outlier: 3.573A pdb=" N LEU J 3 " --> pdb=" O VAL J 19 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 122 through 124 removed outlier: 6.111A pdb=" N VAL M 54 " --> pdb=" O LYS M 123 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP M 15 " --> pdb=" O ILE M 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 73 through 77 Processing sheet with id=AB9, first strand: chain 'N' and resid 7 through 10 removed outlier: 6.068A pdb=" N LYS N 17 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA N 16 " --> pdb=" O ALA N 46 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA N 46 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU N 18 " --> pdb=" O LYS N 44 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL N 40 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL N 24 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL N 38 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYS N 59 " --> pdb=" O ILE N 87 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA N 83 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ALA N 84 " --> pdb=" O ARG N 7 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS N 9 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE N 86 " --> pdb=" O LYS N 9 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 69 through 70 removed outlier: 6.469A pdb=" N THR S 57 " --> pdb=" O ARG S 49 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG S 49 " --> pdb=" O THR S 57 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR S 59 " --> pdb=" O ILE S 47 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLU S 63 " --> pdb=" O LYS S 43 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N LYS S 43 " --> pdb=" O GLU S 63 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG S 38 " --> pdb=" O VAL S 31 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR S 24 " --> pdb=" O LEU S 86 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS S 82 " --> pdb=" O HIS S 28 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS S 30 " --> pdb=" O ILE S 80 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE S 80 " --> pdb=" O LYS S 30 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 76 through 79 removed outlier: 5.994A pdb=" N GLN O 76 " --> pdb=" O LYS O 111 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU O 113 " --> pdb=" O GLN O 76 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL O 78 " --> pdb=" O LEU O 113 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 91 through 93 removed outlier: 7.870A pdb=" N THR O 145 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL O 124 " --> pdb=" O THR O 145 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Q' and resid 33 through 37 removed outlier: 4.231A pdb=" N MET Q 110 " --> pdb=" O VAL Q 100 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 58 through 64 removed outlier: 6.073A pdb=" N THR R 59 " --> pdb=" O ASN R 53 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASN R 53 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA R 61 " --> pdb=" O LEU R 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 89 through 90 removed outlier: 4.373A pdb=" N LYS S 110 " --> pdb=" O ASP S 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 12 through 16 removed outlier: 6.954A pdb=" N TYR U 4 " --> pdb=" O VAL U 42 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL U 42 " --> pdb=" O TYR U 4 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE U 6 " --> pdb=" O ALA U 40 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 21 through 25 removed outlier: 6.365A pdb=" N LEU U 94 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N HIS U 67 " --> pdb=" O LEU U 94 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL U 96 " --> pdb=" O LEU U 65 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR U 61 " --> pdb=" O THR U 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 73 through 79 removed outlier: 4.215A pdb=" N TYR U 84 " --> pdb=" O LYS U 79 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 9 through 17 removed outlier: 5.418A pdb=" N SER V 108 " --> pdb=" O TYR V 16 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU V 115 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL V 78 " --> pdb=" O GLU V 115 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 89 through 94 Processing sheet with id=AD3, first strand: chain 'W' and resid 11 through 14 removed outlier: 4.360A pdb=" N LYS W 80 " --> pdb=" O VAL W 33 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'W' and resid 66 through 68 Processing sheet with id=AD5, first strand: chain 'X' and resid 66 through 67 removed outlier: 3.572A pdb=" N VAL X 25 " --> pdb=" O LEU X 34 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N THR X 8 " --> pdb=" O VAL X 74 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL X 73 " --> pdb=" O THR X 81 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 40 through 43 Processing sheet with id=AD7, first strand: chain 'X' and resid 83 through 87 Processing sheet with id=AD8, first strand: chain 'Z' and resid 22 through 23 removed outlier: 6.765A pdb=" N LEU Z 59 " --> pdb=" O LEU Z 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 30 through 31 Processing sheet with id=AE1, first strand: chain '1' and resid 13 through 18 Processing sheet with id=AE2, first strand: chain '1' and resid 33 through 39 Processing sheet with id=AE3, first strand: chain '3' and resid 34 through 38 Processing sheet with id=AE4, first strand: chain '5' and resid 27 through 32 Processing sheet with id=AE5, first strand: chain '6' and resid 21 through 26 removed outlier: 6.959A pdb=" N ARG 6 21 " --> pdb=" O CYS 6 15 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N CYS 6 15 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR 6 47 " --> pdb=" O CYS 6 42 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '8' and resid 14 through 16 Processing sheet with id=AE7, first strand: chain '4' and resid 21 through 26 removed outlier: 6.967A pdb=" N ILE 4 33 " --> pdb=" O ASP 4 11 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR 4 13 " --> pdb=" O ILE 4 33 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2463 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2823 hydrogen bonds 4500 hydrogen bond angles 0 basepair planarities 1102 basepair parallelities 1641 stacking parallelities Total time for adding SS restraints: 183.49 Time building geometry restraints manager: 44.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 12088 1.33 - 1.45: 45191 1.45 - 1.57: 36136 1.57 - 1.70: 6424 1.70 - 1.82: 76 Bond restraints: 99915 Sorted by residual: bond pdb=" CG1 ILE 3 13 " pdb=" CD1 ILE 3 13 " ideal model delta sigma weight residual 1.513 1.384 0.129 3.90e-02 6.57e+02 1.09e+01 bond pdb=" P C B 89 " pdb=" OP2 C B 89 " ideal model delta sigma weight residual 1.485 1.421 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" P C B 89 " pdb=" OP1 C B 89 " ideal model delta sigma weight residual 1.485 1.548 -0.063 2.00e-02 2.50e+03 9.96e+00 bond pdb=" N3 C B 88 " pdb=" C4 C B 88 " ideal model delta sigma weight residual 1.334 1.275 0.059 2.00e-02 2.50e+03 8.69e+00 bond pdb=" C TRP 1 29 " pdb=" N ASN 1 30 " ideal model delta sigma weight residual 1.329 1.283 0.046 1.86e-02 2.89e+03 6.02e+00 ... (remaining 99910 not shown) Histogram of bond angle deviations from ideal: 96.76 - 104.22: 13018 104.22 - 111.68: 55380 111.68 - 119.14: 33578 119.14 - 126.60: 39881 126.60 - 134.06: 9142 Bond angle restraints: 150999 Sorted by residual: angle pdb=" CA PRO 6 50 " pdb=" N PRO 6 50 " pdb=" CD PRO 6 50 " ideal model delta sigma weight residual 112.00 98.52 13.48 1.40e+00 5.10e-01 9.27e+01 angle pdb=" N ILE F 151 " pdb=" CA ILE F 151 " pdb=" C ILE F 151 " ideal model delta sigma weight residual 113.53 106.82 6.71 9.80e-01 1.04e+00 4.69e+01 angle pdb=" C ASP X 88 " pdb=" CA ASP X 88 " pdb=" CB ASP X 88 " ideal model delta sigma weight residual 109.84 117.25 -7.41 1.63e+00 3.76e-01 2.07e+01 angle pdb=" C ALA R 89 " pdb=" N GLU R 90 " pdb=" CA GLU R 90 " ideal model delta sigma weight residual 121.58 113.25 8.33 1.95e+00 2.63e-01 1.82e+01 angle pdb=" CB MET 4 1 " pdb=" CG MET 4 1 " pdb=" SD MET 4 1 " ideal model delta sigma weight residual 112.70 125.38 -12.68 3.00e+00 1.11e-01 1.79e+01 ... (remaining 150994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 55664 35.88 - 71.75: 7816 71.75 - 107.63: 898 107.63 - 143.51: 24 143.51 - 179.38: 32 Dihedral angle restraints: 64434 sinusoidal: 56298 harmonic: 8136 Sorted by residual: 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 17.63 -177.63 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1535 " pdb=" C1' C A1535 " pdb=" N1 C A1535 " pdb=" C2 C A1535 " ideal model delta sinusoidal sigma weight residual -160.00 16.73 -176.73 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A 139 " pdb=" C1' U A 139 " pdb=" N1 U A 139 " pdb=" C2 U A 139 " ideal model delta sinusoidal sigma weight residual 200.00 31.27 168.73 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 64431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 17053 0.055 - 0.109: 2074 0.109 - 0.164: 295 0.164 - 0.218: 54 0.218 - 0.273: 15 Chirality restraints: 19491 Sorted by residual: 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 2.19 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C1' G A1434 " pdb=" O4' G A1434 " pdb=" C2' G A1434 " pdb=" N9 G A1434 " both_signs ideal model delta sigma weight residual False 2.46 2.19 0.27 2.00e-01 2.50e+01 1.77e+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 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 19488 not shown) Planarity restraints: 7187 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN 6 49 " 0.116 5.00e-02 4.00e+02 1.63e-01 4.27e+01 pdb=" N PRO 6 50 " -0.282 5.00e-02 4.00e+02 pdb=" CA PRO 6 50 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO 6 50 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C B 88 " -0.055 2.00e-02 2.50e+03 2.89e-02 1.89e+01 pdb=" N1 C B 88 " -0.003 2.00e-02 2.50e+03 pdb=" C2 C B 88 " 0.026 2.00e-02 2.50e+03 pdb=" O2 C B 88 " 0.016 2.00e-02 2.50e+03 pdb=" N3 C B 88 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C B 88 " -0.013 2.00e-02 2.50e+03 pdb=" N4 C B 88 " -0.034 2.00e-02 2.50e+03 pdb=" C5 C B 88 " 0.014 2.00e-02 2.50e+03 pdb=" C6 C B 88 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1434 " -0.047 2.00e-02 2.50e+03 2.06e-02 1.27e+01 pdb=" N9 G A1434 " 0.050 2.00e-02 2.50e+03 pdb=" C8 G A1434 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G A1434 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A1434 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G A1434 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G A1434 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G A1434 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G A1434 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G A1434 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G A1434 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G A1434 " 0.008 2.00e-02 2.50e+03 ... (remaining 7184 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 1537 2.59 - 3.16: 70815 3.16 - 3.74: 183381 3.74 - 4.32: 252071 4.32 - 4.90: 338917 Nonbonded interactions: 846721 Sorted by model distance: nonbonded pdb=" O2 U A 329 " pdb=" O6 G A 446 " model vdw 2.008 2.432 nonbonded pdb=" OP1 U A2386 " pdb=" O2' A A2393 " model vdw 2.014 2.440 nonbonded pdb=" OP1 A A2674 " pdb=" O2' A A2721 " model vdw 2.036 2.440 nonbonded pdb=" O4 U A1540 " pdb=" O6 G A1632 " model vdw 2.050 2.432 nonbonded pdb=" OP2 G A 499 " pdb=" O2' A A2630 " model vdw 2.077 2.440 ... (remaining 846716 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 14.170 Check model and map are aligned: 1.030 Set scattering table: 0.650 Process input model: 361.510 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:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 384.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 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 : 0.006 0.129 99915 Z= 0.358 Angle : 0.651 13.476 150999 Z= 0.336 Chirality : 0.038 0.273 19491 Planarity : 0.006 0.163 7187 Dihedral : 24.414 179.384 59216 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.81 % Allowed : 26.45 % Favored : 72.74 % 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: -0.03 (0.16), residues: 2832 helix: 0.75 (0.18), residues: 789 sheet: -0.10 (0.20), residues: 651 loop : -0.32 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 1 29 HIS 0.008 0.002 HIS 7 19 PHE 0.018 0.002 PHE 6 41 TYR 0.025 0.002 TYR J 25 ARG 0.018 0.001 ARG J 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 255 time to evaluate : 3.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 138 ASP cc_start: 0.8256 (t0) cc_final: 0.7925 (t70) REVERT: M 49 ASP cc_start: 0.7769 (p0) cc_final: 0.7113 (p0) REVERT: M 138 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9182 (tp) REVERT: O 97 GLU cc_start: 0.8499 (mp0) cc_final: 0.8221 (mm-30) REVERT: T 59 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8772 (ttmm) outliers start: 19 outliers final: 7 residues processed: 268 average time/residue: 0.8192 time to fit residues: 384.0857 Evaluate side-chains 242 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 233 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain 1 residue 60 LYS Chi-restraints excluded: chain 1 residue 61 VAL Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 37 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 504 optimal weight: 30.0000 chunk 452 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 305 optimal weight: 40.0000 chunk 241 optimal weight: 9.9990 chunk 467 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 284 optimal weight: 10.0000 chunk 348 optimal weight: 10.0000 chunk 542 optimal weight: 30.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN G 151 ASN N 89 ASN R 8 GLN S 2 ASN W 63 GLN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 44 ASN 4 6 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 99915 Z= 0.424 Angle : 0.642 8.628 150999 Z= 0.329 Chirality : 0.039 0.318 19491 Planarity : 0.005 0.081 7187 Dihedral : 24.359 179.764 53690 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.10 % Allowed : 23.12 % Favored : 72.78 % 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: -0.03 (0.15), residues: 2832 helix: 0.94 (0.19), residues: 773 sheet: -0.23 (0.21), residues: 627 loop : -0.36 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 206 HIS 0.008 0.001 HIS 7 19 PHE 0.013 0.002 PHE S 73 TYR 0.014 0.002 TYR Q 47 ARG 0.012 0.001 ARG H 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 233 time to evaluate : 3.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 96 GLU cc_start: 0.8260 (pp20) cc_final: 0.8008 (pp20) REVERT: F 170 MET cc_start: 0.9119 (ttp) cc_final: 0.8883 (ttt) REVERT: G 13 LYS cc_start: 0.9030 (pptt) cc_final: 0.8776 (pptt) REVERT: M 49 ASP cc_start: 0.7995 (p0) cc_final: 0.7342 (p0) REVERT: R 24 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.8927 (ptp-170) REVERT: T 56 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7445 (mm-30) REVERT: V 97 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8822 (mt0) REVERT: W 48 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8891 (tptm) REVERT: X 7 ASP cc_start: 0.8215 (m-30) cc_final: 0.7901 (m-30) REVERT: Z 79 ASN cc_start: 0.9157 (OUTLIER) cc_final: 0.8955 (m-40) REVERT: 1 60 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6902 (tppt) REVERT: 2 53 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7770 (mm-30) REVERT: 8 19 THR cc_start: 0.9247 (p) cc_final: 0.8925 (t) REVERT: 8 30 ARG cc_start: 0.9549 (OUTLIER) cc_final: 0.8718 (mpt180) REVERT: 4 22 PHE cc_start: 0.4312 (OUTLIER) cc_final: 0.3923 (t80) outliers start: 96 outliers final: 42 residues processed: 314 average time/residue: 0.8857 time to fit residues: 486.3662 Evaluate side-chains 265 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 216 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain H residue 45 MET Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 54 HIS Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 97 GLN Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain Z residue 83 VAL Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 1 residue 60 LYS Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 20 HIS Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 6 residue 54 SER Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 8 residue 30 ARG Chi-restraints excluded: chain 4 residue 22 PHE Chi-restraints excluded: chain 4 residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 301 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 451 optimal weight: 10.0000 chunk 369 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 543 optimal weight: 20.0000 chunk 586 optimal weight: 20.0000 chunk 483 optimal weight: 10.0000 chunk 538 optimal weight: 50.0000 chunk 185 optimal weight: 5.9990 chunk 435 optimal weight: 10.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN ** Z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 99915 Z= 0.384 Angle : 0.618 9.233 150999 Z= 0.317 Chirality : 0.038 0.309 19491 Planarity : 0.005 0.063 7187 Dihedral : 24.319 179.788 53681 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.74 % Allowed : 22.70 % Favored : 72.57 % 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: -0.01 (0.16), residues: 2832 helix: 1.08 (0.19), residues: 773 sheet: -0.29 (0.21), residues: 628 loop : -0.40 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 45 HIS 0.006 0.001 HIS 7 19 PHE 0.015 0.002 PHE S 73 TYR 0.015 0.002 TYR Q 47 ARG 0.006 0.001 ARG I 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 234 time to evaluate : 3.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 96 GLU cc_start: 0.8295 (pp20) cc_final: 0.7978 (pp20) REVERT: F 170 MET cc_start: 0.9126 (ttt) cc_final: 0.8825 (ttt) REVERT: G 3 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8544 (tt) REVERT: H 90 MET cc_start: 0.8642 (ptt) cc_final: 0.8411 (ptt) REVERT: I 59 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6709 (pp20) REVERT: I 116 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7632 (mm) REVERT: J 37 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.8016 (pt) REVERT: M 49 ASP cc_start: 0.8118 (p0) cc_final: 0.7431 (p0) REVERT: O 15 GLU cc_start: 0.8207 (tt0) cc_final: 0.7866 (tt0) REVERT: O 96 ASP cc_start: 0.8659 (p0) cc_final: 0.8007 (p0) REVERT: O 97 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8202 (mm-30) REVERT: T 56 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7452 (mm-30) REVERT: T 59 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8615 (ttmm) REVERT: U 53 ASP cc_start: 0.8246 (p0) cc_final: 0.7857 (p0) REVERT: U 57 LYS cc_start: 0.8762 (mtmm) cc_final: 0.8449 (mttp) REVERT: W 48 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8874 (tptm) REVERT: W 70 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6550 (ptt90) REVERT: X 7 ASP cc_start: 0.8260 (m-30) cc_final: 0.7869 (m-30) REVERT: 1 60 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.6976 (tppt) REVERT: 2 16 ASP cc_start: 0.8051 (p0) cc_final: 0.7758 (p0) REVERT: 5 6 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8422 (mtt-85) REVERT: 6 20 HIS cc_start: 0.5758 (OUTLIER) cc_final: 0.5245 (m-70) REVERT: 7 14 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.9038 (ttm-80) REVERT: 4 1 MET cc_start: 0.4776 (tpt) cc_final: 0.4430 (tpt) REVERT: 4 13 THR cc_start: 0.7903 (m) cc_final: 0.7641 (p) REVERT: 4 22 PHE cc_start: 0.4846 (OUTLIER) cc_final: 0.4364 (t80) REVERT: 4 25 ARG cc_start: 0.5474 (OUTLIER) cc_final: 0.4886 (tpp80) outliers start: 111 outliers final: 54 residues processed: 327 average time/residue: 0.8680 time to fit residues: 487.9993 Evaluate side-chains 288 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 222 time to evaluate : 3.695 ------------------------------------------------------------------------------- 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 201 GLN Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 45 MET Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 142 GLN Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 54 HIS Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 83 VAL Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 1 residue 60 LYS Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 6 ARG Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 15 CYS Chi-restraints excluded: chain 6 residue 20 HIS Chi-restraints excluded: chain 6 residue 25 THR Chi-restraints excluded: chain 6 residue 30 ARG Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 4 residue 22 PHE Chi-restraints excluded: chain 4 residue 25 ARG Chi-restraints excluded: chain 4 residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 536 optimal weight: 70.0000 chunk 408 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 364 optimal weight: 10.0000 chunk 545 optimal weight: 10.0000 chunk 577 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 516 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 overall best weight: 8.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 142 GLN N 89 ASN R 3 HIS ** Z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 46 HIS ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 99915 Z= 0.410 Angle : 0.634 8.432 150999 Z= 0.325 Chirality : 0.039 0.315 19491 Planarity : 0.005 0.063 7187 Dihedral : 24.299 179.496 53681 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.61 % Allowed : 22.74 % Favored : 72.65 % 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: -0.09 (0.16), residues: 2832 helix: 1.03 (0.19), residues: 785 sheet: -0.26 (0.21), residues: 626 loop : -0.51 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 206 HIS 0.007 0.001 HIS J 11 PHE 0.014 0.002 PHE S 73 TYR 0.014 0.001 TYR Q 47 ARG 0.009 0.001 ARG 2 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 229 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7702 (ptt90) REVERT: F 96 GLU cc_start: 0.8238 (pp20) cc_final: 0.8021 (pp20) REVERT: G 3 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8182 (tt) REVERT: H 90 MET cc_start: 0.8955 (ptt) cc_final: 0.8660 (ptt) REVERT: H 153 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7618 (pt) REVERT: I 59 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7172 (pp20) REVERT: I 116 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7567 (mm) REVERT: M 49 ASP cc_start: 0.8193 (p0) cc_final: 0.7476 (p0) REVERT: O 15 GLU cc_start: 0.8276 (tt0) cc_final: 0.7927 (tt0) REVERT: O 96 ASP cc_start: 0.8710 (p0) cc_final: 0.8019 (p0) REVERT: O 97 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8278 (mm-30) REVERT: S 48 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8993 (ptt180) REVERT: T 56 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7522 (mm-30) REVERT: T 59 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8626 (ttmm) REVERT: U 53 ASP cc_start: 0.8264 (p0) cc_final: 0.7837 (p0) REVERT: U 57 LYS cc_start: 0.8748 (mtmm) cc_final: 0.8382 (mttp) REVERT: V 97 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8843 (mt0) REVERT: W 70 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6563 (ptt90) REVERT: X 7 ASP cc_start: 0.8232 (m-30) cc_final: 0.7790 (m-30) REVERT: 2 16 ASP cc_start: 0.8175 (p0) cc_final: 0.7956 (p0) REVERT: 2 21 LYS cc_start: 0.9493 (OUTLIER) cc_final: 0.9237 (ttmm) REVERT: 2 53 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7535 (mm-30) REVERT: 3 44 ARG cc_start: 0.8681 (mmm-85) cc_final: 0.8400 (mmm-85) REVERT: 5 6 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8452 (mtt-85) REVERT: 6 20 HIS cc_start: 0.6101 (OUTLIER) cc_final: 0.5304 (m-70) REVERT: 6 53 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7192 (tp30) REVERT: 7 14 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.9018 (ttm-80) REVERT: 8 29 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.7439 (ttp80) REVERT: 4 22 PHE cc_start: 0.5048 (OUTLIER) cc_final: 0.4803 (t80) outliers start: 108 outliers final: 60 residues processed: 320 average time/residue: 0.8738 time to fit residues: 484.6859 Evaluate side-chains 291 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 217 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 201 GLN Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain H residue 45 MET Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 142 GLN Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 54 HIS Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain U residue 44 ASP Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 97 GLN Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 40 ARG Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 83 VAL Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 5 residue 6 ARG Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 15 CYS Chi-restraints excluded: chain 6 residue 20 HIS Chi-restraints excluded: chain 6 residue 25 THR Chi-restraints excluded: chain 6 residue 30 ARG Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 19 THR Chi-restraints excluded: chain 8 residue 28 ASN Chi-restraints excluded: chain 8 residue 29 ARG Chi-restraints excluded: chain 4 residue 22 PHE Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 37 VAL Chi-restraints excluded: chain 4 residue 38 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 480 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 429 optimal weight: 50.0000 chunk 238 optimal weight: 9.9990 chunk 492 optimal weight: 10.0000 chunk 398 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 517 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 overall best weight: 7.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 ASN N 4 GLN N 89 ASN ** Z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 99915 Z= 0.364 Angle : 0.606 8.451 150999 Z= 0.311 Chirality : 0.037 0.316 19491 Planarity : 0.005 0.060 7187 Dihedral : 24.281 179.917 53677 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.99 % Allowed : 23.04 % Favored : 71.97 % 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: -0.07 (0.16), residues: 2832 helix: 1.09 (0.19), residues: 786 sheet: -0.30 (0.21), residues: 641 loop : -0.50 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 206 HIS 0.006 0.001 HIS J 11 PHE 0.014 0.001 PHE S 73 TYR 0.016 0.001 TYR Q 47 ARG 0.011 0.000 ARG 2 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 235 time to evaluate : 3.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 158 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8847 (t) REVERT: F 60 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7721 (ptt90) REVERT: G 3 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8291 (tt) REVERT: H 24 GLN cc_start: 0.9390 (tp40) cc_final: 0.9082 (tp40) REVERT: H 90 MET cc_start: 0.8997 (ptt) cc_final: 0.8687 (ptt) REVERT: I 59 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7402 (pp20) REVERT: I 86 GLN cc_start: 0.8335 (tp40) cc_final: 0.7717 (tp40) REVERT: M 49 ASP cc_start: 0.8233 (p0) cc_final: 0.7485 (p0) REVERT: O 15 GLU cc_start: 0.8281 (tt0) cc_final: 0.7918 (tt0) REVERT: R 12 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7906 (mp0) REVERT: S 48 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8970 (ptt180) REVERT: T 56 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7515 (mm-30) REVERT: T 59 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8594 (ttmm) REVERT: U 30 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8156 (mp0) REVERT: U 53 ASP cc_start: 0.8295 (p0) cc_final: 0.7799 (p0) REVERT: U 57 LYS cc_start: 0.8694 (mtmm) cc_final: 0.8290 (mttp) REVERT: V 97 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8821 (mt0) REVERT: W 70 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6458 (ptt90) REVERT: X 7 ASP cc_start: 0.8227 (m-30) cc_final: 0.7764 (m-30) REVERT: 3 5 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8697 (tptt) REVERT: 5 6 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8460 (mtt-85) REVERT: 7 14 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8979 (ttm-80) REVERT: 8 29 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.7410 (ttp80) outliers start: 117 outliers final: 69 residues processed: 329 average time/residue: 0.8695 time to fit residues: 492.3052 Evaluate side-chains 306 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 226 time to evaluate : 3.680 ------------------------------------------------------------------------------- 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 158 SER Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 45 MET Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 54 HIS Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain U residue 44 ASP Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 97 GLN Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain Z residue 83 VAL Chi-restraints excluded: chain 1 residue 61 VAL Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 3 residue 5 LYS Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 5 residue 6 ARG Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 15 CYS Chi-restraints excluded: chain 6 residue 25 THR Chi-restraints excluded: chain 6 residue 30 ARG Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 19 THR Chi-restraints excluded: chain 8 residue 29 ARG Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 38 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 194 optimal weight: 3.9990 chunk 519 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 338 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 577 optimal weight: 10.0000 chunk 479 optimal weight: 10.0000 chunk 267 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 89 ASN S 28 HIS Z 12 ASN 1 47 GLN ** 4 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 99915 Z= 0.359 Angle : 0.609 10.252 150999 Z= 0.313 Chirality : 0.037 0.320 19491 Planarity : 0.005 0.060 7187 Dihedral : 24.272 179.664 53677 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.86 % Allowed : 23.51 % Favored : 71.63 % 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: -0.14 (0.16), residues: 2832 helix: 1.09 (0.19), residues: 783 sheet: -0.31 (0.21), residues: 631 loop : -0.60 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 206 HIS 0.005 0.001 HIS Q 77 PHE 0.014 0.002 PHE S 73 TYR 0.015 0.001 TYR Q 47 ARG 0.009 0.000 ARG 2 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 231 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 37 THR cc_start: 0.9586 (OUTLIER) cc_final: 0.9235 (t) REVERT: F 60 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7754 (ptt90) REVERT: G 3 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.7859 (tt) REVERT: G 13 LYS cc_start: 0.8951 (pptt) cc_final: 0.8715 (pptt) REVERT: G 50 HIS cc_start: 0.9573 (OUTLIER) cc_final: 0.8934 (p90) REVERT: H 24 GLN cc_start: 0.9383 (tp40) cc_final: 0.9078 (tp40) REVERT: H 90 MET cc_start: 0.9068 (ptt) cc_final: 0.8800 (ptt) REVERT: I 59 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7664 (pp20) REVERT: M 49 ASP cc_start: 0.8203 (p0) cc_final: 0.7423 (p0) REVERT: O 96 ASP cc_start: 0.8709 (p0) cc_final: 0.8055 (p0) REVERT: O 97 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8178 (mm-30) REVERT: S 48 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8972 (ptt180) REVERT: T 56 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7510 (mm-30) REVERT: T 59 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8613 (ttmm) REVERT: U 30 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8207 (mp0) REVERT: U 53 ASP cc_start: 0.8294 (p0) cc_final: 0.7857 (p0) REVERT: U 57 LYS cc_start: 0.8665 (mtmm) cc_final: 0.8355 (mtmm) REVERT: V 97 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8839 (mt0) REVERT: W 70 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6494 (ptt90) REVERT: X 7 ASP cc_start: 0.8236 (m-30) cc_final: 0.7906 (m-30) REVERT: 3 5 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8209 (tptm) REVERT: 5 6 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8467 (mtt-85) REVERT: 6 20 HIS cc_start: 0.6177 (OUTLIER) cc_final: 0.5704 (m-70) REVERT: 7 14 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8997 (ttm-80) REVERT: 8 29 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.8868 (ttp80) outliers start: 114 outliers final: 79 residues processed: 324 average time/residue: 0.8891 time to fit residues: 508.6761 Evaluate side-chains 313 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 221 time to evaluate : 3.684 ------------------------------------------------------------------------------- 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 201 GLN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 192 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 45 MET Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 54 HIS Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 44 ASP Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 97 GLN Chi-restraints excluded: chain W residue 36 ASP Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain Z residue 83 VAL Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 3 residue 5 LYS Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 5 residue 6 ARG Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 20 HIS Chi-restraints excluded: chain 6 residue 25 THR Chi-restraints excluded: chain 6 residue 30 ARG Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 19 THR Chi-restraints excluded: chain 8 residue 28 ASN Chi-restraints excluded: chain 8 residue 29 ARG Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 38 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 556 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 329 optimal weight: 10.0000 chunk 421 optimal weight: 10.0000 chunk 326 optimal weight: 10.0000 chunk 486 optimal weight: 10.0000 chunk 322 optimal weight: 20.0000 chunk 575 optimal weight: 10.0000 chunk 360 optimal weight: 20.0000 chunk 350 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 overall best weight: 9.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN N 89 ASN R 3 HIS ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 99915 Z= 0.444 Angle : 0.652 9.386 150999 Z= 0.334 Chirality : 0.040 0.319 19491 Planarity : 0.005 0.065 7187 Dihedral : 24.293 179.921 53677 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.25 % Allowed : 23.55 % Favored : 71.20 % 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: -0.20 (0.16), residues: 2832 helix: 1.04 (0.19), residues: 777 sheet: -0.34 (0.21), residues: 611 loop : -0.63 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 45 HIS 0.006 0.001 HIS R 3 PHE 0.014 0.002 PHE S 73 TYR 0.016 0.002 TYR Q 47 ARG 0.014 0.001 ARG 2 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 234 time to evaluate : 3.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 37 THR cc_start: 0.9593 (OUTLIER) cc_final: 0.9289 (t) REVERT: F 60 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7730 (ptt180) REVERT: G 13 LYS cc_start: 0.9076 (pptt) cc_final: 0.8751 (pptt) REVERT: G 50 HIS cc_start: 0.9591 (OUTLIER) cc_final: 0.8899 (p90) REVERT: H 90 MET cc_start: 0.9141 (ptt) cc_final: 0.8905 (ptt) REVERT: I 59 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7759 (pp20) REVERT: O 96 ASP cc_start: 0.8736 (p0) cc_final: 0.8127 (p0) REVERT: O 97 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8159 (mm-30) REVERT: R 12 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7985 (mp0) REVERT: S 48 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.9010 (ptt180) REVERT: T 59 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8601 (ttmm) REVERT: U 30 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8197 (mp0) REVERT: U 53 ASP cc_start: 0.8350 (p0) cc_final: 0.7846 (p0) REVERT: U 57 LYS cc_start: 0.8745 (mtmm) cc_final: 0.8346 (mttp) REVERT: V 97 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8847 (mt0) REVERT: W 70 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6642 (ptt90) REVERT: X 7 ASP cc_start: 0.8261 (m-30) cc_final: 0.7929 (m-30) REVERT: 2 21 LYS cc_start: 0.9543 (OUTLIER) cc_final: 0.9299 (ttmm) REVERT: 3 5 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8270 (tptm) REVERT: 5 6 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8481 (mtt-85) REVERT: 6 20 HIS cc_start: 0.6358 (OUTLIER) cc_final: 0.5591 (m-70) REVERT: 7 14 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.9010 (ttm-80) REVERT: 8 29 ARG cc_start: 0.9312 (OUTLIER) cc_final: 0.7538 (ttp80) outliers start: 123 outliers final: 85 residues processed: 337 average time/residue: 0.8423 time to fit residues: 498.5725 Evaluate side-chains 327 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 229 time to evaluate : 3.654 ------------------------------------------------------------------------------- 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 131 LEU Chi-restraints excluded: chain E residue 201 GLN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 192 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 45 MET Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 34 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 54 HIS Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 97 GLN Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain Z residue 83 VAL Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 3 residue 5 LYS Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 34 SER Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 5 residue 6 ARG Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 20 HIS Chi-restraints excluded: chain 6 residue 25 THR Chi-restraints excluded: chain 6 residue 30 ARG Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 19 THR Chi-restraints excluded: chain 8 residue 28 ASN Chi-restraints excluded: chain 8 residue 29 ARG Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 38 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 355 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 chunk 343 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 392 optimal weight: 40.0000 chunk 284 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 452 optimal weight: 10.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 89 ASN 1 47 GLN ** 4 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 99915 Z= 0.286 Angle : 0.577 9.776 150999 Z= 0.296 Chirality : 0.035 0.321 19491 Planarity : 0.004 0.063 7187 Dihedral : 24.268 179.894 53674 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.75 % Allowed : 24.96 % Favored : 71.29 % 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: 0.00 (0.16), residues: 2832 helix: 1.22 (0.19), residues: 780 sheet: -0.23 (0.21), residues: 638 loop : -0.51 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 45 HIS 0.006 0.001 HIS Q 77 PHE 0.013 0.001 PHE S 73 TYR 0.016 0.001 TYR Q 47 ARG 0.014 0.000 ARG 2 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 232 time to evaluate : 3.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 GLN cc_start: 0.8981 (tt0) cc_final: 0.8682 (tt0) REVERT: G 13 LYS cc_start: 0.9060 (pptt) cc_final: 0.8763 (pptt) REVERT: G 50 HIS cc_start: 0.9574 (OUTLIER) cc_final: 0.8866 (p90) REVERT: H 24 GLN cc_start: 0.9443 (tp40) cc_final: 0.9143 (tp40) REVERT: H 90 MET cc_start: 0.9122 (ptt) cc_final: 0.8871 (ptt) REVERT: I 59 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7792 (pp20) REVERT: I 86 GLN cc_start: 0.8564 (tp40) cc_final: 0.8276 (tp40) REVERT: O 96 ASP cc_start: 0.8699 (p0) cc_final: 0.8264 (p0) REVERT: O 97 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8184 (mm-30) REVERT: R 12 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7937 (mp0) REVERT: S 48 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8946 (ptt180) REVERT: S 110 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8762 (ttpp) REVERT: U 30 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8191 (mp0) REVERT: U 53 ASP cc_start: 0.8262 (p0) cc_final: 0.7931 (p0) REVERT: U 57 LYS cc_start: 0.8719 (mtmm) cc_final: 0.8494 (mtmm) REVERT: V 97 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8793 (mt0) REVERT: W 70 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6471 (ptt90) REVERT: X 7 ASP cc_start: 0.8193 (m-30) cc_final: 0.7879 (m-30) REVERT: 5 6 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8521 (mtt-85) REVERT: 7 14 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8968 (ttm-80) REVERT: 8 29 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8856 (ttp80) outliers start: 88 outliers final: 72 residues processed: 304 average time/residue: 0.8385 time to fit residues: 445.5665 Evaluate side-chains 307 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 227 time to evaluate : 3.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 201 GLN Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 192 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 45 MET Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 54 HIS Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain S residue 110 LYS Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain U residue 44 ASP Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 97 GLN Chi-restraints excluded: chain W residue 36 ASP Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 5 residue 6 ARG Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 25 THR Chi-restraints excluded: chain 6 residue 30 ARG Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 19 THR Chi-restraints excluded: chain 8 residue 28 ASN Chi-restraints excluded: chain 8 residue 29 ARG Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 38 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 523 optimal weight: 10.0000 chunk 551 optimal weight: 10.0000 chunk 502 optimal weight: 50.0000 chunk 536 optimal weight: 60.0000 chunk 322 optimal weight: 20.0000 chunk 233 optimal weight: 6.9990 chunk 421 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 484 optimal weight: 10.0000 chunk 507 optimal weight: 40.0000 chunk 534 optimal weight: 20.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 89 ASN ** 4 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 99915 Z= 0.422 Angle : 0.639 9.518 150999 Z= 0.327 Chirality : 0.039 0.320 19491 Planarity : 0.005 0.062 7187 Dihedral : 24.279 179.876 53674 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.31 % Allowed : 24.66 % Favored : 71.03 % 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: -0.14 (0.16), residues: 2832 helix: 1.10 (0.19), residues: 783 sheet: -0.35 (0.20), residues: 656 loop : -0.58 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 45 HIS 0.006 0.001 HIS Q 77 PHE 0.014 0.002 PHE S 73 TYR 0.017 0.001 TYR Q 47 ARG 0.013 0.001 ARG 2 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 229 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 37 THR cc_start: 0.9593 (OUTLIER) cc_final: 0.9289 (t) REVERT: F 60 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7707 (ptt90) REVERT: G 13 LYS cc_start: 0.9057 (pptt) cc_final: 0.8741 (pptt) REVERT: G 50 HIS cc_start: 0.9595 (OUTLIER) cc_final: 0.8930 (p90) REVERT: H 24 GLN cc_start: 0.9471 (tp40) cc_final: 0.9175 (tp40) REVERT: H 90 MET cc_start: 0.9164 (ptt) cc_final: 0.8931 (ptt) REVERT: I 59 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7916 (pp20) REVERT: I 86 GLN cc_start: 0.8572 (tp40) cc_final: 0.8279 (tp40) REVERT: O 96 ASP cc_start: 0.8730 (p0) cc_final: 0.8308 (p0) REVERT: O 97 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8222 (mm-30) REVERT: R 12 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8007 (mp0) REVERT: S 48 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8997 (ptt180) REVERT: T 59 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8599 (ttmm) REVERT: U 30 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8189 (mp0) REVERT: U 53 ASP cc_start: 0.8331 (p0) cc_final: 0.8010 (p0) REVERT: U 57 LYS cc_start: 0.8731 (mtmm) cc_final: 0.8478 (mtmm) REVERT: V 97 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8843 (mt0) REVERT: W 70 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6564 (ptt90) REVERT: X 7 ASP cc_start: 0.8319 (m-30) cc_final: 0.7960 (m-30) REVERT: 5 6 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8486 (mtt-85) REVERT: 6 20 HIS cc_start: 0.5930 (OUTLIER) cc_final: 0.5423 (m-70) REVERT: 7 14 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.9005 (ttm-80) REVERT: 8 29 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.7535 (ttp80) REVERT: 4 1 MET cc_start: 0.8463 (tpp) cc_final: 0.8157 (tpp) outliers start: 101 outliers final: 83 residues processed: 316 average time/residue: 0.8388 time to fit residues: 461.1369 Evaluate side-chains 320 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 226 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 201 GLN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 192 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 45 MET Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 54 HIS Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain U residue 44 ASP Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 97 GLN Chi-restraints excluded: chain W residue 36 ASP Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain 1 residue 53 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 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 5 residue 6 ARG Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 20 HIS Chi-restraints excluded: chain 6 residue 25 THR Chi-restraints excluded: chain 6 residue 30 ARG Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 19 THR Chi-restraints excluded: chain 8 residue 28 ASN Chi-restraints excluded: chain 8 residue 29 ARG Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 38 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 352 optimal weight: 20.0000 chunk 567 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 268 optimal weight: 6.9990 chunk 394 optimal weight: 50.0000 chunk 594 optimal weight: 40.0000 chunk 547 optimal weight: 20.0000 chunk 473 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 365 optimal weight: 10.0000 chunk 290 optimal weight: 10.0000 overall best weight: 8.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 89 ASN R 41 ASN ** 4 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 99915 Z= 0.402 Angle : 0.628 9.199 150999 Z= 0.322 Chirality : 0.038 0.317 19491 Planarity : 0.005 0.062 7187 Dihedral : 24.277 179.982 53674 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.18 % Allowed : 24.83 % Favored : 70.99 % 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: 2832 helix: 1.09 (0.19), residues: 777 sheet: -0.38 (0.20), residues: 656 loop : -0.56 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 45 HIS 0.006 0.001 HIS Q 77 PHE 0.014 0.002 PHE S 73 TYR 0.016 0.001 TYR Q 47 ARG 0.015 0.001 ARG 2 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 233 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 37 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9289 (t) REVERT: F 60 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7709 (ptt90) REVERT: G 13 LYS cc_start: 0.9064 (pptt) cc_final: 0.8739 (pptt) REVERT: G 50 HIS cc_start: 0.9578 (OUTLIER) cc_final: 0.8866 (p90) REVERT: H 24 GLN cc_start: 0.9470 (tp40) cc_final: 0.9175 (tp40) REVERT: H 90 MET cc_start: 0.9168 (ptt) cc_final: 0.8940 (ptt) REVERT: I 59 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8081 (pp20) REVERT: I 86 GLN cc_start: 0.8565 (tp40) cc_final: 0.8242 (tp-100) REVERT: O 96 ASP cc_start: 0.8718 (p0) cc_final: 0.8276 (p0) REVERT: O 97 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8211 (mm-30) REVERT: R 12 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8013 (mp0) REVERT: S 48 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8983 (ptt180) REVERT: T 59 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8593 (ttmm) REVERT: U 30 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8192 (mp0) REVERT: U 53 ASP cc_start: 0.8319 (p0) cc_final: 0.8011 (p0) REVERT: U 57 LYS cc_start: 0.8663 (mtmm) cc_final: 0.8435 (mtmm) REVERT: V 97 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8827 (mt0) REVERT: W 70 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6583 (ptt90) REVERT: 5 6 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8482 (mtt-85) REVERT: 7 14 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.9012 (ttm-80) REVERT: 8 29 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.7595 (ttp80) outliers start: 98 outliers final: 81 residues processed: 315 average time/residue: 0.8542 time to fit residues: 466.1740 Evaluate side-chains 320 residues out of total 2344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 229 time to evaluate : 4.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 201 GLN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 192 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 45 MET Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 54 HIS Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain U residue 44 ASP Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 97 GLN Chi-restraints excluded: chain W residue 36 ASP Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 34 SER Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 5 residue 6 ARG Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 25 THR Chi-restraints excluded: chain 6 residue 30 ARG Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 19 THR Chi-restraints excluded: chain 8 residue 28 ASN Chi-restraints excluded: chain 8 residue 29 ARG Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 38 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 376 optimal weight: 50.0000 chunk 504 optimal weight: 40.0000 chunk 145 optimal weight: 5.9990 chunk 436 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 474 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 487 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 87 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 89 ASN R 41 ASN ** 4 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.043906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.030554 restraints weight = 572733.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.031158 restraints weight = 303565.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.031106 restraints weight = 178389.524| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 99915 Z= 0.292 Angle : 0.583 9.644 150999 Z= 0.299 Chirality : 0.035 0.317 19491 Planarity : 0.004 0.056 7187 Dihedral : 24.250 179.759 53674 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.01 % Allowed : 25.13 % Favored : 70.86 % 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: -0.02 (0.16), residues: 2832 helix: 1.20 (0.19), residues: 780 sheet: -0.32 (0.20), residues: 652 loop : -0.48 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 45 HIS 0.006 0.001 HIS Q 77 PHE 0.014 0.001 PHE S 73 TYR 0.016 0.001 TYR Q 47 ARG 0.013 0.000 ARG 2 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10324.76 seconds wall clock time: 188 minutes 42.55 seconds (11322.55 seconds total)