Starting phenix.real_space_refine on Mon Apr 15 06:35:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wib_37562/04_2024/8wib_37562.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wib_37562/04_2024/8wib_37562.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/8wib_37562/04_2024/8wib_37562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wib_37562/04_2024/8wib_37562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wib_37562/04_2024/8wib_37562.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wib_37562/04_2024/8wib_37562.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= 0.003 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4730 5.49 5 S 78 5.16 5 C 70595 2.51 5 N 26636 2.21 5 O 40208 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" Residue "f GLU 91": "OE1" <-> "OE2" Residue "g GLU 57": "OE1" <-> "OE2" Residue "g GLU 68": "OE1" <-> "OE2" Residue "g GLU 74": "OE1" <-> "OE2" Residue "h GLU 40": "OE1" <-> "OE2" Residue "h GLU 118": "OE1" <-> "OE2" Residue "h GLU 139": "OE1" <-> "OE2" Residue "i GLU 43": "OE1" <-> "OE2" Residue "k GLU 16": "OE1" <-> "OE2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "l GLU 85": "OE1" <-> "OE2" Residue "l GLU 115": "OE1" <-> "OE2" Residue "m GLU 70": "OE1" <-> "OE2" Residue "n GLU 67": "OE1" <-> "OE2" Residue "o GLU 92": "OE1" <-> "OE2" Residue "p GLU 26": "OE1" <-> "OE2" Residue "p GLU 41": "OE1" <-> "OE2" Residue "q GLU 44": "OE1" <-> "OE2" Residue "q GLU 54": "OE1" <-> "OE2" Residue "q GLU 68": "OE1" <-> "OE2" Residue "q GLU 97": "OE1" <-> "OE2" Residue "r GLU 14": "OE1" <-> "OE2" Residue "t GLU 73": "OE1" <-> "OE2" Residue "u GLU 37": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 142247 Number of models: 1 Model: "" Number of chains: 50 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: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} 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: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 458 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain breaks: 1 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} Chain: "a" Number of atoms: 32521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1515, 32521 Classifications: {'RNA': 1515} Modifications used: {'rna2p_pur': 111, 'rna2p_pyr': 85, 'rna3p_pur': 739, 'rna3p_pyr': 580} Link IDs: {'rna2p': 196, 'rna3p': 1318} Chain: "v" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 271 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "d" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1660 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain: "e" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1641 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "f" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1208 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 8, 'TRANS': 157} Chain: "g" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "h" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1207 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "i" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "j" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "k" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 784 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "l" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 855 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "m" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "n" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "o" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 819 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "p" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "q" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 891 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "r" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 748 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "s" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 513 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "t" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 662 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "u" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 660 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "w" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 54.25, per 1000 atoms: 0.38 Number of scatterers: 142247 At special positions: 0 Unit cell: (280.34, 257.87, 245.03, 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 78 16.00 P 4730 15.00 O 40208 8.00 N 26636 7.00 C 70595 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: 60.76 Conformation dependent library (CDL) restraints added in 5.9 seconds 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9508 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 65 sheets defined 37.1% alpha, 21.3% beta 1621 base pairs and 2439 stacking pairs defined. Time for finding SS restraints: 50.64 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: 3.959A 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: 4.670A 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: 3.998A 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: 3.802A 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: 3.893A 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: 3.629A 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: 3.762A 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: 4.348A 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: 4.058A pdb=" N LYS T 13 " --> pdb=" O ASN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.694A pdb=" N ARG T 28 " --> pdb=" O ARG T 25 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER T 29 " --> pdb=" O GLY T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 71 removed outlier: 3.540A pdb=" N ARG T 51 " --> pdb=" O TYR T 47 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS T 54 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 4.481A 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: 3.517A 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: 4.068A 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 helix chain '4' and resid 57 through 65 Processing helix chain 'v' and resid 4 through 24 Processing helix chain 'v' and resid 24 through 32 Processing helix chain 'd' and resid 6 through 11 Processing helix chain 'd' and resid 27 through 46 Processing helix chain 'd' and resid 71 through 76 removed outlier: 3.735A pdb=" N VAL d 75 " --> pdb=" O ARG d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 80 through 92 Processing helix chain 'd' and resid 107 through 110 Processing helix chain 'd' and resid 111 through 126 removed outlier: 3.690A pdb=" N ASN d 125 " --> pdb=" O GLU d 121 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG d 126 " --> pdb=" O GLN d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 128 through 142 Processing helix chain 'd' and resid 156 through 160 Processing helix chain 'e' and resid 8 through 16 removed outlier: 3.547A pdb=" N SER e 12 " --> pdb=" O ALA e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 29 removed outlier: 3.796A pdb=" N GLU e 27 " --> pdb=" O ASP e 23 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 60 removed outlier: 3.623A pdb=" N TYR e 60 " --> pdb=" O ALA e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 63 through 77 Processing helix chain 'e' and resid 80 through 91 Processing helix chain 'e' and resid 92 through 100 Processing helix chain 'e' and resid 105 through 115 Processing helix chain 'e' and resid 142 through 145 Processing helix chain 'e' and resid 147 through 155 Processing helix chain 'e' and resid 182 through 187 removed outlier: 4.510A pdb=" N ASP e 187 " --> pdb=" O ARG e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 200 removed outlier: 3.970A pdb=" N ILE e 195 " --> pdb=" O THR e 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 80 through 95 Processing helix chain 'f' and resid 133 through 144 Processing helix chain 'f' and resid 157 through 171 Processing helix chain 'f' and resid 174 through 183 Processing helix chain 'f' and resid 185 through 190 Processing helix chain 'f' and resid 191 through 200 Processing helix chain 'g' and resid 15 through 17 No H-bonds generated for 'chain 'g' and resid 15 through 17' Processing helix chain 'g' and resid 18 through 35 removed outlier: 4.731A pdb=" N VAL g 29 " --> pdb=" O THR g 25 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE g 30 " --> pdb=" O PHE g 26 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY g 34 " --> pdb=" O ILE g 30 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY g 35 " --> pdb=" O ARG g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 82 Processing helix chain 'h' and resid 20 through 31 removed outlier: 3.947A pdb=" N THR h 24 " --> pdb=" O SER h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 55 Processing helix chain 'h' and resid 57 through 70 removed outlier: 3.829A pdb=" N THR h 61 " --> pdb=" O ASP h 57 " (cutoff:3.500A) Processing helix chain 'h' and resid 92 through 110 Processing helix chain 'h' and resid 115 through 129 Processing helix chain 'h' and resid 132 through 148 Processing helix chain 'h' and resid 149 through 154 removed outlier: 4.423A pdb=" N HIS h 153 " --> pdb=" O ALA h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 20 Processing helix chain 'i' and resid 30 through 43 Processing helix chain 'i' and resid 97 through 101 Processing helix chain 'i' and resid 115 through 122 Processing helix chain 'j' and resid 61 through 76 Proline residue: j 71 - end of helix Processing helix chain 'j' and resid 91 through 111 Processing helix chain 'j' and resid 114 through 121 removed outlier: 3.554A pdb=" N ALA j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 14 through 32 Processing helix chain 'k' and resid 80 through 88 Processing helix chain 'l' and resid 57 through 60 removed outlier: 3.765A pdb=" N GLY l 60 " --> pdb=" O GLY l 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 57 through 60' Processing helix chain 'l' and resid 62 through 67 Processing helix chain 'l' and resid 68 through 85 Processing helix chain 'l' and resid 101 through 112 Processing helix chain 'm' and resid 3 through 11 Processing helix chain 'm' and resid 113 through 117 Processing helix chain 'n' and resid 14 through 21 removed outlier: 3.809A pdb=" N TYR n 21 " --> pdb=" O ILE n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 27 through 38 Processing helix chain 'n' and resid 44 through 48 removed outlier: 3.973A pdb=" N LEU n 48 " --> pdb=" O THR n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 64 Processing helix chain 'n' and resid 67 through 84 Processing helix chain 'n' and resid 86 through 94 Processing helix chain 'n' and resid 107 through 112 Processing helix chain 'o' and resid 3 through 21 removed outlier: 3.516A pdb=" N GLU o 11 " --> pdb=" O ILE o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 33 removed outlier: 3.788A pdb=" N LYS o 28 " --> pdb=" O ARG o 24 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG o 29 " --> pdb=" O ALA o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 38 through 43 removed outlier: 3.735A pdb=" N ALA o 42 " --> pdb=" O PRO o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 43 through 51 removed outlier: 3.607A pdb=" N LEU o 51 " --> pdb=" O ALA o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 52 through 60 Proline residue: o 57 - end of helix Processing helix chain 'o' and resid 81 through 90 Processing helix chain 'p' and resid 4 through 16 Processing helix chain 'p' and resid 24 through 44 Processing helix chain 'p' and resid 49 through 74 Processing helix chain 'p' and resid 74 through 86 Processing helix chain 'q' and resid 52 through 63 Processing helix chain 'q' and resid 67 through 78 Processing helix chain 'q' and resid 78 through 85 Processing helix chain 'q' and resid 101 through 114 Processing helix chain 's' and resid 35 through 40 Processing helix chain 's' and resid 50 through 55 Processing helix chain 's' and resid 57 through 74 Processing helix chain 't' and resid 12 through 24 Processing helix chain 't' and resid 41 through 45 removed outlier: 3.990A pdb=" N ILE t 45 " --> pdb=" O PRO t 42 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 75 Processing helix chain 'u' and resid 4 through 42 Processing helix chain 'u' and resid 43 through 64 removed outlier: 3.892A pdb=" N ALA u 47 " --> pdb=" O ASP u 43 " (cutoff:3.500A) Processing helix chain 'u' and resid 68 through 86 Processing helix chain 'w' and resid 13 through 24 removed outlier: 3.797A pdb=" N ARG w 24 " --> pdb=" O GLU w 20 " (cutoff:3.500A) Processing helix chain 'w' and resid 73 through 93 Processing helix chain 'w' and resid 95 through 99 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: 4.531A 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: 3.587A 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: 5.805A 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: 6.641A 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: 4.838A 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: 5.743A pdb=" N VAL F 112 " --> pdb=" O ASN F 179 " (cutoff:3.500A) removed outlier: 4.616A 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: 6.368A 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: 8.695A 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: 6.188A 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: 7.333A 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: 3.517A 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: 3.540A 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: 3.572A 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: 6.069A 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: 6.338A 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: 5.409A pdb=" N VAL N 24 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 7.570A 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: 8.044A 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: 6.470A 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: 6.748A pdb=" N THR S 24 " --> pdb=" O LEU S 86 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N HIS S 82 " --> pdb=" O HIS S 28 " (cutoff:3.500A) removed outlier: 7.005A 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: 7.378A 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: 6.074A 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: 4.374A 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: 6.478A 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: 6.628A 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: 4.214A 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: 5.656A 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: 6.968A 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) Processing sheet with id=AE8, first strand: chain 'd' and resid 20 through 21 removed outlier: 3.521A pdb=" N ARG d 58 " --> pdb=" O ARG d 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP d 53 " --> pdb=" O HIS d 68 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL d 63 " --> pdb=" O GLN d 99 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ASN d 101 " --> pdb=" O VAL d 63 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL d 65 " --> pdb=" O ASN d 101 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU d 103 " --> pdb=" O VAL d 65 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE d 67 " --> pdb=" O LEU d 103 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'd' and resid 164 through 171 removed outlier: 3.581A pdb=" N GLU d 166 " --> pdb=" O CYS d 153 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS d 204 " --> pdb=" O ASP d 181 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ASP d 181 " --> pdb=" O LYS d 204 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'e' and resid 123 through 124 Processing sheet with id=AF2, first strand: chain 'f' and resid 37 through 49 removed outlier: 5.493A pdb=" N GLU f 38 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLY f 65 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL f 40 " --> pdb=" O ILE f 63 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE f 63 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER f 42 " --> pdb=" O LEU f 61 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'f' and resid 101 through 102 Processing sheet with id=AF4, first strand: chain 'f' and resid 110 through 114 removed outlier: 6.153A pdb=" N ILE f 131 " --> pdb=" O ALA f 150 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N SER f 152 " --> pdb=" O ILE f 131 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'g' and resid 37 through 47 removed outlier: 3.924A pdb=" N VAL g 37 " --> pdb=" O LYS g 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP g 64 " --> pdb=" O LYS g 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR g 60 " --> pdb=" O TRP g 43 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY g 58 " --> pdb=" O ARG g 45 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 73 through 79 Processing sheet with id=AF7, first strand: chain 'i' and resid 24 through 28 removed outlier: 3.738A pdb=" N ASP i 48 " --> pdb=" O GLN i 63 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'i' and resid 76 through 79 Processing sheet with id=AF9, first strand: chain 'i' and resid 76 through 79 removed outlier: 6.032A pdb=" N VAL i 127 " --> pdb=" O SER i 107 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER i 107 " --> pdb=" O VAL i 127 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA i 129 " --> pdb=" O ILE i 105 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'j' and resid 27 through 32 removed outlier: 3.557A pdb=" N THR j 28 " --> pdb=" O VAL j 39 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.092A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS k 11 " --> pdb=" O ASP k 97 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.092A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG o 97 " --> pdb=" O GLU k 66 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'l' and resid 49 through 55 removed outlier: 7.027A pdb=" N ILE l 43 " --> pdb=" O ILE l 51 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TRP l 53 " --> pdb=" O VAL l 41 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL l 41 " --> pdb=" O TRP l 53 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER l 55 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR l 39 " --> pdb=" O SER l 55 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL l 91 " --> pdb=" O GLY l 117 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE l 119 " --> pdb=" O VAL l 91 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL l 93 " --> pdb=" O ILE l 119 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP l 121 " --> pdb=" O VAL l 93 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL l 95 " --> pdb=" O ASP l 121 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'm' and resid 29 through 40 removed outlier: 6.528A pdb=" N ARG m 54 " --> pdb=" O THR m 35 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL m 37 " --> pdb=" O VAL m 52 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL m 52 " --> pdb=" O VAL m 37 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR m 39 " --> pdb=" O ARG m 50 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG m 50 " --> pdb=" O THR m 39 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N TYR m 95 " --> pdb=" O GLU m 62 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N THR m 64 " --> pdb=" O TYR m 95 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ILE m 97 " --> pdb=" O THR m 64 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR m 66 " --> pdb=" O ILE m 97 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'n' and resid 3 through 4 Processing sheet with id=AG7, first strand: chain 'o' and resid 73 through 74 removed outlier: 3.580A pdb=" N LEU o 79 " --> pdb=" O LEU o 74 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'q' and resid 49 through 51 removed outlier: 5.955A pdb=" N VAL q 36 " --> pdb=" O VAL q 22 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL q 22 " --> pdb=" O VAL q 36 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY q 38 " --> pdb=" O ILE q 20 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL q 3 " --> pdb=" O GLN q 65 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'r' and resid 22 through 32 removed outlier: 16.056A pdb=" N THR r 22 " --> pdb=" O ARG r 43 " (cutoff:3.500A) removed outlier: 12.316A pdb=" N ARG r 43 " --> pdb=" O THR r 22 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE r 24 " --> pdb=" O GLU r 41 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU r 41 " --> pdb=" O ILE r 24 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL r 37 " --> pdb=" O VAL r 28 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASP r 30 " --> pdb=" O THR r 35 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR r 35 " --> pdb=" O ASP r 30 " (cutoff:3.500A) removed outlier: 16.371A pdb=" N LYS r 86 " --> pdb=" O THR r 56 " (cutoff:3.500A) removed outlier: 13.567A pdb=" N LYS r 58 " --> pdb=" O LYS r 86 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N TRP r 88 " --> pdb=" O LYS r 58 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS r 60 " --> pdb=" O TRP r 88 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU r 90 " --> pdb=" O LYS r 60 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS r 62 " --> pdb=" O LEU r 90 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N GLU r 92 " --> pdb=" O HIS r 62 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ARG r 87 " --> pdb=" O THR r 79 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER r 75 " --> pdb=" O VAL r 91 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE r 93 " --> pdb=" O ARG r 73 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG r 73 " --> pdb=" O ILE r 93 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 't' and resid 31 through 32 removed outlier: 6.869A pdb=" N ILE t 31 " --> pdb=" O ALA t 50 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N HIS t 52 " --> pdb=" O ILE t 31 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'w' and resid 4 through 6 removed outlier: 3.545A pdb=" N LEU w 40 " --> pdb=" O SER w 6 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP w 59 " --> pdb=" O LEU w 34 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA w 36 " --> pdb=" O ASN w 57 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN w 57 " --> pdb=" O ALA w 36 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL w 38 " --> pdb=" O GLN w 55 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLN w 55 " --> pdb=" O VAL w 38 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU w 40 " --> pdb=" O ILE w 53 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE w 53 " --> pdb=" O LEU w 40 " (cutoff:3.500A) 1809 hydrogen bonds defined for protein. 5106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4146 hydrogen bonds 6544 hydrogen bond angles 0 basepair planarities 1621 basepair parallelities 2439 stacking parallelities Total time for adding SS restraints: 271.99 Time building geometry restraints manager: 66.00 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: 18790 1.33 - 1.45: 68527 1.45 - 1.57: 58082 1.57 - 1.70: 9454 1.70 - 1.82: 133 Bond restraints: 154986 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=" OP1 C B 89 " ideal model delta sigma weight residual 1.485 1.549 -0.064 2.00e-02 2.50e+03 1.02e+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=" 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 8.85e+00 bond pdb=" C TRP 1 29 " pdb=" N ASN 1 30 " ideal model delta sigma weight residual 1.329 1.284 0.045 1.86e-02 2.89e+03 5.90e+00 ... (remaining 154981 not shown) Histogram of bond angle deviations from ideal: 96.76 - 104.23: 19280 104.23 - 111.70: 85197 111.70 - 119.18: 52379 119.18 - 126.65: 62717 126.65 - 134.12: 13318 Bond angle restraints: 232891 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 98.53 13.47 1.40e+00 5.10e-01 9.26e+01 angle pdb=" N ILE F 151 " pdb=" CA ILE F 151 " pdb=" C ILE F 151 " ideal model delta sigma weight residual 113.53 106.83 6.70 9.80e-01 1.04e+00 4.68e+01 angle pdb=" CB MET k 88 " pdb=" CG MET k 88 " pdb=" SD MET k 88 " ideal model delta sigma weight residual 112.70 126.91 -14.21 3.00e+00 1.11e-01 2.24e+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 121.58 113.27 8.31 1.95e+00 2.63e-01 1.82e+01 ... (remaining 232886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 86901 35.88 - 71.75: 11725 71.75 - 107.63: 1326 107.63 - 143.50: 39 143.50 - 179.38: 53 Dihedral angle restraints: 100044 sinusoidal: 85252 harmonic: 14792 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 17.55 -177.55 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 16.76 -176.76 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 31.29 168.71 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 100041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 26377 0.055 - 0.109: 2960 0.109 - 0.164: 420 0.164 - 0.219: 76 0.219 - 0.274: 22 Chirality restraints: 29855 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 2.18 0.27 2.00e-01 2.50e+01 1.87e+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 1.78e+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 1.77e+00 ... (remaining 29852 not shown) Planarity restraints: 11967 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=" CB TRP t 34 " 0.025 2.00e-02 2.50e+03 3.14e-02 2.47e+01 pdb=" CG TRP t 34 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP t 34 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP t 34 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP t 34 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP t 34 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP t 34 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP t 34 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP t 34 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP t 34 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 88 " -0.055 2.00e-02 2.50e+03 2.90e-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 " 0.015 2.00e-02 2.50e+03 pdb=" C6 C B 88 " 0.045 2.00e-02 2.50e+03 ... (remaining 11964 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.82: 9 1.82 - 2.59: 2161 2.59 - 3.36: 168564 3.36 - 4.13: 469574 4.13 - 4.90: 668946 Nonbonded interactions: 1309254 Sorted by model distance: nonbonded pdb=" OE2 GLU 4 36 " pdb=" O ASP n 50 " model vdw 1.044 3.040 nonbonded pdb=" CG1 VAL 4 37 " pdb=" NH1 ARG n 57 " model vdw 1.303 3.540 nonbonded pdb=" O2' U A1560 " pdb=" OE2 GLU g 16 " model vdw 1.304 2.440 nonbonded pdb=" O2 U A1560 " pdb=" CZ ARG g 17 " model vdw 1.477 3.270 nonbonded pdb=" O2 U A1560 " pdb=" NE ARG g 17 " model vdw 1.528 2.520 ... (remaining 1309249 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: 4.980 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: 0.200 Extract box with map and model: 16.450 Check model and map are aligned: 1.520 Set scattering table: 0.990 Process input model: 536.940 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 566.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 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 : 0.005 0.129 154986 Z= 0.316 Angle : 0.631 14.209 232891 Z= 0.327 Chirality : 0.037 0.274 29855 Planarity : 0.005 0.163 11967 Dihedral : 24.186 179.377 90536 Min Nonbonded Distance : 1.044 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.09 % Favored : 96.89 % Rotamer: Outliers : 0.87 % Allowed : 29.37 % Favored : 69.77 % 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: 0.28 (0.12), residues: 5115 helix: 1.22 (0.13), residues: 1709 sheet: 0.04 (0.16), residues: 1074 loop : -0.43 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP t 34 HIS 0.012 0.001 HIS k 15 PHE 0.028 0.002 PHE w 124 TYR 0.025 0.002 TYR J 25 ARG 0.026 0.001 ARG k 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 621 time to evaluate : 5.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 96 GLU cc_start: 0.7430 (pp20) cc_final: 0.7138 (pp20) REVERT: F 99 GLN cc_start: 0.8917 (tt0) cc_final: 0.8709 (tt0) REVERT: H 58 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8775 (m110) REVERT: H 159 MET cc_start: 0.8712 (mtm) cc_final: 0.8497 (mpp) REVERT: M 49 ASP cc_start: 0.7692 (p0) cc_final: 0.6905 (p0) REVERT: M 108 MET cc_start: 0.8830 (mtt) cc_final: 0.8516 (mtt) REVERT: M 138 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9009 (tp) REVERT: O 97 GLU cc_start: 0.8526 (mp0) cc_final: 0.8248 (mp0) REVERT: R 4 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8414 (mppt) REVERT: T 59 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8521 (ttmm) REVERT: 2 12 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8138 (mm-30) REVERT: 2 21 LYS cc_start: 0.9265 (ttmm) cc_final: 0.8998 (tttp) REVERT: 5 23 GLU cc_start: 0.8093 (pm20) cc_final: 0.7815 (pm20) REVERT: 5 38 LYS cc_start: 0.9544 (mmtp) cc_final: 0.9185 (mmmt) REVERT: v 12 MET cc_start: 0.8969 (tpt) cc_final: 0.8611 (tpt) REVERT: v 30 LYS cc_start: 0.7986 (pttt) cc_final: 0.7553 (mtpp) REVERT: d 110 SER cc_start: 0.7851 (t) cc_final: 0.7496 (t) REVERT: f 58 PHE cc_start: 0.7588 (m-80) cc_final: 0.7361 (m-80) REVERT: f 80 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7769 (mt-10) REVERT: g 66 LYS cc_start: 0.8831 (ttmm) cc_final: 0.8573 (ttmm) REVERT: g 68 GLU cc_start: 0.7914 (mp0) cc_final: 0.7086 (mp0) REVERT: g 74 GLU cc_start: 0.8465 (tp30) cc_final: 0.8158 (tp30) REVERT: g 96 HIS cc_start: 0.6869 (m90) cc_final: 0.6578 (m170) REVERT: k 15 HIS cc_start: 0.4883 (t-90) cc_final: 0.3982 (t70) REVERT: k 76 ILE cc_start: 0.7505 (pp) cc_final: 0.7266 (mm) REVERT: k 84 VAL cc_start: 0.7689 (t) cc_final: 0.7407 (t) REVERT: k 88 MET cc_start: 0.8727 (mpp) cc_final: 0.8408 (mpp) REVERT: m 73 ASN cc_start: 0.8016 (p0) cc_final: 0.7369 (p0) REVERT: n 58 ASP cc_start: 0.8609 (p0) cc_final: 0.8297 (p0) REVERT: o 7 ILE cc_start: 0.8687 (mt) cc_final: 0.7913 (mt) REVERT: p 14 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7828 (pp30) REVERT: q 15 ASN cc_start: 0.8517 (m-40) cc_final: 0.8113 (p0) REVERT: q 107 ASN cc_start: 0.9077 (m110) cc_final: 0.8740 (m110) REVERT: s 64 ILE cc_start: 0.9625 (mm) cc_final: 0.9369 (mt) REVERT: w 4 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8438 (p0) outliers start: 37 outliers final: 6 residues processed: 644 average time/residue: 1.2994 time to fit residues: 1490.1247 Evaluate side-chains 498 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 488 time to evaluate : 5.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 ASN Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 1 residue 60 LYS Chi-restraints excluded: chain 1 residue 61 VAL Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain w residue 4 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 820 optimal weight: 8.9990 chunk 736 optimal weight: 20.0000 chunk 408 optimal weight: 10.0000 chunk 251 optimal weight: 9.9990 chunk 496 optimal weight: 20.0000 chunk 393 optimal weight: 50.0000 chunk 761 optimal weight: 30.0000 chunk 294 optimal weight: 20.0000 chunk 463 optimal weight: 30.0000 chunk 567 optimal weight: 20.0000 chunk 882 optimal weight: 5.9990 overall best weight: 10.9994 ------------------------------------------------------------------------------- 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 G 202 ASN N 89 ASN S 2 ASN W 63 GLN X 70 ASN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 35 GLN d 68 HIS ** d 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 51 GLN e 167 GLN ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 78 GLN h 129 ASN ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 61 ASN l 128 ASN o 10 ASN o 12 GLN o 89 HIS p 18 HIS w 35 HIS ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 154986 Z= 0.421 Angle : 0.664 8.392 232891 Z= 0.341 Chirality : 0.040 0.324 29855 Planarity : 0.006 0.066 11967 Dihedral : 24.140 179.885 80295 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.38 % Favored : 96.60 % Rotamer: Outliers : 5.00 % Allowed : 24.32 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.12), residues: 5115 helix: 1.15 (0.12), residues: 1714 sheet: -0.19 (0.16), residues: 1064 loop : -0.51 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP t 34 HIS 0.010 0.002 HIS 7 19 PHE 0.018 0.002 PHE s 79 TYR 0.025 0.002 TYR d 168 ARG 0.014 0.001 ARG g 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 513 time to evaluate : 5.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 96 GLU cc_start: 0.7917 (pp20) cc_final: 0.7475 (pp20) REVERT: F 99 GLN cc_start: 0.8962 (tt0) cc_final: 0.8703 (tt0) REVERT: G 124 ILE cc_start: 0.9721 (OUTLIER) cc_final: 0.9507 (mm) REVERT: G 134 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8289 (mm-40) REVERT: H 40 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.9106 (pttm) REVERT: H 127 LYS cc_start: 0.9148 (mmtt) cc_final: 0.8915 (mmtt) REVERT: H 159 MET cc_start: 0.8986 (mtm) cc_final: 0.8575 (mpp) REVERT: I 30 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8509 (tttt) REVERT: I 120 GLU cc_start: 0.8564 (pm20) cc_final: 0.8124 (pp20) REVERT: M 49 ASP cc_start: 0.7899 (p0) cc_final: 0.7088 (p0) REVERT: N 90 ASP cc_start: 0.8463 (p0) cc_final: 0.8080 (p0) REVERT: R 24 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.8372 (ptp-170) REVERT: T 59 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8565 (ttmm) REVERT: T 97 GLU cc_start: 0.8332 (tp30) cc_final: 0.8031 (tp30) REVERT: 1 60 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7031 (tppt) REVERT: 2 6 THR cc_start: 0.9548 (OUTLIER) cc_final: 0.9276 (p) REVERT: 2 21 LYS cc_start: 0.9423 (ttmm) cc_final: 0.9102 (ttmm) REVERT: 2 24 GLU cc_start: 0.8409 (pt0) cc_final: 0.8115 (pt0) REVERT: 5 38 LYS cc_start: 0.9566 (mmtp) cc_final: 0.9307 (mmmt) REVERT: 6 30 ARG cc_start: 0.8120 (ptp-170) cc_final: 0.7867 (ptm160) REVERT: 7 14 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.8989 (ttm-80) REVERT: v 12 MET cc_start: 0.9098 (tpt) cc_final: 0.8845 (tpt) REVERT: d 53 ASP cc_start: 0.6982 (t0) cc_final: 0.6723 (t0) REVERT: d 107 ASN cc_start: 0.8189 (t0) cc_final: 0.7484 (t0) REVERT: d 110 SER cc_start: 0.8654 (t) cc_final: 0.8393 (m) REVERT: d 183 ASP cc_start: 0.8593 (t0) cc_final: 0.8308 (t70) REVERT: f 58 PHE cc_start: 0.8122 (m-80) cc_final: 0.7791 (m-80) REVERT: f 63 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7871 (mm) REVERT: f 91 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7978 (tm-30) REVERT: f 120 MET cc_start: 0.8405 (ttp) cc_final: 0.8186 (ttp) REVERT: f 176 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7887 (pp20) REVERT: g 5 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7836 (tm-30) REVERT: g 68 GLU cc_start: 0.8068 (mp0) cc_final: 0.7868 (mp0) REVERT: g 74 GLU cc_start: 0.8356 (tp30) cc_final: 0.8115 (tp30) REVERT: h 86 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8435 (mm110) REVERT: j 47 GLN cc_start: 0.7446 (tm-30) cc_final: 0.6577 (tm-30) REVERT: j 58 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.7938 (t80) REVERT: j 82 ASP cc_start: 0.8326 (m-30) cc_final: 0.8111 (t70) REVERT: k 10 LEU cc_start: 0.8848 (mt) cc_final: 0.8642 (tp) REVERT: k 18 ILE cc_start: 0.8505 (tt) cc_final: 0.8049 (tt) REVERT: k 84 VAL cc_start: 0.7820 (t) cc_final: 0.7411 (t) REVERT: k 88 MET cc_start: 0.8838 (mpp) cc_final: 0.8138 (mpp) REVERT: l 115 GLU cc_start: 0.7429 (tp30) cc_final: 0.6961 (tp30) REVERT: m 73 ASN cc_start: 0.7999 (p0) cc_final: 0.7470 (p0) REVERT: o 11 GLU cc_start: 0.9048 (mp0) cc_final: 0.8814 (mp0) REVERT: q 52 ASP cc_start: 0.8107 (t0) cc_final: 0.7001 (t0) REVERT: q 107 ASN cc_start: 0.9159 (m110) cc_final: 0.8755 (m110) REVERT: t 73 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: u 45 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7834 (p0) outliers start: 214 outliers final: 87 residues processed: 686 average time/residue: 1.2828 time to fit residues: 1569.5464 Evaluate side-chains 567 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 467 time to evaluate : 5.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 96 ARG Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 143 SER 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 R residue 65 SER Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain S residue 2 ASN Chi-restraints excluded: chain S residue 56 GLU 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 U residue 34 SER Chi-restraints excluded: chain U residue 44 ASP Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 115 GLU Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 75 ARG Chi-restraints excluded: chain Z residue 81 VAL Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 1 residue 60 LYS Chi-restraints excluded: chain 1 residue 61 VAL Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 14 THR Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 6 residue 24 ILE 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 37 VAL Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 25 ASP Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 99 GLN Chi-restraints excluded: chain d residue 206 ASP Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 101 LEU Chi-restraints excluded: chain f residue 152 SER Chi-restraints excluded: chain f residue 176 GLU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 86 GLN Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 63 VAL Chi-restraints excluded: chain j residue 150 ARG Chi-restraints excluded: chain k residue 16 GLU Chi-restraints excluded: chain k residue 76 ILE Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 43 MET Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain s residue 56 ASN Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 2 ASP Chi-restraints excluded: chain w residue 41 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 490 optimal weight: 10.0000 chunk 273 optimal weight: 0.0270 chunk 734 optimal weight: 10.0000 chunk 601 optimal weight: 20.0000 chunk 243 optimal weight: 10.0000 chunk 884 optimal weight: 10.0000 chunk 955 optimal weight: 10.0000 chunk 787 optimal weight: 30.0000 chunk 876 optimal weight: 7.9990 chunk 301 optimal weight: 10.0000 chunk 709 optimal weight: 40.0000 overall best weight: 7.6052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 202 ASN H 58 ASN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 GLN ** R 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 70 ASN Z 12 ASN d 27 GLN d 107 ASN ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 143 GLN e 95 ASN ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 47 GLN k 99 ASN l 128 ASN m 105 GLN o 49 GLN r 33 GLN t 22 GLN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 154986 Z= 0.289 Angle : 0.577 9.083 232891 Z= 0.298 Chirality : 0.036 0.310 29855 Planarity : 0.005 0.059 11967 Dihedral : 24.144 179.323 80287 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.05 % Favored : 96.93 % Rotamer: Outliers : 3.79 % Allowed : 25.51 % Favored : 70.70 % 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: 0.34 (0.12), residues: 5115 helix: 1.40 (0.13), residues: 1718 sheet: -0.11 (0.16), residues: 1073 loop : -0.42 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP t 34 HIS 0.008 0.001 HIS k 15 PHE 0.016 0.001 PHE f 96 TYR 0.020 0.001 TYR d 168 ARG 0.010 0.000 ARG k 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 487 time to evaluate : 5.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 MET cc_start: 0.8663 (mtp) cc_final: 0.8414 (mtp) REVERT: F 99 GLN cc_start: 0.8986 (tt0) cc_final: 0.8776 (tt0) REVERT: F 198 ILE cc_start: 0.9540 (OUTLIER) cc_final: 0.9315 (pt) REVERT: G 124 ILE cc_start: 0.9712 (OUTLIER) cc_final: 0.9505 (mm) REVERT: H 108 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8554 (m-30) REVERT: H 159 MET cc_start: 0.8923 (mtm) cc_final: 0.8477 (mpp) REVERT: I 102 GLN cc_start: 0.7623 (pp30) cc_final: 0.7372 (pp30) REVERT: I 120 GLU cc_start: 0.8582 (pm20) cc_final: 0.8330 (pp20) REVERT: M 49 ASP cc_start: 0.8017 (p0) cc_final: 0.7290 (p0) REVERT: N 90 ASP cc_start: 0.8471 (p0) cc_final: 0.8177 (p0) REVERT: R 24 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8560 (ptp-170) REVERT: R 122 GLU cc_start: 0.8622 (pp20) cc_final: 0.8418 (pp20) REVERT: S 56 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8105 (tp30) REVERT: T 97 GLU cc_start: 0.8349 (tp30) cc_final: 0.8006 (tp30) REVERT: V 66 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8530 (tm-30) REVERT: W 48 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8795 (tppt) REVERT: 1 60 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6939 (tppt) REVERT: 2 21 LYS cc_start: 0.9368 (ttmm) cc_final: 0.9032 (ttmm) REVERT: 5 38 LYS cc_start: 0.9548 (mmtp) cc_final: 0.9257 (mmmt) REVERT: 6 10 LYS cc_start: 0.8560 (mppt) cc_final: 0.8326 (mppt) REVERT: 7 14 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.7978 (ttp80) REVERT: v 12 MET cc_start: 0.9070 (tpt) cc_final: 0.8817 (tpt) REVERT: d 27 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8387 (pm20) REVERT: d 53 ASP cc_start: 0.7326 (t0) cc_final: 0.7008 (t0) REVERT: d 99 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7587 (pp30) REVERT: d 107 ASN cc_start: 0.8236 (t160) cc_final: 0.7168 (t0) REVERT: d 110 SER cc_start: 0.8658 (t) cc_final: 0.8103 (m) REVERT: d 183 ASP cc_start: 0.8555 (t0) cc_final: 0.8215 (t70) REVERT: f 63 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7626 (mm) REVERT: f 80 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7998 (mt-10) REVERT: f 91 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8062 (tm-30) REVERT: g 5 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7818 (tm-30) REVERT: g 16 GLU cc_start: 0.7195 (pm20) cc_final: 0.6580 (pm20) REVERT: g 74 GLU cc_start: 0.8331 (tp30) cc_final: 0.8040 (tp30) REVERT: j 47 GLN cc_start: 0.7592 (tm130) cc_final: 0.6745 (tm-30) REVERT: j 58 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.7899 (t80) REVERT: j 82 ASP cc_start: 0.8377 (m-30) cc_final: 0.8041 (t0) REVERT: k 88 MET cc_start: 0.8833 (mpp) cc_final: 0.8076 (mpp) REVERT: n 12 ASP cc_start: 0.8539 (p0) cc_final: 0.8260 (m-30) REVERT: n 41 LYS cc_start: 0.7876 (mptt) cc_final: 0.7663 (mmtt) REVERT: n 60 ILE cc_start: 0.9434 (mm) cc_final: 0.9223 (mt) REVERT: o 11 GLU cc_start: 0.9055 (mp0) cc_final: 0.8763 (mp0) REVERT: q 39 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7751 (ptp-110) REVERT: q 52 ASP cc_start: 0.8007 (t0) cc_final: 0.6903 (t0) REVERT: q 107 ASN cc_start: 0.9163 (m110) cc_final: 0.8743 (m110) REVERT: t 22 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8319 (mm-40) REVERT: t 73 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8030 (mp0) outliers start: 162 outliers final: 80 residues processed: 614 average time/residue: 1.2402 time to fit residues: 1348.7289 Evaluate side-chains 554 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 459 time to evaluate : 5.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain Q residue 14 SER 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 65 SER Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 115 GLU Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain 1 residue 60 LYS Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 42 SER Chi-restraints excluded: chain 2 residue 66 LEU Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 6 residue 25 THR 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 19 THR Chi-restraints excluded: chain 8 residue 54 ASP Chi-restraints excluded: chain 4 residue 37 VAL Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 27 GLN Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 99 GLN Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 63 VAL Chi-restraints excluded: chain j residue 150 ARG Chi-restraints excluded: chain k residue 16 GLU Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 76 ILE Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain q residue 39 ARG Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain s residue 56 ASN Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 22 GLN Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 2 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 873 optimal weight: 9.9990 chunk 664 optimal weight: 20.0000 chunk 458 optimal weight: 10.0000 chunk 97 optimal weight: 30.0000 chunk 422 optimal weight: 10.0000 chunk 593 optimal weight: 50.0000 chunk 887 optimal weight: 2.9990 chunk 939 optimal weight: 6.9990 chunk 463 optimal weight: 30.0000 chunk 841 optimal weight: 9.9990 chunk 253 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 202 ASN M 136 GLN N 4 GLN N 89 ASN ** R 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 27 GLN ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 95 ASN ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 86 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 128 ASN m 73 ASN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 154986 Z= 0.297 Angle : 0.577 11.184 232891 Z= 0.297 Chirality : 0.036 0.316 29855 Planarity : 0.005 0.060 11967 Dihedral : 24.089 179.922 80280 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 4.54 % Allowed : 24.69 % Favored : 70.77 % 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: 0.39 (0.12), residues: 5115 helix: 1.49 (0.13), residues: 1727 sheet: -0.13 (0.16), residues: 1101 loop : -0.42 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP t 34 HIS 0.009 0.001 HIS J 11 PHE 0.024 0.002 PHE 4 61 TYR 0.033 0.001 TYR d 28 ARG 0.015 0.000 ARG n 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 487 time to evaluate : 5.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 GLN cc_start: 0.9019 (tt0) cc_final: 0.8750 (tt0) REVERT: F 198 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9316 (pt) REVERT: G 124 ILE cc_start: 0.9707 (OUTLIER) cc_final: 0.9490 (mm) REVERT: H 108 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8584 (m-30) REVERT: H 127 LYS cc_start: 0.9157 (mmtt) cc_final: 0.8919 (mmtt) REVERT: H 159 MET cc_start: 0.8862 (mtm) cc_final: 0.8259 (mpp) REVERT: I 86 GLN cc_start: 0.8390 (tp-100) cc_final: 0.8185 (tp-100) REVERT: I 102 GLN cc_start: 0.7746 (pp30) cc_final: 0.7408 (pp30) REVERT: I 120 GLU cc_start: 0.8598 (pm20) cc_final: 0.8379 (pp20) REVERT: J 2 LYS cc_start: 0.6994 (mmmt) cc_final: 0.6337 (mmmt) REVERT: J 23 ASP cc_start: 0.7520 (p0) cc_final: 0.6786 (t0) REVERT: M 49 ASP cc_start: 0.8062 (p0) cc_final: 0.7425 (p0) REVERT: N 90 ASP cc_start: 0.8542 (p0) cc_final: 0.8174 (p0) REVERT: R 24 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8700 (ptp-170) REVERT: R 90 GLU cc_start: 0.8851 (pm20) cc_final: 0.8611 (pm20) REVERT: S 56 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8034 (tp30) REVERT: T 97 GLU cc_start: 0.8351 (tp30) cc_final: 0.8015 (tp30) REVERT: V 66 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8497 (tm-30) REVERT: W 48 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8810 (tppt) REVERT: 1 60 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7039 (tppt) REVERT: 2 6 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.9372 (p) REVERT: 2 41 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8498 (pt) REVERT: 5 6 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8414 (mtt-85) REVERT: 5 38 LYS cc_start: 0.9554 (mmtp) cc_final: 0.9220 (mmmt) REVERT: 7 14 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8016 (ttp80) REVERT: 8 3 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9084 (ptmt) REVERT: d 53 ASP cc_start: 0.7576 (t0) cc_final: 0.7264 (t0) REVERT: d 99 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7388 (pp30) REVERT: d 183 ASP cc_start: 0.8588 (t0) cc_final: 0.8182 (t70) REVERT: f 63 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8064 (mm) REVERT: f 80 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8168 (mt-10) REVERT: f 113 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: g 5 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7874 (tm-30) REVERT: g 43 TRP cc_start: 0.8234 (OUTLIER) cc_final: 0.7856 (p-90) REVERT: g 74 GLU cc_start: 0.8179 (tp30) cc_final: 0.7748 (tp30) REVERT: j 47 GLN cc_start: 0.7630 (tm130) cc_final: 0.6795 (tm-30) REVERT: j 58 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7885 (t80) REVERT: j 103 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9118 (mp) REVERT: k 88 MET cc_start: 0.8943 (mpp) cc_final: 0.8208 (mpp) REVERT: n 41 LYS cc_start: 0.8031 (mptt) cc_final: 0.7811 (mmtt) REVERT: o 10 ASN cc_start: 0.8083 (m-40) cc_final: 0.7593 (t0) REVERT: o 11 GLU cc_start: 0.9168 (mp0) cc_final: 0.8892 (mp0) REVERT: o 46 SER cc_start: 0.8477 (t) cc_final: 0.8205 (p) REVERT: p 19 ASP cc_start: 0.8302 (p0) cc_final: 0.8085 (p0) REVERT: q 39 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7674 (ptp-110) REVERT: q 45 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7250 (tp30) REVERT: q 107 ASN cc_start: 0.9152 (m110) cc_final: 0.8720 (m110) REVERT: s 59 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8620 (mt0) REVERT: t 73 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8027 (mp0) outliers start: 194 outliers final: 117 residues processed: 630 average time/residue: 1.2117 time to fit residues: 1357.4843 Evaluate side-chains 602 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 464 time to evaluate : 5.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER 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 40 VAL Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 115 GLU Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 40 ARG Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain 1 residue 60 LYS Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 2 residue 42 SER Chi-restraints excluded: chain 2 residue 66 LEU Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 6 ARG Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 8 residue 3 LYS Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 19 THR Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain 4 residue 37 VAL Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 25 ASP Chi-restraints excluded: chain d residue 30 ASP Chi-restraints excluded: chain d residue 61 ASP Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 99 GLN Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 113 GLU Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 66 LYS Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain j residue 108 ILE Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 16 GLU Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 76 ILE Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 75 GLN Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain n residue 75 GLN Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 39 ARG Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 18 ARG Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain s residue 56 ASN Chi-restraints excluded: chain s residue 59 GLN Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain t residue 29 GLN Chi-restraints excluded: chain t residue 30 VAL Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 2 ASP Chi-restraints excluded: chain w residue 41 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 782 optimal weight: 7.9990 chunk 533 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 699 optimal weight: 30.0000 chunk 387 optimal weight: 10.0000 chunk 801 optimal weight: 40.0000 chunk 649 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 479 optimal weight: 20.0000 chunk 843 optimal weight: 20.0000 chunk 237 optimal weight: 0.8980 overall best weight: 7.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 202 ASN N 4 GLN N 89 ASN ** R 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 128 ASN m 73 ASN t 47 HIS ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 154986 Z= 0.279 Angle : 0.564 11.444 232891 Z= 0.290 Chirality : 0.035 0.313 29855 Planarity : 0.004 0.060 11967 Dihedral : 24.073 179.787 80280 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.11 % Favored : 96.87 % Rotamer: Outliers : 4.65 % Allowed : 25.09 % Favored : 70.26 % 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: 0.47 (0.12), residues: 5115 helix: 1.60 (0.13), residues: 1721 sheet: -0.12 (0.16), residues: 1074 loop : -0.40 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP t 34 HIS 0.008 0.001 HIS k 15 PHE 0.016 0.001 PHE 4 61 TYR 0.018 0.001 TYR d 168 ARG 0.012 0.000 ARG s 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 488 time to evaluate : 5.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 LYS cc_start: 0.9066 (pptt) cc_final: 0.8784 (pptt) REVERT: G 124 ILE cc_start: 0.9685 (OUTLIER) cc_final: 0.9476 (mm) REVERT: H 108 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8573 (m-30) REVERT: H 127 LYS cc_start: 0.9183 (mmtt) cc_final: 0.8940 (mmtt) REVERT: H 159 MET cc_start: 0.8888 (mtm) cc_final: 0.8304 (mpp) REVERT: I 102 GLN cc_start: 0.7679 (pp30) cc_final: 0.7374 (pp30) REVERT: J 2 LYS cc_start: 0.7428 (mmmt) cc_final: 0.6823 (mmmt) REVERT: J 23 ASP cc_start: 0.7645 (p0) cc_final: 0.7149 (t0) REVERT: M 49 ASP cc_start: 0.8107 (p0) cc_final: 0.7454 (p0) REVERT: N 90 ASP cc_start: 0.8520 (p0) cc_final: 0.8118 (p0) REVERT: R 24 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8729 (ptp-170) REVERT: S 56 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8049 (tp30) REVERT: T 97 GLU cc_start: 0.8344 (tp30) cc_final: 0.8009 (tp30) REVERT: V 66 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8567 (tm-30) REVERT: W 48 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8813 (tppt) REVERT: 1 60 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7090 (tppt) REVERT: 2 41 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8347 (pt) REVERT: 5 6 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8419 (mtt-85) REVERT: 5 38 LYS cc_start: 0.9496 (mmtp) cc_final: 0.9196 (mmmt) REVERT: 7 14 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.8003 (ttp80) REVERT: 8 3 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9092 (ptmt) REVERT: d 101 ASN cc_start: 0.8051 (m-40) cc_final: 0.7496 (p0) REVERT: d 183 ASP cc_start: 0.8661 (t0) cc_final: 0.8261 (t70) REVERT: f 63 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7969 (mm) REVERT: f 80 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7947 (mt-10) REVERT: f 120 MET cc_start: 0.8348 (ttp) cc_final: 0.8128 (ttp) REVERT: g 5 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7897 (tm-30) REVERT: g 43 TRP cc_start: 0.8196 (OUTLIER) cc_final: 0.7777 (p-90) REVERT: g 74 GLU cc_start: 0.8080 (tp30) cc_final: 0.7629 (tp30) REVERT: h 22 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9190 (tt) REVERT: j 58 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7859 (t80) REVERT: j 82 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8158 (t0) REVERT: n 15 MET cc_start: 0.7839 (mmm) cc_final: 0.7507 (tpp) REVERT: o 10 ASN cc_start: 0.8136 (m-40) cc_final: 0.7603 (t0) REVERT: o 11 GLU cc_start: 0.9167 (mp0) cc_final: 0.8916 (mp0) REVERT: o 46 SER cc_start: 0.8483 (t) cc_final: 0.8233 (p) REVERT: p 19 ASP cc_start: 0.8384 (p0) cc_final: 0.8085 (p0) REVERT: q 39 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7593 (ptp-110) REVERT: q 107 ASN cc_start: 0.9193 (m110) cc_final: 0.8742 (m110) REVERT: r 30 ASP cc_start: 0.8379 (p0) cc_final: 0.8177 (p0) REVERT: s 59 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8601 (mt0) REVERT: t 22 GLN cc_start: 0.9069 (tp40) cc_final: 0.8765 (mm-40) REVERT: t 34 TRP cc_start: 0.8589 (OUTLIER) cc_final: 0.7279 (t-100) REVERT: t 73 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: w 43 HIS cc_start: 0.9157 (OUTLIER) cc_final: 0.8952 (m-70) outliers start: 199 outliers final: 123 residues processed: 637 average time/residue: 1.1935 time to fit residues: 1357.3938 Evaluate side-chains 612 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 469 time to evaluate : 5.725 ------------------------------------------------------------------------------- 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 161 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain N residue 115 VAL 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 143 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 98 ILE 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 65 SER Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 115 GLU Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain 1 residue 40 THR 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 2 residue 66 LEU Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 5 residue 6 ARG Chi-restraints excluded: chain 6 residue 25 THR Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 8 residue 3 LYS Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 19 THR Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain 4 residue 37 VAL Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 25 ASP Chi-restraints excluded: chain d residue 30 ASP Chi-restraints excluded: chain d residue 61 ASP Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 7 MET Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 66 LYS Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 82 ASP Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 16 GLU Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 40 VAL Chi-restraints excluded: chain k residue 76 ILE Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 51 ILE Chi-restraints excluded: chain l residue 85 GLU Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 39 ARG Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain s residue 56 ASN Chi-restraints excluded: chain s residue 59 GLN Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain t residue 30 VAL Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 2 ASP Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 43 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 316 optimal weight: 20.0000 chunk 846 optimal weight: 30.0000 chunk 185 optimal weight: 8.9990 chunk 551 optimal weight: 20.0000 chunk 231 optimal weight: 20.0000 chunk 940 optimal weight: 0.6980 chunk 780 optimal weight: 5.9990 chunk 435 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 311 optimal weight: 50.0000 chunk 493 optimal weight: 20.0000 overall best weight: 8.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 202 ASN N 89 ASN ** R 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 61 ASN k 99 ASN l 128 ASN m 73 ASN ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 154986 Z= 0.328 Angle : 0.591 10.800 232891 Z= 0.304 Chirality : 0.036 0.314 29855 Planarity : 0.005 0.059 11967 Dihedral : 24.058 179.927 80280 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.58 % Favored : 96.40 % Rotamer: Outliers : 4.72 % Allowed : 25.46 % Favored : 69.82 % 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: 0.42 (0.12), residues: 5115 helix: 1.57 (0.13), residues: 1723 sheet: -0.15 (0.16), residues: 1070 loop : -0.42 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP t 34 HIS 0.007 0.001 HIS k 15 PHE 0.015 0.001 PHE 4 61 TYR 0.017 0.001 TYR d 168 ARG 0.010 0.000 ARG s 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 483 time to evaluate : 5.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 LYS cc_start: 0.9088 (pptt) cc_final: 0.8828 (pptt) REVERT: G 124 ILE cc_start: 0.9686 (OUTLIER) cc_final: 0.9476 (mm) REVERT: H 127 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8930 (mmtt) REVERT: H 159 MET cc_start: 0.8842 (mtm) cc_final: 0.8120 (mpp) REVERT: J 2 LYS cc_start: 0.7618 (mmmt) cc_final: 0.7151 (mmmt) REVERT: J 23 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7393 (t0) REVERT: M 49 ASP cc_start: 0.8096 (p0) cc_final: 0.7436 (p0) REVERT: N 90 ASP cc_start: 0.8518 (p0) cc_final: 0.8118 (p0) REVERT: O 96 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8484 (p0) REVERT: R 24 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8872 (ptp-170) REVERT: S 56 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8156 (tp30) REVERT: T 59 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8549 (ttmm) REVERT: T 97 GLU cc_start: 0.8351 (tp30) cc_final: 0.8015 (tp30) REVERT: V 66 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8572 (tm-30) REVERT: W 48 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8837 (tppt) REVERT: X 7 ASP cc_start: 0.8208 (m-30) cc_final: 0.7876 (m-30) REVERT: 1 60 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.6974 (tppt) REVERT: 2 20 ASP cc_start: 0.8474 (t0) cc_final: 0.8154 (t0) REVERT: 2 24 GLU cc_start: 0.8413 (pt0) cc_final: 0.8209 (pt0) REVERT: 2 41 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8425 (pt) REVERT: 5 6 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8472 (mtt-85) REVERT: 5 38 LYS cc_start: 0.9503 (mmtp) cc_final: 0.9199 (mmmt) REVERT: 7 14 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.7984 (ttp80) REVERT: 8 3 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9113 (ptmt) REVERT: d 66 ASP cc_start: 0.7340 (m-30) cc_final: 0.6731 (m-30) REVERT: d 84 ASP cc_start: 0.8594 (t0) cc_final: 0.8266 (m-30) REVERT: d 183 ASP cc_start: 0.8662 (t0) cc_final: 0.8249 (t70) REVERT: f 80 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8004 (mt-10) REVERT: f 120 MET cc_start: 0.8526 (ttp) cc_final: 0.8299 (ttp) REVERT: g 5 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7946 (tm-30) REVERT: g 43 TRP cc_start: 0.8179 (OUTLIER) cc_final: 0.7783 (p-90) REVERT: h 22 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9214 (tt) REVERT: j 47 GLN cc_start: 0.7208 (tm-30) cc_final: 0.6725 (tm-30) REVERT: j 58 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7928 (t80) REVERT: j 82 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8023 (t0) REVERT: k 88 MET cc_start: 0.9012 (mpp) cc_final: 0.8408 (mpp) REVERT: n 12 ASP cc_start: 0.8257 (m-30) cc_final: 0.7772 (m-30) REVERT: n 46 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.8995 (ptpp) REVERT: o 10 ASN cc_start: 0.8106 (m-40) cc_final: 0.7568 (t0) REVERT: o 46 SER cc_start: 0.8529 (t) cc_final: 0.8319 (p) REVERT: p 19 ASP cc_start: 0.8483 (p0) cc_final: 0.8157 (p0) REVERT: q 39 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7611 (ptp-110) REVERT: q 107 ASN cc_start: 0.9224 (m110) cc_final: 0.8765 (m110) REVERT: r 30 ASP cc_start: 0.8458 (p0) cc_final: 0.8250 (p0) REVERT: s 59 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8586 (mt0) REVERT: t 34 TRP cc_start: 0.8695 (OUTLIER) cc_final: 0.7145 (t-100) REVERT: t 73 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: w 43 HIS cc_start: 0.9101 (OUTLIER) cc_final: 0.8630 (m90) outliers start: 202 outliers final: 132 residues processed: 631 average time/residue: 1.3139 time to fit residues: 1493.2911 Evaluate side-chains 619 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 465 time to evaluate : 5.824 ------------------------------------------------------------------------------- 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 161 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER 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 R residue 65 SER Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 56 GLU 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 61 THR Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 115 GLU Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain Z residue 81 VAL Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 1 residue 60 LYS Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 6 ARG Chi-restraints excluded: chain 6 residue 25 THR Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 3 LYS Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 19 THR Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 25 ASP Chi-restraints excluded: chain d residue 61 ASP Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 206 ASP Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 7 MET Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 66 LYS Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 63 VAL Chi-restraints excluded: chain j residue 82 ASP Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 16 GLU Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 40 VAL Chi-restraints excluded: chain k residue 76 ILE Chi-restraints excluded: chain k residue 99 ASN Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 51 ILE Chi-restraints excluded: chain l residue 85 GLU Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 122 GLU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 39 ARG Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain s residue 56 ASN Chi-restraints excluded: chain s residue 59 GLN Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain t residue 29 GLN Chi-restraints excluded: chain t residue 30 VAL Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 2 ASP Chi-restraints excluded: chain w residue 43 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 906 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 535 optimal weight: 20.0000 chunk 686 optimal weight: 10.0000 chunk 532 optimal weight: 10.0000 chunk 791 optimal weight: 10.0000 chunk 525 optimal weight: 20.0000 chunk 936 optimal weight: 9.9990 chunk 586 optimal weight: 30.0000 chunk 571 optimal weight: 20.0000 chunk 432 optimal weight: 20.0000 overall best weight: 9.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 202 ASN N 89 ASN ** R 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 128 ASN m 73 ASN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 154986 Z= 0.353 Angle : 0.604 10.748 232891 Z= 0.310 Chirality : 0.037 0.313 29855 Planarity : 0.005 0.059 11967 Dihedral : 24.060 179.909 80280 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.66 % Favored : 96.32 % Rotamer: Outliers : 4.65 % Allowed : 25.86 % Favored : 69.49 % 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: 0.35 (0.12), residues: 5115 helix: 1.53 (0.13), residues: 1721 sheet: -0.25 (0.16), residues: 1081 loop : -0.45 (0.13), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP t 34 HIS 0.007 0.001 HIS k 15 PHE 0.014 0.002 PHE 4 61 TYR 0.015 0.001 TYR Q 47 ARG 0.014 0.001 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 480 time to evaluate : 5.601 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: G 13 LYS cc_start: 0.9064 (pptt) cc_final: 0.8798 (pptt) REVERT: H 127 LYS cc_start: 0.9203 (mmtt) cc_final: 0.8989 (mmtt) REVERT: H 159 MET cc_start: 0.8841 (mtm) cc_final: 0.8222 (mpp) REVERT: J 2 LYS cc_start: 0.7732 (mmmt) cc_final: 0.7370 (mmmt) REVERT: J 23 ASP cc_start: 0.7646 (p0) cc_final: 0.7391 (t0) REVERT: M 49 ASP cc_start: 0.8089 (p0) cc_final: 0.7449 (p0) REVERT: N 90 ASP cc_start: 0.8542 (p0) cc_final: 0.8138 (p0) REVERT: R 24 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8868 (ptp-170) REVERT: S 56 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8109 (tp30) REVERT: T 97 GLU cc_start: 0.8345 (tp30) cc_final: 0.8010 (tp30) REVERT: V 66 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8601 (tm-30) REVERT: W 48 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8850 (tppt) REVERT: X 7 ASP cc_start: 0.8259 (m-30) cc_final: 0.7954 (m-30) REVERT: 2 20 ASP cc_start: 0.8491 (t0) cc_final: 0.8189 (t0) REVERT: 2 24 GLU cc_start: 0.8410 (pt0) cc_final: 0.8209 (pt0) REVERT: 2 41 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8420 (pt) REVERT: 5 6 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8479 (mtt-85) REVERT: 5 38 LYS cc_start: 0.9501 (mmtp) cc_final: 0.9207 (mmmt) REVERT: 7 14 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.7985 (ttp80) REVERT: 8 3 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9055 (ptmt) REVERT: v 16 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8066 (mptp) REVERT: d 66 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6673 (m-30) REVERT: d 84 ASP cc_start: 0.8652 (t0) cc_final: 0.8418 (m-30) REVERT: d 183 ASP cc_start: 0.8640 (t0) cc_final: 0.8223 (t70) REVERT: e 42 LYS cc_start: 0.5144 (OUTLIER) cc_final: 0.3961 (pttt) REVERT: g 5 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7916 (tm-30) REVERT: g 43 TRP cc_start: 0.8229 (OUTLIER) cc_final: 0.7810 (p-90) REVERT: g 74 GLU cc_start: 0.8420 (tp30) cc_final: 0.8171 (tp30) REVERT: h 22 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9151 (tt) REVERT: j 47 GLN cc_start: 0.7251 (tm-30) cc_final: 0.6694 (tm-30) REVERT: j 58 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7891 (t80) REVERT: j 82 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8066 (t70) REVERT: j 120 LYS cc_start: 0.8999 (mmtt) cc_final: 0.8682 (mmtt) REVERT: k 10 LEU cc_start: 0.8748 (mt) cc_final: 0.8433 (tp) REVERT: k 88 MET cc_start: 0.9052 (mpp) cc_final: 0.8560 (mpp) REVERT: n 65 LYS cc_start: 0.8484 (ptmm) cc_final: 0.8218 (ptmm) REVERT: n 75 GLN cc_start: 0.8608 (pp30) cc_final: 0.8355 (pp30) REVERT: o 10 ASN cc_start: 0.8022 (m-40) cc_final: 0.7409 (t0) REVERT: p 19 ASP cc_start: 0.8501 (p0) cc_final: 0.8155 (p0) REVERT: q 39 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7627 (ptp-110) REVERT: q 107 ASN cc_start: 0.9245 (m110) cc_final: 0.8785 (m110) REVERT: s 59 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8587 (mt0) REVERT: t 34 TRP cc_start: 0.8762 (OUTLIER) cc_final: 0.6743 (t-100) REVERT: t 73 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: w 43 HIS cc_start: 0.9096 (OUTLIER) cc_final: 0.8624 (m90) outliers start: 199 outliers final: 137 residues processed: 629 average time/residue: 1.1526 time to fit residues: 1294.1548 Evaluate side-chains 626 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 470 time to evaluate : 5.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 15 VAL 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 M residue 12 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 60 ASP 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 94 ARG Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 98 ILE 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 R residue 65 SER Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 115 GLU Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain Z residue 81 VAL Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 2 residue 5 THR 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 6 residue 25 THR Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 3 LYS Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 19 THR Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain v residue 16 LYS Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 25 ASP Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 206 ASP Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 42 LYS Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 7 MET Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 66 LYS Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 82 ASP Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 16 GLU Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 76 ILE Chi-restraints excluded: chain k residue 98 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 51 ILE Chi-restraints excluded: chain l residue 85 GLU Chi-restraints excluded: chain l residue 96 LYS Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 122 GLU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 39 ARG Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 18 ARG Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain s residue 56 ASN Chi-restraints excluded: chain s residue 59 GLN Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain t residue 30 VAL Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 2 ASP Chi-restraints excluded: chain w residue 40 LEU Chi-restraints excluded: chain w residue 43 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 579 optimal weight: 20.0000 chunk 374 optimal weight: 20.0000 chunk 559 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 595 optimal weight: 50.0000 chunk 638 optimal weight: 30.0000 chunk 463 optimal weight: 30.0000 chunk 87 optimal weight: 5.9990 chunk 736 optimal weight: 20.0000 overall best weight: 7.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 202 ASN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 122 GLN ** e 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 128 ASN m 73 ASN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 154986 Z= 0.291 Angle : 0.577 11.910 232891 Z= 0.296 Chirality : 0.035 0.315 29855 Planarity : 0.004 0.060 11967 Dihedral : 24.059 179.668 80276 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 4.12 % Allowed : 26.47 % Favored : 69.42 % 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: 0.41 (0.12), residues: 5115 helix: 1.58 (0.13), residues: 1721 sheet: -0.23 (0.16), residues: 1075 loop : -0.41 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP t 34 HIS 0.009 0.001 HIS J 11 PHE 0.014 0.001 PHE f 97 TYR 0.017 0.001 TYR d 168 ARG 0.015 0.000 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 483 time to evaluate : 7.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8309 (mtp) REVERT: G 13 LYS cc_start: 0.9078 (pptt) cc_final: 0.8871 (pptt) REVERT: H 90 MET cc_start: 0.9026 (ptp) cc_final: 0.8787 (ptp) REVERT: H 127 LYS cc_start: 0.9231 (mmtt) cc_final: 0.8991 (mmtt) REVERT: H 159 MET cc_start: 0.8844 (mtm) cc_final: 0.8269 (mpp) REVERT: I 55 ARG cc_start: 0.4328 (OUTLIER) cc_final: 0.3932 (ptt180) REVERT: I 88 MET cc_start: 0.7752 (mmm) cc_final: 0.7456 (tpp) REVERT: J 2 LYS cc_start: 0.7944 (mmmt) cc_final: 0.7712 (mmmt) REVERT: J 23 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7450 (t0) REVERT: M 49 ASP cc_start: 0.8111 (p0) cc_final: 0.7483 (p0) REVERT: N 90 ASP cc_start: 0.8558 (p0) cc_final: 0.8167 (p0) REVERT: O 96 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8433 (p0) REVERT: R 24 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8885 (ptp-170) REVERT: T 59 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8547 (ttmm) REVERT: T 97 GLU cc_start: 0.8352 (tp30) cc_final: 0.8019 (tp30) REVERT: V 66 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8586 (tm-30) REVERT: W 48 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8827 (tppt) REVERT: X 7 ASP cc_start: 0.8260 (m-30) cc_final: 0.7896 (m-30) REVERT: 2 20 ASP cc_start: 0.8462 (t0) cc_final: 0.8159 (t0) REVERT: 2 24 GLU cc_start: 0.8398 (pt0) cc_final: 0.8127 (pt0) REVERT: 2 41 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8362 (pt) REVERT: 5 6 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8427 (mtt-85) REVERT: 5 38 LYS cc_start: 0.9501 (mmtp) cc_final: 0.9194 (mmmt) REVERT: 7 14 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.7976 (ttp80) REVERT: 8 3 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.9046 (ptmt) REVERT: d 66 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6686 (m-30) REVERT: d 84 ASP cc_start: 0.8676 (t0) cc_final: 0.8443 (m-30) REVERT: d 183 ASP cc_start: 0.8618 (t0) cc_final: 0.8182 (t70) REVERT: e 42 LYS cc_start: 0.5420 (OUTLIER) cc_final: 0.5209 (pttm) REVERT: e 119 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8613 (mp) REVERT: f 120 MET cc_start: 0.8507 (ttp) cc_final: 0.8186 (ttp) REVERT: g 5 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7902 (tm-30) REVERT: g 43 TRP cc_start: 0.8183 (OUTLIER) cc_final: 0.7766 (p-90) REVERT: g 74 GLU cc_start: 0.8210 (tp30) cc_final: 0.7925 (tp30) REVERT: j 47 GLN cc_start: 0.7154 (tm-30) cc_final: 0.6736 (tm-30) REVERT: j 58 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7889 (t80) REVERT: j 82 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8027 (t0) REVERT: j 120 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8706 (mmtt) REVERT: k 88 MET cc_start: 0.9043 (mpp) cc_final: 0.8625 (mpp) REVERT: o 10 ASN cc_start: 0.8019 (m-40) cc_final: 0.7483 (t0) REVERT: p 19 ASP cc_start: 0.8435 (p0) cc_final: 0.8072 (p0) REVERT: q 39 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7548 (ptp-110) REVERT: q 107 ASN cc_start: 0.9238 (m110) cc_final: 0.8782 (m110) REVERT: s 59 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8560 (mt0) REVERT: t 34 TRP cc_start: 0.8697 (OUTLIER) cc_final: 0.6660 (t-100) REVERT: t 73 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: w 43 HIS cc_start: 0.9098 (OUTLIER) cc_final: 0.8629 (m90) outliers start: 176 outliers final: 126 residues processed: 615 average time/residue: 1.2069 time to fit residues: 1326.5242 Evaluate side-chains 619 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 471 time to evaluate : 5.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 55 ARG Chi-restraints excluded: chain I residue 69 SER 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 23 ASP Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 98 ILE 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 R residue 65 SER Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 115 GLU Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 40 ARG Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain Z residue 81 VAL Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 2 residue 5 THR 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 6 residue 25 THR Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 8 residue 3 LYS Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 19 THR Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 25 ASP Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 206 ASP Chi-restraints excluded: chain e residue 42 LYS Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 119 LEU Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 7 MET Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 66 LYS Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 82 ASP Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 16 GLU Chi-restraints excluded: chain k residue 76 ILE Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 51 ILE Chi-restraints excluded: chain l residue 85 GLU Chi-restraints excluded: chain l residue 96 LYS Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 122 GLU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 39 ARG Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 18 ARG Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain s residue 56 ASN Chi-restraints excluded: chain s residue 59 GLN Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain t residue 30 VAL Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 2 ASP Chi-restraints excluded: chain w residue 40 LEU Chi-restraints excluded: chain w residue 43 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 852 optimal weight: 10.0000 chunk 897 optimal weight: 6.9990 chunk 818 optimal weight: 0.8980 chunk 873 optimal weight: 20.0000 chunk 525 optimal weight: 20.0000 chunk 380 optimal weight: 20.0000 chunk 685 optimal weight: 10.0000 chunk 267 optimal weight: 20.0000 chunk 788 optimal weight: 10.0000 chunk 825 optimal weight: 20.0000 chunk 869 optimal weight: 20.0000 overall best weight: 7.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 202 ASN H 62 ASN ** R 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 128 ASN m 73 ASN o 49 GLN p 37 GLN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 154986 Z= 0.288 Angle : 0.577 13.483 232891 Z= 0.297 Chirality : 0.035 0.316 29855 Planarity : 0.004 0.059 11967 Dihedral : 24.041 179.883 80276 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.62 % Favored : 96.36 % Rotamer: Outliers : 3.95 % Allowed : 26.61 % Favored : 69.44 % 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: 0.42 (0.12), residues: 5115 helix: 1.60 (0.13), residues: 1714 sheet: -0.24 (0.16), residues: 1069 loop : -0.38 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP t 34 HIS 0.011 0.001 HIS J 11 PHE 0.014 0.001 PHE S 73 TYR 0.014 0.001 TYR Q 47 ARG 0.014 0.000 ARG k 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 484 time to evaluate : 5.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 127 LYS cc_start: 0.9234 (mmtt) cc_final: 0.9003 (mmtt) REVERT: H 159 MET cc_start: 0.8845 (mtm) cc_final: 0.8254 (mpp) REVERT: J 23 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7492 (t0) REVERT: J 33 ARG cc_start: 0.8876 (ptp-170) cc_final: 0.8665 (ptp90) REVERT: N 90 ASP cc_start: 0.8570 (p0) cc_final: 0.8183 (p0) REVERT: O 96 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8413 (p0) REVERT: R 24 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8872 (ptp-170) REVERT: T 59 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8553 (ttmm) REVERT: T 97 GLU cc_start: 0.8355 (tp30) cc_final: 0.8021 (tp30) REVERT: V 66 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8588 (tm-30) REVERT: W 48 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8827 (tppt) REVERT: X 7 ASP cc_start: 0.8258 (m-30) cc_final: 0.7883 (m-30) REVERT: 2 20 ASP cc_start: 0.8405 (t0) cc_final: 0.8074 (t0) REVERT: 2 24 GLU cc_start: 0.8396 (pt0) cc_final: 0.8122 (pt0) REVERT: 2 41 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8381 (pt) REVERT: 5 6 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8423 (mtt-85) REVERT: 5 38 LYS cc_start: 0.9497 (mmtp) cc_final: 0.9198 (mmmt) REVERT: 7 14 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.7993 (ttp80) REVERT: 8 3 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.9050 (ptmt) REVERT: v 16 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.7993 (mptp) REVERT: d 66 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.6855 (m-30) REVERT: d 84 ASP cc_start: 0.8742 (t0) cc_final: 0.8531 (m-30) REVERT: d 183 ASP cc_start: 0.8635 (t0) cc_final: 0.8211 (t70) REVERT: e 119 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8607 (mp) REVERT: f 120 MET cc_start: 0.8518 (ttp) cc_final: 0.8231 (ttp) REVERT: g 5 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7937 (tm-30) REVERT: g 43 TRP cc_start: 0.8230 (OUTLIER) cc_final: 0.7971 (p-90) REVERT: g 74 GLU cc_start: 0.8182 (tp30) cc_final: 0.7898 (tp30) REVERT: j 47 GLN cc_start: 0.7107 (tm-30) cc_final: 0.6795 (tm-30) REVERT: j 58 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7892 (t80) REVERT: j 82 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7977 (t0) REVERT: j 120 LYS cc_start: 0.9021 (mmtt) cc_final: 0.8749 (mmtt) REVERT: k 23 ARG cc_start: 0.8144 (mtm110) cc_final: 0.7881 (mtm110) REVERT: k 88 MET cc_start: 0.9017 (mpp) cc_final: 0.8603 (mpp) REVERT: m 75 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8541 (pp30) REVERT: n 75 GLN cc_start: 0.8602 (pp30) cc_final: 0.8343 (pp30) REVERT: o 10 ASN cc_start: 0.7845 (m-40) cc_final: 0.7372 (t0) REVERT: p 19 ASP cc_start: 0.8465 (p0) cc_final: 0.8115 (p0) REVERT: q 39 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7513 (ptp-110) REVERT: q 45 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6929 (tp30) REVERT: q 107 ASN cc_start: 0.9214 (m110) cc_final: 0.8743 (m110) REVERT: s 59 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8542 (mt0) REVERT: t 34 TRP cc_start: 0.8653 (OUTLIER) cc_final: 0.6621 (t-100) REVERT: t 73 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: w 43 HIS cc_start: 0.9097 (OUTLIER) cc_final: 0.8631 (m90) REVERT: w 124 PHE cc_start: 0.6371 (t80) cc_final: 0.5954 (t80) outliers start: 169 outliers final: 132 residues processed: 612 average time/residue: 1.2277 time to fit residues: 1349.1294 Evaluate side-chains 626 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 473 time to evaluate : 5.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 69 SER 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 23 ASP Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 60 ASP 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 M residue 143 LYS Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 98 ILE 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 R residue 73 ILE Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 115 GLU Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 40 ARG Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain Z residue 81 VAL Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 10 LEU 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 37 ARG Chi-restraints excluded: chain 6 residue 25 THR Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 3 LYS Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 19 THR Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain v residue 16 LYS Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 25 ASP Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 206 ASP Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 119 LEU Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain f residue 152 SER Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 7 MET Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 66 LYS Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 82 ASP Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 16 GLU Chi-restraints excluded: chain k residue 76 ILE Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 51 ILE Chi-restraints excluded: chain l residue 85 GLU Chi-restraints excluded: chain l residue 96 LYS Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 75 GLN Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain q residue 39 ARG Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 18 ARG Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain s residue 56 ASN Chi-restraints excluded: chain s residue 59 GLN Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain t residue 30 VAL Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 2 ASP Chi-restraints excluded: chain w residue 40 LEU Chi-restraints excluded: chain w residue 43 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 573 optimal weight: 10.0000 chunk 923 optimal weight: 8.9990 chunk 563 optimal weight: 10.0000 chunk 437 optimal weight: 20.0000 chunk 641 optimal weight: 30.0000 chunk 968 optimal weight: 9.9990 chunk 891 optimal weight: 4.9990 chunk 771 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 595 optimal weight: 50.0000 chunk 472 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 202 ASN H 62 ASN ** R 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 122 GLN ** e 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 99 ASN l 128 ASN m 73 ASN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 154986 Z= 0.313 Angle : 0.590 12.124 232891 Z= 0.303 Chirality : 0.036 0.318 29855 Planarity : 0.005 0.075 11967 Dihedral : 24.036 179.851 80276 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.13 % Rotamer: Outliers : 3.88 % Allowed : 26.72 % Favored : 69.39 % 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: 0.37 (0.12), residues: 5115 helix: 1.52 (0.13), residues: 1721 sheet: -0.24 (0.16), residues: 1055 loop : -0.42 (0.13), residues: 2339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP t 34 HIS 0.012 0.001 HIS J 11 PHE 0.013 0.002 PHE f 97 TYR 0.017 0.001 TYR d 168 ARG 0.013 0.000 ARG k 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 484 time to evaluate : 5.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 90 MET cc_start: 0.9059 (ptp) cc_final: 0.8783 (ptp) REVERT: H 127 LYS cc_start: 0.9245 (mmtt) cc_final: 0.9009 (mmtt) REVERT: H 159 MET cc_start: 0.8847 (mtm) cc_final: 0.8255 (mpp) REVERT: J 23 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7611 (t0) REVERT: J 33 ARG cc_start: 0.9008 (ptp-170) cc_final: 0.8797 (ptp90) REVERT: N 90 ASP cc_start: 0.8576 (p0) cc_final: 0.8193 (p0) REVERT: O 96 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8395 (p0) REVERT: O 97 GLU cc_start: 0.8345 (mp0) cc_final: 0.7823 (mm-30) REVERT: R 24 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8899 (ptp-170) REVERT: T 59 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8553 (ttmm) REVERT: T 97 GLU cc_start: 0.8349 (tp30) cc_final: 0.8009 (tp30) REVERT: V 66 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8588 (tm-30) REVERT: W 48 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8845 (tppt) REVERT: X 7 ASP cc_start: 0.8259 (m-30) cc_final: 0.7877 (m-30) REVERT: 2 20 ASP cc_start: 0.8420 (t0) cc_final: 0.8104 (t0) REVERT: 2 24 GLU cc_start: 0.8395 (pt0) cc_final: 0.8134 (pt0) REVERT: 2 41 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8392 (pt) REVERT: 5 6 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8468 (mtt-85) REVERT: 5 38 LYS cc_start: 0.9499 (mmtp) cc_final: 0.9201 (mmmt) REVERT: 7 14 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.7994 (ttp80) REVERT: 8 3 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9058 (ptmt) REVERT: v 16 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.7995 (mptp) REVERT: d 66 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.6774 (m-30) REVERT: d 84 ASP cc_start: 0.8779 (t0) cc_final: 0.8577 (m-30) REVERT: d 183 ASP cc_start: 0.8598 (t0) cc_final: 0.8172 (t70) REVERT: e 42 LYS cc_start: 0.5588 (OUTLIER) cc_final: 0.5301 (pttm) REVERT: e 119 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8632 (mp) REVERT: f 120 MET cc_start: 0.8534 (ttp) cc_final: 0.8288 (ttp) REVERT: g 5 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7942 (tm-30) REVERT: g 43 TRP cc_start: 0.8216 (OUTLIER) cc_final: 0.7939 (p-90) REVERT: g 51 GLU cc_start: 0.8344 (tp30) cc_final: 0.8088 (tp30) REVERT: g 73 SER cc_start: 0.9293 (m) cc_final: 0.9076 (p) REVERT: h 4 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8759 (mttp) REVERT: j 47 GLN cc_start: 0.7111 (tm-30) cc_final: 0.6817 (tm-30) REVERT: j 58 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7895 (t80) REVERT: j 82 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7983 (t0) REVERT: k 15 HIS cc_start: 0.6221 (OUTLIER) cc_final: 0.5936 (t-170) REVERT: k 88 MET cc_start: 0.9035 (mpp) cc_final: 0.8663 (mpp) REVERT: n 75 GLN cc_start: 0.8602 (pp30) cc_final: 0.8335 (pp30) REVERT: o 10 ASN cc_start: 0.7845 (m-40) cc_final: 0.7331 (t0) REVERT: p 19 ASP cc_start: 0.8529 (p0) cc_final: 0.8168 (p0) REVERT: q 39 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7550 (ptp-110) REVERT: q 107 ASN cc_start: 0.9213 (m110) cc_final: 0.8697 (m110) REVERT: s 59 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8548 (mt0) REVERT: t 34 TRP cc_start: 0.8642 (OUTLIER) cc_final: 0.6572 (t-100) REVERT: t 73 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: w 43 HIS cc_start: 0.9098 (OUTLIER) cc_final: 0.8625 (m90) REVERT: w 59 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: w 124 PHE cc_start: 0.6522 (t80) cc_final: 0.6076 (t80) outliers start: 166 outliers final: 132 residues processed: 606 average time/residue: 1.1523 time to fit residues: 1251.2319 Evaluate side-chains 629 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 473 time to evaluate : 5.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 69 SER 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 I residue 120 GLU Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 60 ASP 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 94 ARG Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 98 ILE 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 R residue 65 SER Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 115 GLU Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 40 ARG Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain Z residue 81 VAL Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 6 ARG Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 25 THR Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 3 LYS Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 19 THR Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain v residue 16 LYS Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 25 ASP Chi-restraints excluded: chain d residue 61 ASP Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 206 ASP Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 42 LYS Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 119 LEU Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain f residue 152 SER Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 7 MET Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 66 LYS Chi-restraints excluded: chain h residue 4 LYS Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 82 ASP Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 76 ILE Chi-restraints excluded: chain k residue 99 ASN Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 51 ILE Chi-restraints excluded: chain l residue 85 GLU Chi-restraints excluded: chain l residue 96 LYS Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain q residue 39 ARG Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 18 ARG Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain s residue 56 ASN Chi-restraints excluded: chain s residue 59 GLN Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain t residue 30 VAL Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 2 ASP Chi-restraints excluded: chain w residue 40 LEU Chi-restraints excluded: chain w residue 43 HIS Chi-restraints excluded: chain w residue 59 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 612 optimal weight: 20.0000 chunk 821 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 711 optimal weight: 40.0000 chunk 113 optimal weight: 8.9990 chunk 214 optimal weight: 0.0870 chunk 772 optimal weight: 0.7980 chunk 323 optimal weight: 20.0000 chunk 793 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 overall best weight: 2.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 202 ASN H 62 ASN ** R 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 122 GLN ** e 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 128 ASN ** m 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.040570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.029043 restraints weight = 970468.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.029735 restraints weight = 484181.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.029558 restraints weight = 329537.941| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.210 154986 Z= 0.262 Angle : 0.612 59.196 232891 Z= 0.319 Chirality : 0.035 1.349 29855 Planarity : 0.004 0.071 11967 Dihedral : 24.039 179.842 80276 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.13 % Rotamer: Outliers : 3.83 % Allowed : 26.86 % Favored : 69.30 % Cbeta Deviations : 0.02 % 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: 0.37 (0.12), residues: 5115 helix: 1.53 (0.13), residues: 1721 sheet: -0.24 (0.16), residues: 1055 loop : -0.41 (0.13), residues: 2339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP t 34 HIS 0.012 0.001 HIS J 11 PHE 0.012 0.001 PHE S 73 TYR 0.015 0.001 TYR d 168 ARG 0.010 0.000 ARG l 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23312.27 seconds wall clock time: 414 minutes 26.99 seconds (24866.99 seconds total)