Starting phenix.real_space_refine on Tue Apr 16 16:55:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi7_37559/04_2024/8wi7_37559.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi7_37559/04_2024/8wi7_37559.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/8wi7_37559/04_2024/8wi7_37559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi7_37559/04_2024/8wi7_37559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi7_37559/04_2024/8wi7_37559.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi7_37559/04_2024/8wi7_37559.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 4658 5.49 5 S 94 5.16 5 C 72514 2.51 5 N 27065 2.21 5 O 40477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "G GLU 23": "OE1" <-> "OE2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G GLU 163": "OE1" <-> "OE2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "I GLU 117": "OE1" <-> "OE2" Residue "J TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 97": "OE1" <-> "OE2" Residue "Q GLU 30": "OE1" <-> "OE2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 82": "OE1" <-> "OE2" Residue "Q GLU 114": "OE1" <-> "OE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R GLU 98": "OE1" <-> "OE2" Residue "S PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "S PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 56": "OE1" <-> "OE2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S GLU 101": "OE1" <-> "OE2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T GLU 97": "OE1" <-> "OE2" Residue "U GLU 25": "OE1" <-> "OE2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W GLU 47": "OE1" <-> "OE2" Residue "X GLU 36": "OE1" <-> "OE2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "2 GLU 9": "OE1" <-> "OE2" Residue "2 GLU 24": "OE1" <-> "OE2" Residue "2 GLU 27": "OE1" <-> "OE2" Residue "2 GLU 28": "OE1" <-> "OE2" Residue "2 GLU 63": "OE1" <-> "OE2" Residue "2 GLU 65": "OE1" <-> "OE2" Residue "3 GLU 38": "OE1" <-> "OE2" Residue "6 GLU 16": "OE1" <-> "OE2" Residue "6 GLU 37": "OE1" <-> "OE2" Residue "6 GLU 53": "OE1" <-> "OE2" Residue "4 GLU 8": "OE1" <-> "OE2" Residue "g GLU 5": "OE1" <-> "OE2" Residue "g GLU 24": "OE1" <-> "OE2" Residue "g GLU 83": "OE1" <-> "OE2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k GLU 63": "OE1" <-> "OE2" Residue "n GLU 67": "OE1" <-> "OE2" Residue "n GLU 83": "OE1" <-> "OE2" Residue "o GLU 92": "OE1" <-> "OE2" Residue "q GLU 45": "OE1" <-> "OE2" Residue "q GLU 54": "OE1" <-> "OE2" Residue "q GLU 90": "OE1" <-> "OE2" Residue "r GLU 14": "OE1" <-> "OE2" Residue "u GLU 49": "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: 144808 Number of models: 1 Model: "" Number of chains: 51 Chain: "E" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2110 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 19, 'TRANS': 255} Chain: "F" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "G" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1569 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "H" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1445 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "I" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1260 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 11, 'TRANS': 153} Chain: "J" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 308 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "M" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "N" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "O" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "Q" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "S" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 907 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "T" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "U" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "V" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "W" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 747 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "X" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 710 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain breaks: 1 Chain: "Z" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 568 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "1" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "2" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "3" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 474 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} 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: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 498 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} 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: 64965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3025, 64965 Classifications: {'RNA': 3025} Modifications used: {'rna2p_pur': 293, 'rna2p_pyr': 148, 'rna3p_pur': 1438, 'rna3p_pyr': 1146} Link IDs: {'rna2p': 441, 'rna3p': 2583} Chain breaks: 2 Chain: "B" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2522 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 47} Link IDs: {'rna2p': 14, 'rna3p': 103} 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: "b" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1193 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 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: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1656 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} 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: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1223 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 8, 'TRANS': 159} 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: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} 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: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 949 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} 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: "c" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1793 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "w" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2030 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 20, 'TRANS': 234} Time building chain proxies: 53.00, per 1000 atoms: 0.37 Number of scatterers: 144808 At special positions: 0 Unit cell: (279.27, 263.22, 243.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 P 4658 15.00 O 40477 8.00 N 27065 7.00 C 72514 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: 59.05 Conformation dependent library (CDL) restraints added in 6.3 seconds 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10472 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 73 sheets defined 37.3% alpha, 21.2% beta 1596 base pairs and 2353 stacking pairs defined. Time for finding SS restraints: 48.99 Creating SS restraints... Processing helix chain 'E' and resid 10 through 14 removed outlier: 3.719A 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 198 through 204 removed outlier: 4.244A pdb=" N SER E 202 " --> pdb=" O ALA E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 removed outlier: 4.042A pdb=" N MET E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 266 removed outlier: 4.088A pdb=" N LYS E 266 " --> pdb=" O PRO E 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 62 removed outlier: 3.853A pdb=" N VAL F 62 " --> pdb=" O PRO F 59 " (cutoff:3.500A) 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: 3.577A 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 removed outlier: 3.703A pdb=" N ASN G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 149 Processing helix chain 'G' and resid 162 through 169 Processing helix chain 'G' and resid 179 through 183 removed outlier: 3.779A pdb=" N LEU G 183 " --> pdb=" O PRO G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 191 removed outlier: 3.543A 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 18 Processing helix chain 'H' and resid 18 through 28 Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.936A pdb=" N ILE H 35 " --> pdb=" O VAL H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 53 removed outlier: 3.511A pdb=" N ALA H 51 " --> pdb=" O GLY H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 69 removed outlier: 3.557A pdb=" N ASN H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 113 removed outlier: 3.560A pdb=" N MET H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'I' and resid 3 through 7 Processing helix chain 'I' and resid 59 through 83 removed outlier: 4.524A pdb=" N GLY I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU I 68 " --> pdb=" O SER I 64 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU I 82 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 151 Processing helix chain 'J' and resid 22 through 29 Processing helix chain 'M' and resid 24 through 38 Processing helix chain 'M' and resid 58 through 62 Processing helix chain 'M' and resid 89 through 96 Processing helix chain 'M' and resid 96 through 107 removed outlier: 3.982A pdb=" N VAL M 100 " --> pdb=" O HIS M 96 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL M 101 " --> pdb=" O PRO M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 120 removed outlier: 3.799A pdb=" N LYS M 120 " --> pdb=" O ARG M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 136 removed outlier: 4.594A pdb=" N ALA M 134 " --> pdb=" O PRO M 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 109 removed outlier: 4.156A 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: 3.841A pdb=" N LEU O 9 " --> pdb=" O LEU O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 87 Processing helix chain 'O' and resid 94 through 102 Processing helix chain 'O' and resid 130 through 140 removed outlier: 3.505A 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: 3.608A pdb=" N LYS Q 57 " --> pdb=" O THR Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 71 removed outlier: 4.040A pdb=" N LYS Q 69 " --> pdb=" O GLU Q 65 " (cutoff:3.500A) removed outlier: 3.562A 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: 3.545A pdb=" N LEU R 25 " --> pdb=" O ARG R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 72 Processing helix chain 'R' and resid 76 through 95 Processing helix chain 'R' and resid 111 through 123 Processing helix chain 'S' and resid 4 through 12 removed outlier: 4.171A pdb=" N ALA S 10 " --> pdb=" O PHE S 6 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER S 11 " --> pdb=" O VAL S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 55 removed outlier: 3.831A 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 removed outlier: 3.571A pdb=" N GLU S 101 " --> pdb=" O TYR S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 108 removed outlier: 3.650A pdb=" N LYS S 108 " --> pdb=" O LYS S 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 21 removed outlier: 3.867A pdb=" N LYS T 13 " --> pdb=" O ASN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.771A pdb=" N ARG T 28 " --> pdb=" O ARG T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 72 removed outlier: 3.538A pdb=" N ARG T 51 " --> pdb=" O TYR T 47 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS T 54 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY T 55 " --> pdb=" O ARG T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 87 Processing helix chain 'T' and resid 91 through 102 Processing helix chain 'T' and resid 102 through 117 Processing helix chain 'U' and resid 51 through 57 Processing helix chain 'V' and resid 20 through 29 removed outlier: 3.532A pdb=" N VAL V 27 " --> pdb=" O LYS V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 45 Processing helix chain 'V' and resid 50 through 68 removed outlier: 3.716A 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 17 through 25 Processing helix chain 'W' and resid 38 through 51 Processing helix chain '1' and resid 53 through 58 Processing helix chain '2' and resid 6 through 11 removed outlier: 3.503A pdb=" N LEU 2 10 " --> pdb=" O THR 2 6 " (cutoff:3.500A) Processing helix chain '2' and resid 14 through 39 Processing helix chain '2' and resid 44 through 67 removed outlier: 4.243A pdb=" N ARG 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) Processing helix chain '3' and resid 16 through 27 Processing helix chain '3' and resid 40 through 50 Processing helix chain '5' and resid 9 through 18 Processing helix chain '5' and resid 43 through 49 Processing helix chain '7' and resid 11 through 20 Processing helix chain '7' and resid 20 through 27 removed outlier: 3.803A pdb=" N THR 7 27 " --> pdb=" O LEU 7 23 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 41 Processing helix chain '8' and resid 7 through 14 Processing helix chain '8' and resid 37 through 44 Processing helix chain '8' and resid 51 through 63 removed outlier: 4.519A pdb=" N SER 8 56 " --> pdb=" O ALA 8 52 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ARG 8 57 " --> pdb=" O ALA 8 53 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 6 removed outlier: 3.848A pdb=" N ILE 4 5 " --> pdb=" O LYS 4 2 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS 4 6 " --> pdb=" O THR 4 3 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 2 through 6' Processing helix chain '4' and resid 42 through 47 Processing helix chain '4' and resid 57 through 65 Processing helix chain 'b' and resid 19 through 30 removed outlier: 3.686A pdb=" N ILE b 30 " --> pdb=" O ILE b 26 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 80 Processing helix chain 'b' and resid 104 through 118 Processing helix chain 'b' and resid 151 through 153 No H-bonds generated for 'chain 'b' and resid 151 through 153' Processing helix chain 'v' and resid 4 through 32 removed outlier: 5.394A pdb=" N VAL v 26 " --> pdb=" O ARG v 22 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLN v 27 " --> pdb=" O ARG v 23 " (cutoff:3.500A) 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: 3.726A 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 111 through 126 removed outlier: 3.966A pdb=" N ASN d 125 " --> pdb=" O GLU d 121 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG d 126 " --> pdb=" O GLN d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 128 through 143 removed outlier: 3.698A pdb=" N ARG d 142 " --> pdb=" O GLN d 138 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN d 143 " --> pdb=" O SER d 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 160 removed outlier: 3.558A pdb=" N ALA d 160 " --> pdb=" O LEU d 157 " (cutoff:3.500A) Processing helix chain 'e' and resid 8 through 16 Processing helix chain 'e' and resid 24 through 29 Processing helix chain 'e' and resid 44 through 60 removed outlier: 3.642A 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 removed outlier: 3.545A pdb=" N LEU e 145 " --> pdb=" O GLU e 142 " (cutoff:3.500A) No H-bonds generated for '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: 4.824A pdb=" N ASP e 187 " --> pdb=" O ARG e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 200 removed outlier: 4.000A 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 202 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: 4.366A pdb=" N VAL g 29 " --> pdb=" O THR g 25 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE g 30 " --> pdb=" O PHE g 26 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY g 34 " --> pdb=" O ILE g 30 " (cutoff:3.500A) removed outlier: 3.941A 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: 3.851A 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: 3.668A pdb=" N THR h 61 " --> pdb=" O ASP h 57 " (cutoff:3.500A) Processing helix chain 'h' and resid 92 through 110 removed outlier: 3.548A pdb=" N GLN h 110 " --> pdb=" O ASN h 106 " (cutoff:3.500A) 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: 4.347A pdb=" N HIS h 153 " --> pdb=" O ALA h 150 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR h 154 " --> pdb=" O PHE h 151 " (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 122 Processing helix chain 'k' and resid 14 through 32 Processing helix chain 'k' and resid 80 through 89 Processing helix chain 'l' and resid 57 through 60 removed outlier: 3.738A 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 removed outlier: 3.612A pdb=" N ARG l 65 " --> pdb=" O LYS l 62 " (cutoff:3.500A) 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 21 through 25 Processing helix chain 'm' and resid 113 through 118 removed outlier: 3.750A pdb=" N GLY m 118 " --> pdb=" O SER m 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 14 through 20 Processing helix chain 'n' and resid 27 through 38 Processing helix chain 'n' and resid 44 through 48 removed outlier: 3.533A pdb=" N ASP n 47 " --> pdb=" O ARG n 44 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU n 48 " --> pdb=" O THR n 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 44 through 48' 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: 3.606A 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 62 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 removed outlier: 3.609A pdb=" N GLU q 114 " --> pdb=" O LEU q 110 " (cutoff:3.500A) Processing helix chain 's' and resid 34 through 40 removed outlier: 3.775A pdb=" N LEU s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) 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: 3.664A 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: 3.994A 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 'c' and resid 7 through 13 removed outlier: 3.858A pdb=" N SER c 12 " --> pdb=" O GLN c 8 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY c 13 " --> pdb=" O LEU c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 24 through 29 removed outlier: 4.375A pdb=" N ARG c 29 " --> pdb=" O LYS c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 63 removed outlier: 3.880A pdb=" N THR c 46 " --> pdb=" O ASP c 42 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS c 52 " --> pdb=" O THR c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 73 through 75 No H-bonds generated for 'chain 'c' and resid 73 through 75' Processing helix chain 'c' and resid 76 through 88 removed outlier: 3.807A pdb=" N ILE c 80 " --> pdb=" O ALA c 76 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 124 removed outlier: 3.936A pdb=" N LYS c 109 " --> pdb=" O SER c 105 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG c 110 " --> pdb=" O THR c 106 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 148 Processing helix chain 'c' and resid 150 through 154 removed outlier: 4.027A pdb=" N ASP c 153 " --> pdb=" O GLY c 150 " (cutoff:3.500A) Processing helix chain 'c' and resid 169 through 180 Processing helix chain 'c' and resid 206 through 227 Processing helix chain 'w' and resid 13 through 23 Processing helix chain 'w' and resid 24 through 26 No H-bonds generated for 'chain 'w' and resid 24 through 26' Processing helix chain 'w' and resid 73 through 93 Processing helix chain 'w' and resid 95 through 100 Processing helix chain 'w' and resid 145 through 157 removed outlier: 3.717A pdb=" N LEU w 156 " --> pdb=" O GLU w 152 " (cutoff:3.500A) Processing helix chain 'w' and resid 178 through 180 No H-bonds generated for 'chain 'w' and resid 178 through 180' Processing helix chain 'w' and resid 213 through 225 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: 6.609A pdb=" N ILE E 92 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE E 82 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU E 94 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 130 through 132 removed outlier: 5.818A pdb=" N LEU E 165 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG E 176 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY E 167 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG E 184 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 5.865A 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: 6.115A 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: 6.701A pdb=" N VAL F 28 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N MET F 13 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL F 26 " --> pdb=" O MET F 13 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLN F 15 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL F 24 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS F 195 " --> pdb=" O VAL F 182 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL F 182 " --> pdb=" O LYS F 195 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL F 112 " --> pdb=" O ASN F 179 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR F 117 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 7.228A 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: 3.776A pdb=" N ARG F 38 " --> pdb=" O GLN F 51 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA F 53 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 5.881A 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: 3.739A pdb=" N GLY F 122 " --> pdb=" O MET F 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 14 through 20 removed outlier: 4.029A pdb=" N GLY G 16 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU G 3 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ILE G 124 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP G 6 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA G 126 " --> pdb=" O ASP G 6 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N HIS G 125 " --> pdb=" O PHE G 196 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU G 155 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N SER G 197 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 7.375A 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: 3.565A pdb=" N GLY H 93 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA H 94 " --> pdb=" O MET H 45 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS H 40 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR H 135 " --> pdb=" O VAL H 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 16 through 20 Processing sheet with id=AB3, first strand: chain 'I' and resid 42 through 46 removed outlier: 3.676A pdb=" N SER I 42 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR I 54 " --> pdb=" O SER I 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 122 through 125 removed outlier: 4.219A pdb=" N GLU I 89 " --> pdb=" O ARG I 164 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG I 164 " --> pdb=" O GLU I 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 96 through 100 removed outlier: 3.547A pdb=" N ARG I 96 " --> pdb=" O ALA I 107 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN I 98 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU I 105 " --> pdb=" O GLN I 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 18 through 20 removed outlier: 3.754A 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: 6.212A pdb=" N VAL M 54 " --> pdb=" O LYS M 123 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR M 16 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE M 57 " --> pdb=" O TYR M 16 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE M 18 " --> pdb=" O ILE M 57 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TRP M 15 " --> pdb=" O ILE M 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'M' and resid 73 through 77 removed outlier: 3.616A pdb=" N ARG M 87 " --> pdb=" O ALA M 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 7 through 10 removed outlier: 6.312A pdb=" N LYS N 17 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA N 16 " --> pdb=" O ALA N 46 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA N 46 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU N 18 " --> pdb=" O LYS N 44 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL N 40 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL N 24 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL N 38 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS N 59 " --> pdb=" O ILE N 87 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA N 83 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA N 84 " --> pdb=" O ARG N 7 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS N 9 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 7.767A 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: 6.523A pdb=" N THR S 57 " --> pdb=" O ARG S 49 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG S 49 " --> pdb=" O THR S 57 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR S 59 " --> pdb=" O ILE S 47 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU S 63 " --> pdb=" O LYS S 43 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N LYS S 43 " --> pdb=" O GLU S 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG S 38 " --> pdb=" O VAL S 31 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR S 24 " --> pdb=" O LEU S 86 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP S 84 " --> pdb=" O ASN S 26 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS S 82 " --> pdb=" O HIS S 28 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS S 30 " --> pdb=" O ILE S 80 " (cutoff:3.500A) removed outlier: 6.460A 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: 6.180A pdb=" N GLN O 76 " --> pdb=" O LYS O 111 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU O 113 " --> pdb=" O GLN O 76 " (cutoff:3.500A) removed outlier: 6.303A 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: 7.780A pdb=" N THR O 145 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 5.903A 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 Processing sheet with id=AC5, first strand: chain 'R' and resid 58 through 64 removed outlier: 6.070A pdb=" N THR R 59 " --> pdb=" O ASN R 53 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN R 53 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.934A 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: 4.398A 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: 6.971A pdb=" N TYR U 4 " --> pdb=" O VAL U 42 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL U 42 " --> pdb=" O TYR U 4 " (cutoff:3.500A) removed outlier: 6.301A 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: 6.576A pdb=" N LEU U 94 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS U 67 " --> pdb=" O LEU U 94 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL U 96 " --> pdb=" O LEU U 65 " (cutoff:3.500A) removed outlier: 7.193A 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 78 Processing sheet with id=AD1, first strand: chain 'V' and resid 9 through 17 removed outlier: 6.591A pdb=" N SER V 9 " --> pdb=" O SER V 116 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N SER V 116 " --> pdb=" O SER V 9 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N THR V 11 " --> pdb=" O VAL V 114 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL V 114 " --> pdb=" O THR V 11 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LYS V 13 " --> pdb=" O VAL V 112 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL V 112 " --> pdb=" O LYS V 13 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ARG V 15 " --> pdb=" O ILE V 110 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE V 110 " --> pdb=" O ARG V 15 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU V 115 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 5.509A 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: 4.500A pdb=" N LYS W 80 " --> pdb=" O VAL W 33 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER W 56 " --> pdb=" O LYS W 85 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'W' and resid 66 through 69 Processing sheet with id=AD5, first strand: chain 'X' and resid 66 through 67 removed outlier: 3.593A pdb=" N VAL X 25 " --> pdb=" O LEU X 34 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR X 8 " --> pdb=" O VAL X 74 " (cutoff:3.500A) removed outlier: 4.051A 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 88 Processing sheet with id=AD8, first strand: chain 'Z' and resid 22 through 23 removed outlier: 6.850A 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 removed outlier: 3.579A pdb=" N THR 1 25 " --> pdb=" O SER 1 17 " (cutoff:3.500A) 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 31 Processing sheet with id=AE5, first strand: chain '6' and resid 21 through 26 removed outlier: 6.632A pdb=" N ARG 6 21 " --> pdb=" O CYS 6 15 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N CYS 6 15 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR 6 47 " --> pdb=" O CYS 6 42 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '8' and resid 15 through 16 Processing sheet with id=AE7, first strand: chain '4' and resid 21 through 26 Processing sheet with id=AE8, first strand: chain 'b' and resid 38 through 42 removed outlier: 6.795A pdb=" N ILE b 101 " --> pdb=" O LEU b 91 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'b' and resid 50 through 53 Processing sheet with id=AF1, first strand: chain 'b' and resid 168 through 169 removed outlier: 3.752A pdb=" N GLY b 128 " --> pdb=" O ILE b 169 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR b 129 " --> pdb=" O ASP b 141 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE b 139 " --> pdb=" O ILE b 131 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG b 145 " --> pdb=" O VAL b 183 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU b 185 " --> pdb=" O ARG b 145 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE b 147 " --> pdb=" O LEU b 185 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL b 184 " --> pdb=" O ILE b 174 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'd' and resid 20 through 21 removed outlier: 3.582A pdb=" N ARG d 58 " --> pdb=" O ARG d 21 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP d 53 " --> pdb=" O HIS d 68 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL d 63 " --> pdb=" O GLN d 99 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ASN d 101 " --> pdb=" O VAL d 63 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL d 65 " --> pdb=" O ASN d 101 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU d 103 " --> pdb=" O VAL d 65 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE d 67 " --> pdb=" O LEU d 103 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 164 through 171 removed outlier: 3.936A pdb=" N LYS d 204 " --> pdb=" O ASP d 181 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ASP d 181 " --> pdb=" O LYS d 204 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'e' and resid 123 through 124 Processing sheet with id=AF5, first strand: chain 'f' and resid 37 through 49 removed outlier: 5.339A pdb=" N GLU f 38 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLY f 65 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL f 40 " --> pdb=" O ILE f 63 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE f 63 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER f 42 " --> pdb=" O LEU f 61 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'f' and resid 101 through 102 removed outlier: 3.551A pdb=" N THR f 105 " --> pdb=" O ILE f 102 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'f' and resid 110 through 114 removed outlier: 6.399A pdb=" N ILE f 131 " --> pdb=" O ALA f 150 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N SER f 152 " --> pdb=" O ILE f 131 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'g' and resid 37 through 42 removed outlier: 3.789A pdb=" N VAL g 37 " --> pdb=" O LYS g 66 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 37 through 42 removed outlier: 3.789A pdb=" N VAL g 37 " --> pdb=" O LYS g 66 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 73 through 79 Processing sheet with id=AG2, first strand: chain 'i' and resid 24 through 28 removed outlier: 3.670A pdb=" N ASP i 48 " --> pdb=" O GLN i 63 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'i' and resid 76 through 79 Processing sheet with id=AG4, first strand: chain 'i' and resid 76 through 79 removed outlier: 6.931A pdb=" N ILE i 105 " --> pdb=" O LEU i 128 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR i 130 " --> pdb=" O VAL i 103 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL i 103 " --> pdb=" O TYR i 130 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'j' and resid 27 through 32 removed outlier: 6.689A pdb=" N ASN j 49 " --> pdb=" O ALA j 85 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU j 87 " --> pdb=" O ASN j 49 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.023A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS k 11 " --> pdb=" O ASP k 97 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.023A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'l' and resid 49 through 55 removed outlier: 5.583A pdb=" N VAL l 50 " --> pdb=" O ASP l 45 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASP l 45 " --> pdb=" O VAL l 50 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA l 52 " --> pdb=" O ILE l 43 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY l 28 " --> pdb=" O ASP l 92 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N PHE l 94 " --> pdb=" O GLY l 28 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA l 30 " --> pdb=" O PHE l 94 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LYS l 96 " --> pdb=" O ALA l 30 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE l 32 " --> pdb=" O LYS l 96 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL l 91 " --> pdb=" O GLY l 117 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE l 119 " --> pdb=" O VAL l 91 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL l 93 " --> pdb=" O ILE l 119 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASP l 121 " --> pdb=" O VAL l 93 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL l 95 " --> pdb=" O ASP l 121 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'm' and resid 29 through 40 removed outlier: 5.970A pdb=" N CYS m 34 " --> pdb=" O LYS m 56 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS m 56 " --> pdb=" O CYS m 34 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N TYR m 95 " --> pdb=" O GLU m 62 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR m 64 " --> pdb=" O TYR m 95 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE m 97 " --> pdb=" O THR m 64 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR m 66 " --> pdb=" O ILE m 97 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'n' and resid 3 through 4 Processing sheet with id=AH2, first strand: chain 'o' and resid 73 through 74 removed outlier: 3.581A pdb=" N LEU o 79 " --> pdb=" O LEU o 74 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'q' and resid 49 through 51 removed outlier: 5.965A pdb=" N VAL q 36 " --> pdb=" O VAL q 22 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL q 22 " --> pdb=" O VAL q 36 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL q 3 " --> pdb=" O GLN q 65 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'r' and resid 22 through 32 removed outlier: 15.914A pdb=" N THR r 22 " --> pdb=" O ARG r 43 " (cutoff:3.500A) removed outlier: 12.292A pdb=" N ARG r 43 " --> pdb=" O THR r 22 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE r 24 " --> pdb=" O GLU r 41 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU r 41 " --> pdb=" O ILE r 24 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL r 37 " --> pdb=" O VAL r 28 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASP r 30 " --> pdb=" O THR r 35 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR r 35 " --> pdb=" O ASP r 30 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LYS r 86 " --> pdb=" O LYS r 58 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LYS r 60 " --> pdb=" O LYS r 86 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU r 90 " --> pdb=" O HIS r 62 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG r 87 " --> pdb=" O PRO r 81 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG r 89 " --> pdb=" O THR r 79 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N THR r 79 " --> pdb=" O ARG r 89 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL r 91 " --> pdb=" O MET r 77 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N MET r 77 " --> pdb=" O VAL r 91 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE r 93 " --> pdb=" O SER r 75 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER r 75 " --> pdb=" O ILE r 93 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 't' and resid 31 through 33 removed outlier: 7.100A pdb=" N ILE t 31 " --> pdb=" O ALA t 50 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N HIS t 52 " --> pdb=" O ILE t 31 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N THR t 33 " --> pdb=" O HIS t 52 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'c' and resid 16 through 19 removed outlier: 5.916A pdb=" N PHE c 16 " --> pdb=" O ILE c 41 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE c 41 " --> pdb=" O PHE c 16 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS c 18 " --> pdb=" O TYR c 39 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE c 38 " --> pdb=" O ASP c 34 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP c 34 " --> pdb=" O ILE c 38 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE c 40 " --> pdb=" O PHE c 32 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'c' and resid 91 through 92 removed outlier: 8.400A pdb=" N VAL c 92 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE c 69 " --> pdb=" O VAL c 92 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU c 68 " --> pdb=" O TRP c 162 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL c 164 " --> pdb=" O LEU c 68 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL c 70 " --> pdb=" O VAL c 164 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL c 161 " --> pdb=" O ILE c 184 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ILE c 186 " --> pdb=" O VAL c 161 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL c 163 " --> pdb=" O ILE c 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'w' and resid 3 through 6 removed outlier: 5.500A pdb=" N HIS w 35 " --> pdb=" O ASP w 59 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ASP w 59 " --> pdb=" O HIS w 35 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'w' and resid 143 through 144 Processing sheet with id=AI1, first strand: chain 'w' and resid 211 through 212 1969 hydrogen bonds defined for protein. 5565 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4078 hydrogen bonds 6430 hydrogen bond angles 0 basepair planarities 1596 basepair parallelities 2353 stacking parallelities Total time for adding SS restraints: 231.91 Time building geometry restraints manager: 64.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 18963 1.33 - 1.45: 68875 1.45 - 1.57: 60120 1.57 - 1.70: 9314 1.70 - 1.82: 161 Bond restraints: 157433 Sorted by residual: bond pdb=" CB PRO c 182 " pdb=" CG PRO c 182 " ideal model delta sigma weight residual 1.492 1.625 -0.133 5.00e-02 4.00e+02 7.07e+00 bond pdb=" C ARG w 131 " pdb=" O ARG w 131 " ideal model delta sigma weight residual 1.236 1.206 0.030 1.16e-02 7.43e+03 6.85e+00 bond pdb=" CB PRO d 108 " pdb=" CG PRO d 108 " ideal model delta sigma weight residual 1.492 1.616 -0.124 5.00e-02 4.00e+02 6.17e+00 bond pdb=" CB PRO h 58 " pdb=" CG PRO h 58 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.78e+00 bond pdb=" C ASP o 33 " pdb=" N PRO o 34 " ideal model delta sigma weight residual 1.335 1.351 -0.016 8.70e-03 1.32e+04 3.58e+00 ... (remaining 157428 not shown) Histogram of bond angle deviations from ideal: 97.23 - 105.02: 21512 105.02 - 112.80: 94197 112.80 - 120.59: 68524 120.59 - 128.37: 45092 128.37 - 136.15: 6512 Bond angle restraints: 235837 Sorted by residual: angle pdb=" CA PRO c 182 " pdb=" N PRO c 182 " pdb=" CD PRO c 182 " ideal model delta sigma weight residual 112.00 100.71 11.29 1.40e+00 5.10e-01 6.50e+01 angle pdb=" CA PRO h 58 " pdb=" N PRO h 58 " pdb=" CD PRO h 58 " ideal model delta sigma weight residual 112.00 100.74 11.26 1.40e+00 5.10e-01 6.47e+01 angle pdb=" CA PRO d 108 " pdb=" N PRO d 108 " pdb=" CD PRO d 108 " ideal model delta sigma weight residual 112.00 102.36 9.64 1.40e+00 5.10e-01 4.74e+01 angle pdb=" C4' G a1425 " pdb=" C3' G a1425 " pdb=" O3' G a1425 " ideal model delta sigma weight residual 113.00 105.34 7.66 1.50e+00 4.44e-01 2.61e+01 angle pdb=" C THR F 156 " pdb=" N PRO F 157 " pdb=" CA PRO F 157 " ideal model delta sigma weight residual 119.19 114.00 5.19 1.06e+00 8.90e-01 2.40e+01 ... (remaining 235832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 88298 35.99 - 71.97: 11744 71.97 - 107.96: 1334 107.96 - 143.95: 35 143.95 - 179.93: 48 Dihedral angle restraints: 101459 sinusoidal: 85165 harmonic: 16294 Sorted by residual: dihedral pdb=" O4' C A1535 " pdb=" C1' C A1535 " pdb=" N1 C A1535 " pdb=" C2 C A1535 " ideal model delta sinusoidal sigma weight residual -160.00 15.44 -175.44 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C A3046 " pdb=" C1' C A3046 " pdb=" N1 C A3046 " pdb=" C2 C A3046 " ideal model delta sinusoidal sigma weight residual -160.00 11.99 -171.99 1 1.50e+01 4.44e-03 8.49e+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 28.94 171.06 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 101456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 27773 0.058 - 0.116: 2072 0.116 - 0.174: 247 0.174 - 0.232: 42 0.232 - 0.290: 8 Chirality restraints: 30142 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 2.17 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1' U a1206 " pdb=" O4' U a1206 " pdb=" C2' U a1206 " pdb=" N1 U a1206 " both_signs ideal model delta sigma weight residual False 2.47 2.19 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU n 56 " pdb=" CB LEU n 56 " pdb=" CD1 LEU n 56 " pdb=" CD2 LEU n 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 30139 not shown) Planarity restraints: 12620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP h 57 " 0.100 5.00e-02 4.00e+02 1.43e-01 3.26e+01 pdb=" N PRO h 58 " -0.246 5.00e-02 4.00e+02 pdb=" CA PRO h 58 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO h 58 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE c 181 " 0.065 5.00e-02 4.00e+02 9.21e-02 1.36e+01 pdb=" N PRO c 182 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO c 182 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO c 182 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN d 107 " 0.061 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO d 108 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO d 108 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO d 108 " 0.048 5.00e-02 4.00e+02 ... (remaining 12617 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.96: 19 1.96 - 2.70: 9588 2.70 - 3.43: 190560 3.43 - 4.17: 472231 4.17 - 4.90: 647060 Nonbonded interactions: 1319458 Sorted by model distance: nonbonded pdb=" OE1 GLU 4 36 " pdb=" N THR n 54 " model vdw 1.231 2.520 nonbonded pdb=" OE1 GLU 4 36 " pdb=" C VAL n 53 " model vdw 1.444 3.270 nonbonded pdb=" OE2 GLU 4 36 " pdb=" O ASP n 50 " model vdw 1.530 3.040 nonbonded pdb=" OG SER H 143 " pdb=" NH2 ARG n 3 " model vdw 1.706 2.520 nonbonded pdb=" O2 C a 598 " pdb=" NZ LYS q 12 " model vdw 1.746 2.520 ... (remaining 1319453 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: 3.340 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: 0.080 Extract box with map and model: 16.130 Check model and map are aligned: 1.560 Set scattering table: 0.970 Process input model: 491.870 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.390 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 519.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 : 0.002 0.133 157433 Z= 0.153 Angle : 0.539 11.900 235837 Z= 0.283 Chirality : 0.033 0.290 30142 Planarity : 0.004 0.143 12620 Dihedral : 24.048 179.931 90987 Min Nonbonded Distance : 1.231 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 0.45 % Allowed : 28.34 % Favored : 71.22 % 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: 0.46 (0.11), residues: 5634 helix: 1.51 (0.12), residues: 1861 sheet: -0.03 (0.15), residues: 1141 loop : -0.35 (0.12), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP w 96 HIS 0.017 0.001 HIS J 11 PHE 0.042 0.001 PHE b 22 TYR 0.040 0.001 TYR c 49 ARG 0.014 0.000 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 4719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 623 time to evaluate : 5.391 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: F 100 GLU cc_start: 0.8100 (tp30) cc_final: 0.7738 (mm-30) REVERT: G 106 MET cc_start: 0.8397 (mtt) cc_final: 0.7948 (mtt) REVERT: I 141 LYS cc_start: 0.9303 (mmpt) cc_final: 0.8982 (mmtm) REVERT: R 90 GLU cc_start: 0.8798 (pm20) cc_final: 0.8506 (pm20) REVERT: T 107 THR cc_start: 0.9275 (m) cc_final: 0.9041 (p) REVERT: W 36 ASP cc_start: 0.8446 (m-30) cc_final: 0.8215 (m-30) REVERT: 1 60 LYS cc_start: 0.8086 (mttt) cc_final: 0.7247 (tptt) REVERT: 2 20 ASP cc_start: 0.8444 (m-30) cc_final: 0.8085 (m-30) REVERT: 2 23 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.7954 (ttm-80) REVERT: 5 37 ARG cc_start: 0.7847 (ptp-110) cc_final: 0.7602 (ptp-110) REVERT: 5 53 ASP cc_start: 0.8147 (m-30) cc_final: 0.7703 (p0) REVERT: 5 54 LEU cc_start: 0.8499 (mt) cc_final: 0.8247 (mt) REVERT: 6 47 THR cc_start: 0.4944 (p) cc_final: 0.4447 (p) REVERT: 4 25 ARG cc_start: 0.2227 (ppt170) cc_final: 0.1900 (ttp80) REVERT: d 114 LEU cc_start: 0.7242 (mm) cc_final: 0.6815 (tp) REVERT: d 124 SER cc_start: 0.7224 (t) cc_final: 0.6994 (p) REVERT: d 201 TRP cc_start: 0.3662 (m-90) cc_final: 0.3192 (m-90) REVERT: e 139 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7110 (m-30) REVERT: f 196 LYS cc_start: 0.8892 (pttp) cc_final: 0.7914 (mmmt) REVERT: g 1 MET cc_start: 0.7817 (mmm) cc_final: 0.6984 (mmm) REVERT: g 11 ASP cc_start: 0.8272 (p0) cc_final: 0.7916 (p0) REVERT: g 41 ASP cc_start: 0.8250 (t70) cc_final: 0.8045 (p0) REVERT: g 66 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8403 (tmtt) REVERT: j 82 ASP cc_start: 0.8301 (t70) cc_final: 0.7995 (t0) REVERT: j 84 TYR cc_start: 0.8120 (m-80) cc_final: 0.7839 (m-80) REVERT: j 111 GLN cc_start: 0.8518 (tp-100) cc_final: 0.8283 (tp40) REVERT: k 45 GLU cc_start: 0.8157 (tt0) cc_final: 0.7819 (tt0) REVERT: l 90 LYS cc_start: 0.8335 (ttpt) cc_final: 0.8085 (ttpt) REVERT: n 15 MET cc_start: 0.7590 (tpp) cc_final: 0.7169 (tpt) REVERT: o 4 LYS cc_start: 0.9098 (tppp) cc_final: 0.8587 (tttm) REVERT: o 9 LYS cc_start: 0.8339 (tptm) cc_final: 0.7701 (ttpp) REVERT: p 14 GLN cc_start: 0.8109 (tt0) cc_final: 0.7862 (tt0) REVERT: p 15 TYR cc_start: 0.8277 (m-80) cc_final: 0.7989 (m-80) REVERT: q 98 PRO cc_start: 0.8955 (Cg_exo) cc_final: 0.8296 (Cg_endo) outliers start: 21 outliers final: 8 residues processed: 637 average time/residue: 1.2466 time to fit residues: 1377.7766 Evaluate side-chains 475 residues out of total 4719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 466 time to evaluate : 5.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 16 GLU Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain w residue 131 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 857 optimal weight: 6.9990 chunk 770 optimal weight: 30.0000 chunk 427 optimal weight: 50.0000 chunk 263 optimal weight: 9.9990 chunk 519 optimal weight: 20.0000 chunk 411 optimal weight: 10.0000 chunk 796 optimal weight: 1.9990 chunk 308 optimal weight: 50.0000 chunk 484 optimal weight: 20.0000 chunk 592 optimal weight: 20.0000 chunk 922 optimal weight: 2.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 ASN H 187 ASN I 22 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 GLN ** S 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 40 GLN 5 36 GLN ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 117 GLN h 49 GLN ** i 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 61 ASN l 31 HIS n 88 GLN o 12 GLN p 28 GLN q 107 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 157433 Z= 0.255 Angle : 0.572 9.732 235837 Z= 0.294 Chirality : 0.034 0.323 30142 Planarity : 0.005 0.082 12620 Dihedral : 24.003 179.295 79730 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 3.79 % Allowed : 25.33 % Favored : 70.88 % 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 (0.11), residues: 5634 helix: 1.49 (0.12), residues: 1891 sheet: -0.04 (0.16), residues: 1126 loop : -0.32 (0.12), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP w 96 HIS 0.006 0.001 HIS 7 19 PHE 0.015 0.002 PHE d 129 TYR 0.036 0.002 TYR c 49 ARG 0.012 0.001 ARG g 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 4719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 517 time to evaluate : 6.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 100 GLU cc_start: 0.8105 (tp30) cc_final: 0.7850 (mm-30) REVERT: G 106 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8502 (mtt) REVERT: H 85 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8322 (pptt) REVERT: Q 89 ASP cc_start: 0.8509 (p0) cc_final: 0.8241 (p0) REVERT: R 4 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8487 (mmmt) REVERT: R 24 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8105 (ptp90) REVERT: X 88 ASP cc_start: 0.5297 (OUTLIER) cc_final: 0.4460 (t0) REVERT: Z 68 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7028 (tm-30) REVERT: 1 60 LYS cc_start: 0.8159 (mttt) cc_final: 0.7271 (tptt) REVERT: 2 20 ASP cc_start: 0.8611 (m-30) cc_final: 0.8024 (m-30) REVERT: 2 41 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8243 (pt) REVERT: 5 53 ASP cc_start: 0.8162 (m-30) cc_final: 0.7718 (p0) REVERT: 8 57 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.7773 (mtm-85) REVERT: 4 65 TYR cc_start: 0.8034 (m-80) cc_final: 0.7823 (m-80) REVERT: d 124 SER cc_start: 0.7481 (t) cc_final: 0.7221 (p) REVERT: d 133 MET cc_start: 0.7492 (mpp) cc_final: 0.7198 (mpp) REVERT: e 42 LYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6508 (pttm) REVERT: e 139 ASP cc_start: 0.7203 (OUTLIER) cc_final: 0.6961 (m-30) REVERT: f 196 LYS cc_start: 0.9041 (pttp) cc_final: 0.8128 (mmmt) REVERT: g 1 MET cc_start: 0.7638 (mmm) cc_final: 0.7075 (mmm) REVERT: g 11 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8034 (p0) REVERT: g 24 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8537 (mp0) REVERT: g 64 ASP cc_start: 0.8231 (m-30) cc_final: 0.7977 (m-30) REVERT: g 66 LYS cc_start: 0.8975 (ttmm) cc_final: 0.8554 (tmtt) REVERT: j 82 ASP cc_start: 0.8329 (t70) cc_final: 0.8083 (t0) REVERT: j 84 TYR cc_start: 0.8161 (m-80) cc_final: 0.7773 (m-80) REVERT: j 111 GLN cc_start: 0.8398 (tp-100) cc_final: 0.7956 (tp-100) REVERT: k 45 GLU cc_start: 0.8109 (tt0) cc_final: 0.7751 (tt0) REVERT: k 66 GLU cc_start: 0.6970 (pm20) cc_final: 0.6717 (pm20) REVERT: l 45 ASP cc_start: 0.8859 (t70) cc_final: 0.8417 (t0) REVERT: l 47 GLN cc_start: 0.8412 (mp10) cc_final: 0.8073 (mp10) REVERT: l 115 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7322 (tp30) REVERT: o 9 LYS cc_start: 0.8402 (tptm) cc_final: 0.7735 (ttpt) REVERT: p 11 ILE cc_start: 0.9286 (mt) cc_final: 0.8990 (mp) REVERT: s 52 ARG cc_start: 0.8287 (mpp80) cc_final: 0.7834 (ptt-90) REVERT: c 1 MET cc_start: 0.5140 (ptp) cc_final: 0.4509 (ptp) REVERT: c 54 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: c 59 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8488 (tm-30) REVERT: w 57 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.7860 (m-40) outliers start: 179 outliers final: 70 residues processed: 655 average time/residue: 1.2237 time to fit residues: 1406.5475 Evaluate side-chains 543 residues out of total 4719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 461 time to evaluate : 5.962 ------------------------------------------------------------------------------- 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 190 ARG Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 6 residue 8 ARG Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 49 THR Chi-restraints excluded: chain 8 residue 54 ASP Chi-restraints excluded: chain 8 residue 57 ARG Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain e residue 42 LYS Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain f residue 201 SER Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 114 ASP Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 76 ILE Chi-restraints excluded: chain l residue 85 GLU Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain n residue 117 ILE Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain o residue 86 GLU Chi-restraints excluded: chain p residue 37 GLN Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain t residue 56 LYS Chi-restraints excluded: chain t residue 63 THR Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain c residue 54 TYR Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 142 ASN Chi-restraints excluded: chain w residue 57 ASN Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 145 THR Chi-restraints excluded: chain w residue 146 VAL Chi-restraints excluded: chain w residue 147 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 512 optimal weight: 20.0000 chunk 286 optimal weight: 20.0000 chunk 767 optimal weight: 6.9990 chunk 628 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 924 optimal weight: 10.0000 chunk 998 optimal weight: 10.0000 chunk 823 optimal weight: 6.9990 chunk 916 optimal weight: 30.0000 chunk 315 optimal weight: 40.0000 chunk 741 optimal weight: 20.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 46 HIS ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 25 GLN h 68 ASN o 12 GLN ** q 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 84 ASN ** c 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 167 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 157433 Z= 0.307 Angle : 0.593 10.210 235837 Z= 0.307 Chirality : 0.037 0.311 30142 Planarity : 0.005 0.079 12620 Dihedral : 23.986 179.162 79715 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.08 % Favored : 95.90 % Rotamer: Outliers : 5.32 % Allowed : 24.25 % Favored : 70.43 % 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: 0.43 (0.11), residues: 5634 helix: 1.47 (0.12), residues: 1888 sheet: 0.03 (0.16), residues: 1080 loop : -0.41 (0.12), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP w 96 HIS 0.005 0.001 HIS d 8 PHE 0.019 0.002 PHE j 59 TYR 0.041 0.002 TYR c 49 ARG 0.011 0.001 ARG 2 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 488 time to evaluate : 6.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 85 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.7952 (pptt) REVERT: N 80 ASP cc_start: 0.8203 (t0) cc_final: 0.7787 (t0) REVERT: R 4 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8328 (tptt) REVERT: R 24 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8108 (ptp90) REVERT: S 56 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8113 (tp30) REVERT: Z 68 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7280 (tm-30) REVERT: 1 60 LYS cc_start: 0.8333 (mttt) cc_final: 0.7507 (tptt) REVERT: 2 20 ASP cc_start: 0.8713 (m-30) cc_final: 0.7877 (m-30) REVERT: 3 38 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7715 (tm-30) REVERT: 5 53 ASP cc_start: 0.8221 (m-30) cc_final: 0.7758 (p0) REVERT: 7 28 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8083 (ttm-80) REVERT: 8 34 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8129 (tm-30) REVERT: 8 45 ASP cc_start: 0.7975 (t0) cc_final: 0.7741 (t0) REVERT: 8 57 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7632 (mtm-85) REVERT: 4 65 TYR cc_start: 0.8290 (m-80) cc_final: 0.8024 (m-80) REVERT: d 124 SER cc_start: 0.8097 (t) cc_final: 0.7810 (p) REVERT: e 111 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: e 139 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7203 (m-30) REVERT: f 120 MET cc_start: 0.8726 (ppp) cc_final: 0.8428 (ppp) REVERT: f 196 LYS cc_start: 0.9195 (pttp) cc_final: 0.8354 (mmmt) REVERT: g 57 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7693 (mm-30) REVERT: g 74 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8236 (tm-30) REVERT: h 68 ASN cc_start: 0.8954 (t160) cc_final: 0.8385 (t0) REVERT: h 116 MET cc_start: 0.8337 (tpp) cc_final: 0.8114 (tpp) REVERT: j 82 ASP cc_start: 0.8431 (t70) cc_final: 0.8105 (t0) REVERT: j 84 TYR cc_start: 0.8110 (m-80) cc_final: 0.7736 (m-80) REVERT: j 111 GLN cc_start: 0.8022 (tp-100) cc_final: 0.7472 (tp-100) REVERT: k 45 GLU cc_start: 0.8108 (tt0) cc_final: 0.7759 (tt0) REVERT: o 9 LYS cc_start: 0.8560 (tptm) cc_final: 0.8021 (ttpp) REVERT: t 15 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7619 (pt) REVERT: t 18 LYS cc_start: 0.8230 (mttp) cc_final: 0.7934 (mptp) REVERT: c 1 MET cc_start: 0.4984 (ptp) cc_final: 0.4471 (ptp) REVERT: c 44 GLN cc_start: 0.8808 (mp10) cc_final: 0.8540 (mp10) REVERT: c 49 TYR cc_start: 0.8632 (m-80) cc_final: 0.8281 (m-80) REVERT: c 54 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: c 59 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8831 (mm-30) REVERT: c 100 MET cc_start: 0.8427 (mtt) cc_final: 0.8166 (mtt) REVERT: w 34 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8773 (mt) REVERT: w 159 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8334 (p0) outliers start: 251 outliers final: 125 residues processed: 697 average time/residue: 1.2425 time to fit residues: 1523.0051 Evaluate side-chains 576 residues out of total 4719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 439 time to evaluate : 5.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 THR 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 163 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 15 ASP Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain W residue 26 ASP Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 16 LYS Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 28 ARG Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 48 THR Chi-restraints excluded: chain 8 residue 49 THR Chi-restraints excluded: chain 8 residue 54 ASP Chi-restraints excluded: chain 8 residue 57 ARG Chi-restraints excluded: chain 4 residue 26 SER Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 163 SER Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 97 PHE Chi-restraints excluded: chain f residue 155 SER Chi-restraints excluded: chain f residue 186 ILE Chi-restraints excluded: chain f residue 201 SER Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 41 LYS Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 114 ASP Chi-restraints excluded: chain j residue 131 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 76 ILE Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain m residue 109 ASN Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 12 ASP Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 103 THR Chi-restraints excluded: chain n residue 117 ILE Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 53 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain t residue 17 LYS Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain t residue 56 LYS Chi-restraints excluded: chain t residue 63 THR Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain c residue 54 TYR Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 142 ASN Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 139 PHE Chi-restraints excluded: chain w residue 145 THR Chi-restraints excluded: chain w residue 146 VAL Chi-restraints excluded: chain w residue 159 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 913 optimal weight: 4.9990 chunk 694 optimal weight: 20.0000 chunk 479 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 441 optimal weight: 20.0000 chunk 620 optimal weight: 20.0000 chunk 927 optimal weight: 8.9990 chunk 982 optimal weight: 20.0000 chunk 484 optimal weight: 20.0000 chunk 879 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN ** S 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 36 GLN 6 20 HIS 8 25 GLN ** h 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 ASN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 12 GLN p 28 GLN ** q 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 157433 Z= 0.290 Angle : 0.571 10.018 235837 Z= 0.294 Chirality : 0.036 0.314 30142 Planarity : 0.005 0.074 12620 Dihedral : 23.935 179.741 79715 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.94 % Favored : 96.04 % Rotamer: Outliers : 4.56 % Allowed : 25.58 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.11), residues: 5634 helix: 1.57 (0.12), residues: 1883 sheet: 0.05 (0.16), residues: 1093 loop : -0.47 (0.12), residues: 2658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP w 96 HIS 0.015 0.001 HIS w 249 PHE 0.014 0.001 PHE c 104 TYR 0.026 0.001 TYR c 49 ARG 0.026 0.001 ARG w 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 4719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 466 time to evaluate : 6.151 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: H 85 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.7838 (pptt) REVERT: H 103 MET cc_start: 0.8669 (ptm) cc_final: 0.8420 (ptm) REVERT: I 27 LYS cc_start: 0.7702 (tppt) cc_final: 0.7346 (tppt) REVERT: J 1 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.5215 (mmm) REVERT: N 80 ASP cc_start: 0.8153 (t0) cc_final: 0.7703 (t0) REVERT: N 88 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8525 (ptpp) REVERT: N 92 ASP cc_start: 0.8259 (t0) cc_final: 0.8002 (t0) REVERT: O 97 GLU cc_start: 0.8464 (mp0) cc_final: 0.8110 (mp0) REVERT: R 4 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8441 (tptt) REVERT: R 24 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8124 (ptp90) REVERT: R 116 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8832 (pt) REVERT: S 48 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8775 (ptt180) REVERT: X 7 ASP cc_start: 0.8507 (m-30) cc_final: 0.8197 (m-30) REVERT: X 88 ASP cc_start: 0.5602 (OUTLIER) cc_final: 0.5004 (t0) REVERT: Z 68 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7393 (tm-30) REVERT: 2 20 ASP cc_start: 0.8609 (m-30) cc_final: 0.7932 (m-30) REVERT: 2 41 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8432 (pt) REVERT: 3 38 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7716 (tm-30) REVERT: 5 53 ASP cc_start: 0.8213 (m-30) cc_final: 0.7729 (p0) REVERT: 6 53 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7797 (mm-30) REVERT: 8 57 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7703 (mtm-85) REVERT: e 111 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: f 120 MET cc_start: 0.8751 (ppp) cc_final: 0.8406 (ppp) REVERT: f 196 LYS cc_start: 0.9205 (pttp) cc_final: 0.8353 (mmmt) REVERT: g 66 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8664 (tmtt) REVERT: i 72 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8973 (mtt-85) REVERT: j 82 ASP cc_start: 0.8452 (t70) cc_final: 0.7917 (t0) REVERT: j 84 TYR cc_start: 0.8134 (m-80) cc_final: 0.7791 (m-80) REVERT: j 111 GLN cc_start: 0.8147 (tp-100) cc_final: 0.7785 (tp-100) REVERT: k 45 GLU cc_start: 0.8111 (tt0) cc_final: 0.7778 (tt0) REVERT: l 103 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8015 (mm-30) REVERT: n 15 MET cc_start: 0.8747 (tpp) cc_final: 0.8165 (tpp) REVERT: n 41 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8095 (ptpp) REVERT: o 9 LYS cc_start: 0.8535 (tptm) cc_final: 0.8071 (ttpt) REVERT: o 32 ARG cc_start: 0.4343 (mtp180) cc_final: 0.3345 (mmm160) REVERT: c 1 MET cc_start: 0.5133 (ptp) cc_final: 0.4676 (ptp) REVERT: c 54 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.7764 (m-80) REVERT: c 111 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8639 (mt) outliers start: 215 outliers final: 140 residues processed: 641 average time/residue: 1.2325 time to fit residues: 1390.7943 Evaluate side-chains 592 residues out of total 4719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 438 time to evaluate : 6.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 201 GLN Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 88 LYS Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 135 GLU Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 82 GLU Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 15 ASP Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 97 GLN Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 75 ASP Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 83 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 6 residue 32 ASP Chi-restraints excluded: chain 7 residue 28 ARG Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 49 THR Chi-restraints excluded: chain 8 residue 54 ASP Chi-restraints excluded: chain 8 residue 57 ARG Chi-restraints excluded: chain 4 residue 33 ILE Chi-restraints excluded: chain 4 residue 37 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain d residue 32 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 111 GLN Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain e residue 44 SER Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 186 ILE Chi-restraints excluded: chain f residue 201 SER Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 76 ASP Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 72 ARG Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 114 ASP Chi-restraints excluded: chain j residue 131 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 76 ILE Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 85 GLU Chi-restraints excluded: chain l residue 137 ARG Chi-restraints excluded: chain m residue 58 THR Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 109 ASN Chi-restraints excluded: chain n residue 19 LEU Chi-restraints excluded: chain n residue 39 ILE Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 103 THR Chi-restraints excluded: chain n residue 117 ILE Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 37 GLN Chi-restraints excluded: chain p residue 80 SER Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain r residue 94 LEU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain t residue 5 LEU Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain t residue 56 LYS Chi-restraints excluded: chain t residue 63 THR Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 43 ASP Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain c residue 54 TYR Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 142 ASN Chi-restraints excluded: chain c residue 159 SER Chi-restraints excluded: chain w residue 33 VAL Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 139 PHE Chi-restraints excluded: chain w residue 145 THR Chi-restraints excluded: chain w residue 146 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 817 optimal weight: 9.9990 chunk 557 optimal weight: 50.0000 chunk 14 optimal weight: 8.9990 chunk 731 optimal weight: 20.0000 chunk 405 optimal weight: 10.0000 chunk 838 optimal weight: 30.0000 chunk 678 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 501 optimal weight: 20.0000 chunk 881 optimal weight: 9.9990 chunk 247 optimal weight: 20.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 189 ASN ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 25 GLN e 167 GLN ** h 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 12 GLN ** q 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 157433 Z= 0.343 Angle : 0.606 10.142 235837 Z= 0.311 Chirality : 0.037 0.311 30142 Planarity : 0.005 0.066 12620 Dihedral : 23.956 179.248 79713 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.33 % Favored : 95.65 % Rotamer: Outliers : 5.07 % Allowed : 25.52 % 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: 0.36 (0.11), residues: 5634 helix: 1.52 (0.12), residues: 1900 sheet: -0.08 (0.16), residues: 1084 loop : -0.51 (0.12), residues: 2650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP w 96 HIS 0.007 0.001 HIS 6 20 PHE 0.028 0.002 PHE b 22 TYR 0.033 0.001 TYR c 49 ARG 0.010 0.001 ARG 6 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 467 time to evaluate : 5.472 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: E 226 MET cc_start: 0.8931 (mtt) cc_final: 0.8658 (mtt) REVERT: H 85 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.7859 (pptt) REVERT: I 27 LYS cc_start: 0.7741 (tppt) cc_final: 0.7525 (tppt) REVERT: J 1 MET cc_start: 0.6141 (OUTLIER) cc_final: 0.4897 (mmm) REVERT: N 80 ASP cc_start: 0.8146 (t0) cc_final: 0.7662 (t0) REVERT: N 88 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8503 (ptpp) REVERT: N 92 ASP cc_start: 0.8264 (t0) cc_final: 0.7948 (t0) REVERT: R 4 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8450 (tptt) REVERT: R 24 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.7966 (ptp90) REVERT: R 116 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8864 (pt) REVERT: S 48 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8790 (ptt180) REVERT: X 88 ASP cc_start: 0.5899 (OUTLIER) cc_final: 0.5237 (t0) REVERT: Z 68 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7440 (tm-30) REVERT: 2 20 ASP cc_start: 0.8656 (m-30) cc_final: 0.7868 (m-30) REVERT: 2 41 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8444 (pt) REVERT: 3 38 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7730 (tm-30) REVERT: 5 53 ASP cc_start: 0.8245 (m-30) cc_final: 0.7744 (p0) REVERT: 6 8 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8359 (mtp180) REVERT: 6 11 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8599 (tp) REVERT: 6 50 PRO cc_start: 0.9079 (Cg_exo) cc_final: 0.8671 (Cg_endo) REVERT: 7 3 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7816 (tptp) REVERT: 8 21 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8332 (mtmm) REVERT: 8 45 ASP cc_start: 0.8214 (t0) cc_final: 0.7922 (t0) REVERT: 8 57 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7682 (mtm-85) REVERT: b 99 ARG cc_start: 0.5558 (OUTLIER) cc_final: 0.5152 (ptt180) REVERT: e 42 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.5733 (pttt) REVERT: e 111 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: f 120 MET cc_start: 0.8812 (ppp) cc_final: 0.8456 (ppp) REVERT: f 196 LYS cc_start: 0.9222 (pttp) cc_final: 0.8484 (mmmt) REVERT: g 66 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8820 (tttp) REVERT: g 75 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9364 (tp) REVERT: i 72 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8993 (mtt-85) REVERT: j 95 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8740 (mt0) REVERT: k 45 GLU cc_start: 0.8105 (tt0) cc_final: 0.7785 (tt0) REVERT: m 9 ARG cc_start: 0.9418 (OUTLIER) cc_final: 0.8937 (mtm110) REVERT: o 9 LYS cc_start: 0.8630 (tptm) cc_final: 0.8140 (ttpt) REVERT: o 12 GLN cc_start: 0.8691 (mt0) cc_final: 0.8475 (mt0) REVERT: o 32 ARG cc_start: 0.4596 (mtp180) cc_final: 0.3449 (mmm160) REVERT: t 17 LYS cc_start: 0.9114 (mmtp) cc_final: 0.8891 (mmtm) REVERT: c 49 TYR cc_start: 0.8766 (m-80) cc_final: 0.8548 (m-80) REVERT: c 54 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: c 111 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8529 (mt) REVERT: w 34 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8772 (mt) REVERT: w 159 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8179 (p0) outliers start: 239 outliers final: 159 residues processed: 662 average time/residue: 1.1750 time to fit residues: 1368.0502 Evaluate side-chains 621 residues out of total 4719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 439 time to evaluate : 5.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 201 GLN Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 88 LYS Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 135 GLU Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 82 GLU Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 15 ASP Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 26 ASP Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 75 ASP Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 6 residue 8 ARG Chi-restraints excluded: chain 6 residue 11 ILE Chi-restraints excluded: chain 7 residue 3 LYS Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 25 GLN Chi-restraints excluded: chain 8 residue 49 THR Chi-restraints excluded: chain 8 residue 54 ASP Chi-restraints excluded: chain 8 residue 57 ARG Chi-restraints excluded: chain 4 residue 33 ILE Chi-restraints excluded: chain 4 residue 34 VAL Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 99 ARG Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain d residue 32 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 111 GLN Chi-restraints excluded: chain d residue 163 SER Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 42 LYS Chi-restraints excluded: chain e residue 44 SER Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 96 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 97 PHE Chi-restraints excluded: chain f residue 186 ILE Chi-restraints excluded: chain f residue 201 SER Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 76 ASP Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain h residue 144 MET Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 72 ARG Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 95 GLN Chi-restraints excluded: chain j residue 114 ASP Chi-restraints excluded: chain j residue 131 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 76 ILE Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 85 GLU Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 137 ARG Chi-restraints excluded: chain m residue 9 ARG Chi-restraints excluded: chain m residue 58 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 97 ILE Chi-restraints excluded: chain m residue 109 ASN Chi-restraints excluded: chain n residue 103 THR Chi-restraints excluded: chain n residue 117 ILE Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 62 ASN Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 19 ASP Chi-restraints excluded: chain p residue 37 GLN Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain r residue 94 LEU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 53 VAL Chi-restraints excluded: chain t residue 5 LEU Chi-restraints excluded: chain t residue 13 ASP Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 35 SER Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain t residue 56 LYS Chi-restraints excluded: chain t residue 63 THR Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 43 ASP Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain c residue 54 TYR Chi-restraints excluded: chain c residue 60 THR Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 142 ASN Chi-restraints excluded: chain w residue 33 VAL Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 139 PHE Chi-restraints excluded: chain w residue 145 THR Chi-restraints excluded: chain w residue 146 VAL Chi-restraints excluded: chain w residue 159 ASP Chi-restraints excluded: chain w residue 173 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 330 optimal weight: 20.0000 chunk 884 optimal weight: 20.0000 chunk 194 optimal weight: 5.9990 chunk 576 optimal weight: 10.0000 chunk 242 optimal weight: 20.0000 chunk 983 optimal weight: 8.9990 chunk 816 optimal weight: 0.6980 chunk 455 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 325 optimal weight: 10.0000 chunk 516 optimal weight: 20.0000 overall best weight: 7.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 46 HIS ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 25 GLN ** e 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 47 GLN ** q 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 157433 Z= 0.256 Angle : 0.560 10.932 235837 Z= 0.288 Chirality : 0.035 0.309 30142 Planarity : 0.004 0.066 12620 Dihedral : 23.933 179.877 79713 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.04 % Rotamer: Outliers : 4.30 % Allowed : 26.52 % Favored : 69.18 % 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 (0.11), residues: 5634 helix: 1.63 (0.12), residues: 1888 sheet: 0.02 (0.16), residues: 1074 loop : -0.47 (0.12), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP w 96 HIS 0.005 0.001 HIS X 4 PHE 0.032 0.001 PHE b 22 TYR 0.023 0.001 TYR c 49 ARG 0.016 0.000 ARG d 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 479 time to evaluate : 6.005 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: E 226 MET cc_start: 0.8973 (mtt) cc_final: 0.8669 (mtt) REVERT: G 69 LYS cc_start: 0.4675 (OUTLIER) cc_final: 0.4422 (mtpp) REVERT: H 85 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7990 (pptt) REVERT: J 1 MET cc_start: 0.6282 (OUTLIER) cc_final: 0.5356 (mmm) REVERT: M 91 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7752 (pm20) REVERT: N 80 ASP cc_start: 0.8096 (t0) cc_final: 0.7633 (t0) REVERT: N 88 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8503 (ptpp) REVERT: N 92 ASP cc_start: 0.8258 (t0) cc_final: 0.7920 (t0) REVERT: R 24 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.7950 (ptp90) REVERT: R 118 ASP cc_start: 0.8934 (m-30) cc_final: 0.8703 (m-30) REVERT: R 126 LYS cc_start: 0.8807 (pptt) cc_final: 0.8604 (pttp) REVERT: S 48 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8751 (ptt180) REVERT: S 56 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8073 (tp30) REVERT: X 7 ASP cc_start: 0.8471 (m-30) cc_final: 0.8162 (m-30) REVERT: X 88 ASP cc_start: 0.5851 (OUTLIER) cc_final: 0.5225 (t0) REVERT: Z 68 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7452 (tm-30) REVERT: 2 20 ASP cc_start: 0.8678 (m-30) cc_final: 0.8020 (m-30) REVERT: 2 41 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8337 (pt) REVERT: 3 38 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7661 (tm-30) REVERT: 5 53 ASP cc_start: 0.8187 (m-30) cc_final: 0.7661 (p0) REVERT: 6 53 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7675 (mm-30) REVERT: 8 45 ASP cc_start: 0.8082 (t0) cc_final: 0.7793 (t0) REVERT: 8 57 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.7700 (mtm-85) REVERT: d 34 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6612 (tp30) REVERT: d 35 ASP cc_start: 0.7286 (t0) cc_final: 0.6897 (m-30) REVERT: d 48 ARG cc_start: 0.6153 (mtm-85) cc_final: 0.5773 (ptt-90) REVERT: e 42 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.5739 (pttt) REVERT: e 111 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: f 120 MET cc_start: 0.8820 (ppp) cc_final: 0.8457 (ppp) REVERT: f 137 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8158 (ttm-80) REVERT: f 196 LYS cc_start: 0.9254 (pttp) cc_final: 0.8519 (mmmt) REVERT: h 116 MET cc_start: 0.8413 (tpp) cc_final: 0.8212 (tpp) REVERT: j 120 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8869 (mmtt) REVERT: k 45 GLU cc_start: 0.8092 (tt0) cc_final: 0.7762 (tt0) REVERT: m 9 ARG cc_start: 0.9398 (OUTLIER) cc_final: 0.8868 (mtm110) REVERT: n 41 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8143 (ptpp) REVERT: o 9 LYS cc_start: 0.8595 (tptm) cc_final: 0.8198 (ttpp) REVERT: o 32 ARG cc_start: 0.4509 (mtp180) cc_final: 0.3387 (mmm160) REVERT: t 56 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8795 (ptpt) REVERT: c 54 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: c 111 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8462 (mt) REVERT: w 34 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8762 (mt) outliers start: 203 outliers final: 143 residues processed: 647 average time/residue: 1.1903 time to fit residues: 1355.7478 Evaluate side-chains 618 residues out of total 4719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 454 time to evaluate : 5.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain M residue 91 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 88 LYS Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 135 GLU Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain Q residue 82 GLU Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain S residue 15 ASP Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 48 ARG Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 97 GLN Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 75 ASP Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 83 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 54 ASP Chi-restraints excluded: chain 8 residue 57 ARG Chi-restraints excluded: chain 4 residue 26 SER Chi-restraints excluded: chain 4 residue 33 ILE Chi-restraints excluded: chain 4 residue 37 VAL Chi-restraints excluded: chain b residue 32 TYR Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain d residue 34 GLU Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 125 ASN Chi-restraints excluded: chain d residue 163 SER Chi-restraints excluded: chain e residue 42 LYS Chi-restraints excluded: chain e residue 44 SER Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 137 ARG Chi-restraints excluded: chain f residue 186 ILE Chi-restraints excluded: chain f residue 201 SER Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 76 ASP Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain h residue 135 VAL Chi-restraints excluded: chain h residue 136 LYS Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 114 ASP Chi-restraints excluded: chain j residue 131 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 76 ILE Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 85 GLU Chi-restraints excluded: chain m residue 9 ARG Chi-restraints excluded: chain m residue 58 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 97 ILE Chi-restraints excluded: chain m residue 109 ASN Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 117 ILE Chi-restraints excluded: chain o residue 62 ASN Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 19 ASP Chi-restraints excluded: chain p residue 37 GLN Chi-restraints excluded: chain p residue 80 SER Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain r residue 94 LEU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 53 VAL Chi-restraints excluded: chain t residue 5 LEU Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 35 SER Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain t residue 56 LYS Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 43 ASP Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain c residue 54 TYR Chi-restraints excluded: chain c residue 60 THR Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 142 ASN Chi-restraints excluded: chain w residue 33 VAL Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 139 PHE Chi-restraints excluded: chain w residue 145 THR Chi-restraints excluded: chain w residue 146 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 947 optimal weight: 20.0000 chunk 110 optimal weight: 0.9990 chunk 560 optimal weight: 10.0000 chunk 717 optimal weight: 30.0000 chunk 556 optimal weight: 20.0000 chunk 827 optimal weight: 2.9990 chunk 548 optimal weight: 20.0000 chunk 979 optimal weight: 20.0000 chunk 612 optimal weight: 20.0000 chunk 597 optimal weight: 20.0000 chunk 452 optimal weight: 20.0000 overall best weight: 10.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 111 GLN ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 12 GLN ** q 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3688 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: