Starting phenix.real_space_refine on Sun Feb 18 15:16:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlw_11276/02_2024/6zlw_11276.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlw_11276/02_2024/6zlw_11276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlw_11276/02_2024/6zlw_11276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlw_11276/02_2024/6zlw_11276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlw_11276/02_2024/6zlw_11276.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlw_11276/02_2024/6zlw_11276.pdb" } resolution = 2.6 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= 0.000 sd= 0.716 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1665 5.49 5 S 182 5.16 5 C 40518 2.51 5 N 13743 2.21 5 O 18457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 136": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F ARG 116": "NH1" <-> "NH2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "H GLU 188": "OE1" <-> "OE2" Residue "H GLU 191": "OE1" <-> "OE2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I GLU 194": "OE1" <-> "OE2" Residue "J GLU 21": "OE1" <-> "OE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "K GLU 176": "OE1" <-> "OE2" Residue "K TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 195": "OE1" <-> "OE2" Residue "L GLU 52": "OE1" <-> "OE2" Residue "O GLU 97": "OE1" <-> "OE2" Residue "O GLU 117": "OE1" <-> "OE2" Residue "Q TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 31": "OE1" <-> "OE2" Residue "R GLU 61": "OE1" <-> "OE2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "S GLU 77": "OE1" <-> "OE2" Residue "S GLU 97": "OE1" <-> "OE2" Residue "S GLU 104": "OE1" <-> "OE2" Residue "U TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 107": "OE1" <-> "OE2" Residue "V GLU 111": "OE1" <-> "OE2" Residue "X GLU 53": "OE1" <-> "OE2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y GLU 98": "OE1" <-> "OE2" Residue "e ARG 31": "NH1" <-> "NH2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 223": "OE1" <-> "OE2" Residue "i GLU 155": "OE1" <-> "OE2" Residue "i GLU 159": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 74568 Number of models: 1 Model: "" Number of chains: 39 Chain: "B" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 12, 'TRANS': 193} Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1682 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "F" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "K" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "M" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 816 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "P" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1006 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 984 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "R" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1109 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "S" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "U" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "V" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "Z" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "a" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "c" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "d" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "e" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 403 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "f" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "g" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 591 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "h" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 213 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "j" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "2" Number of atoms: 35552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1665, 35552 Classifications: {'RNA': 1665} Modifications used: {'rna2p_pur': 134, 'rna2p_pyr': 115, 'rna3p_pur': 750, 'rna3p_pyr': 666} Link IDs: {'rna2p': 248, 'rna3p': 1416} Chain breaks: 11 Chain: "i" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 261 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 31} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33535 SG CYS c 23 88.287 166.198 106.511 1.00 22.51 S ATOM 33939 SG CYS c 74 90.208 162.989 105.114 1.00 19.71 S ATOM 33958 SG CYS c 77 91.080 166.331 103.643 1.00 19.98 S ATOM 35215 SG CYS f 21 157.793 161.006 69.425 1.00 9.67 S ATOM 35239 SG CYS f 24 155.053 158.545 68.158 1.00 12.82 S ATOM 35386 SG CYS f 42 155.673 158.736 72.009 1.00 17.06 S ATOM 36041 SG CYS g 141 179.837 153.338 27.237 1.00 32.13 S Time building chain proxies: 28.42, per 1000 atoms: 0.38 Number of scatterers: 74568 At special positions: 0 Unit cell: (216.036, 250.983, 203.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 182 16.00 P 1665 15.00 O 18457 8.00 N 13743 7.00 C 40518 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: 25.36 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 201 " pdb="ZN ZN c 201 " - pdb=" SG CYS c 74 " pdb="ZN ZN c 201 " - pdb=" SG CYS c 77 " pdb="ZN ZN c 201 " - pdb=" SG CYS c 23 " pdb=" ZN f 201 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 42 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 24 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 21 " pdb=" ZN g 500 " pdb="ZN ZN g 500 " - pdb=" SG CYS g 141 " 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9058 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 56 sheets defined 35.1% alpha, 18.7% beta 515 base pairs and 914 stacking pairs defined. Time for finding SS restraints: 22.87 Creating SS restraints... Processing helix chain 'B' and resid 5 through 9 removed outlier: 3.647A pdb=" N GLN B 9 " --> pdb=" O ASP B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.528A pdb=" N LYS B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 50 through 67 removed outlier: 3.597A pdb=" N ILE B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 167 through 186 removed outlier: 3.696A pdb=" N VAL B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.516A pdb=" N GLY C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 157 through 178 removed outlier: 3.549A pdb=" N ILE C 171 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET C 172 " --> pdb=" O MET C 168 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.546A pdb=" N VAL C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 202 Processing helix chain 'C' and resid 224 through 233 removed outlier: 3.574A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 77 through 84 removed outlier: 4.025A pdb=" N ILE D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 98 Processing helix chain 'D' and resid 99 through 102 removed outlier: 3.576A pdb=" N LEU D 102 " --> pdb=" O GLY D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 102' Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.647A pdb=" N ILE D 156 " --> pdb=" O ARG D 152 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 217 removed outlier: 3.713A pdb=" N LYS D 212 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU D 213 " --> pdb=" O VAL D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'D' and resid 269 through 274 removed outlier: 3.813A pdb=" N VAL D 274 " --> pdb=" O THR D 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 43 through 50 Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.645A pdb=" N LYS E 62 " --> pdb=" O GLY E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 247 through 259 removed outlier: 3.742A pdb=" N LYS E 254 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG E 255 " --> pdb=" O GLU E 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 removed outlier: 3.564A pdb=" N PHE F 11 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS F 18 " --> pdb=" O ASP F 14 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN F 22 " --> pdb=" O LYS F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 60 removed outlier: 3.860A pdb=" N VAL F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 78 removed outlier: 3.521A pdb=" N ARG F 67 " --> pdb=" O GLY F 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 96 Processing helix chain 'F' and resid 97 through 111 Processing helix chain 'F' and resid 114 through 130 removed outlier: 3.665A pdb=" N TYR F 120 " --> pdb=" O ARG F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 167 Processing helix chain 'G' and resid 137 through 145 removed outlier: 3.573A pdb=" N ARG G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 157 removed outlier: 4.040A pdb=" N VAL G 157 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 192 Processing helix chain 'G' and resid 192 through 217 removed outlier: 3.617A pdb=" N LYS G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU G 208 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 223 removed outlier: 3.847A pdb=" N LYS G 223 " --> pdb=" O GLU G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 230 removed outlier: 4.109A pdb=" N ILE G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA G 229 " --> pdb=" O GLN G 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 25 removed outlier: 3.530A pdb=" N ILE H 23 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 28 No H-bonds generated for 'chain 'H' and resid 26 through 28' Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 36 through 41 removed outlier: 3.637A pdb=" N ARG H 41 " --> pdb=" O LYS H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 74 removed outlier: 3.634A pdb=" N LYS H 74 " --> pdb=" O LYS H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 85 removed outlier: 3.769A pdb=" N ARG H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS H 85 " --> pdb=" O ARG H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 120 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.736A pdb=" N LEU H 130 " --> pdb=" O HIS H 126 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU H 131 " --> pdb=" O ASP H 127 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 169 through 181 removed outlier: 3.629A pdb=" N GLY H 175 " --> pdb=" O GLU H 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 88 through 93 removed outlier: 4.085A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR I 93 " --> pdb=" O GLU I 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 88 through 93' Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 133 through 138 Processing helix chain 'I' and resid 142 through 152 removed outlier: 3.881A pdb=" N LYS I 147 " --> pdb=" O LYS I 143 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG I 152 " --> pdb=" O LYS I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 164 removed outlier: 3.646A pdb=" N GLU I 164 " --> pdb=" O SER I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 169 removed outlier: 3.893A pdb=" N GLN I 168 " --> pdb=" O GLU I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 191 through 206 removed outlier: 3.684A pdb=" N ARG I 200 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS I 203 " --> pdb=" O LEU I 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 36 Processing helix chain 'J' and resid 40 through 61 removed outlier: 3.879A pdb=" N VAL J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.986A pdb=" N MET J 92 " --> pdb=" O GLU J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 100 Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.855A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 Processing helix chain 'J' and resid 122 through 132 removed outlier: 3.565A pdb=" N ARG J 127 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL J 128 " --> pdb=" O HIS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 181 removed outlier: 3.666A pdb=" N LYS J 180 " --> pdb=" O LYS J 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 22 removed outlier: 3.732A pdb=" N GLY K 21 " --> pdb=" O LYS K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 77 removed outlier: 3.507A pdb=" N LEU K 72 " --> pdb=" O ILE K 68 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET K 77 " --> pdb=" O THR K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.957A pdb=" N ASN K 83 " --> pdb=" O GLY K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 104 removed outlier: 3.564A pdb=" N THR K 89 " --> pdb=" O LYS K 85 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG K 91 " --> pdb=" O LEU K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'K' and resid 142 through 162 Processing helix chain 'K' and resid 168 through 182 Processing helix chain 'K' and resid 187 through 197 Processing helix chain 'L' and resid 23 through 28 removed outlier: 3.702A pdb=" N THR L 28 " --> pdb=" O LEU L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 52 Processing helix chain 'M' and resid 4 through 19 removed outlier: 3.628A pdb=" N ALA M 10 " --> pdb=" O LYS M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 55 removed outlier: 3.534A pdb=" N VAL M 45 " --> pdb=" O PRO M 41 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG M 55 " --> pdb=" O SER M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 84 removed outlier: 3.510A pdb=" N TYR M 78 " --> pdb=" O GLU M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 95 removed outlier: 3.837A pdb=" N ARG M 95 " --> pdb=" O ALA M 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 42 removed outlier: 3.632A pdb=" N LYS N 34 " --> pdb=" O SER N 30 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS N 39 " --> pdb=" O GLU N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 57 Processing helix chain 'N' and resid 62 through 68 removed outlier: 3.563A pdb=" N VAL N 66 " --> pdb=" O GLN N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 79 removed outlier: 3.543A pdb=" N SER N 77 " --> pdb=" O ARG N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 105 removed outlier: 4.099A pdb=" N ARG N 104 " --> pdb=" O LYS N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 132 removed outlier: 3.554A pdb=" N ILE N 116 " --> pdb=" O LYS N 112 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR N 128 " --> pdb=" O ARG N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 150 removed outlier: 3.730A pdb=" N VAL N 150 " --> pdb=" O ALA N 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 29 removed outlier: 3.738A pdb=" N THR O 24 " --> pdb=" O GLU O 20 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU O 26 " --> pdb=" O LEU O 22 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE O 27 " --> pdb=" O LYS O 23 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS O 28 " --> pdb=" O THR O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 43 removed outlier: 3.759A pdb=" N LYS O 40 " --> pdb=" O ARG O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 72 removed outlier: 4.180A pdb=" N VAL O 62 " --> pdb=" O GLU O 58 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS O 63 " --> pdb=" O PRO O 59 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL O 65 " --> pdb=" O TYR O 61 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU O 66 " --> pdb=" O VAL O 62 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA O 67 " --> pdb=" O LYS O 63 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS O 72 " --> pdb=" O LEU O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 86 removed outlier: 4.066A pdb=" N LEU O 85 " --> pdb=" O ASP O 81 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY O 86 " --> pdb=" O ASN O 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 81 through 86' Processing helix chain 'O' and resid 120 through 125 removed outlier: 3.908A pdb=" N ILE O 124 " --> pdb=" O ALA O 120 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 120 through 125' Processing helix chain 'P' and resid 65 through 69 removed outlier: 3.684A pdb=" N GLU P 68 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER P 69 " --> pdb=" O ARG P 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 65 through 69' Processing helix chain 'P' and resid 70 through 88 removed outlier: 3.578A pdb=" N ARG P 84 " --> pdb=" O ASP P 80 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS P 86 " --> pdb=" O ALA P 82 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU P 87 " --> pdb=" O GLN P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 121 removed outlier: 3.721A pdb=" N ALA P 120 " --> pdb=" O LEU P 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 27 Processing helix chain 'Q' and resid 32 through 37 removed outlier: 3.633A pdb=" N LEU Q 36 " --> pdb=" O GLN Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 48 removed outlier: 3.608A pdb=" N LEU Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 66 removed outlier: 3.757A pdb=" N LEU Q 56 " --> pdb=" O LYS Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 90 removed outlier: 3.633A pdb=" N VAL Q 90 " --> pdb=" O PRO Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 112 removed outlier: 3.705A pdb=" N MET Q 111 " --> pdb=" O LYS Q 108 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE Q 112 " --> pdb=" O PRO Q 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 108 through 112' Processing helix chain 'Q' and resid 115 through 119 Processing helix chain 'R' and resid 40 through 42 No H-bonds generated for 'chain 'R' and resid 40 through 42' Processing helix chain 'R' and resid 44 through 46 No H-bonds generated for 'chain 'R' and resid 44 through 46' Processing helix chain 'R' and resid 47 through 59 removed outlier: 3.610A pdb=" N LEU R 51 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 60 through 63 Processing helix chain 'R' and resid 76 through 100 removed outlier: 3.748A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.611A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS R 106 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU R 107 " --> pdb=" O ALA R 103 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 27 through 39 removed outlier: 3.860A pdb=" N ARG S 33 " --> pdb=" O HIS S 29 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU S 36 " --> pdb=" O LYS S 32 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU S 37 " --> pdb=" O ARG S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 60 removed outlier: 3.520A pdb=" N LYS S 49 " --> pdb=" O LYS S 45 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG S 60 " --> pdb=" O HIS S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 81 removed outlier: 3.877A pdb=" N ARG S 80 " --> pdb=" O GLU S 76 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG S 81 " --> pdb=" O GLU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 108 removed outlier: 3.901A pdb=" N LEU S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.871A pdb=" N ILE T 30 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.575A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 59 removed outlier: 3.638A pdb=" N GLU T 58 " --> pdb=" O ARG T 55 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU T 59 " --> pdb=" O ALA T 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 55 through 59' Processing helix chain 'T' and resid 64 through 73 Processing helix chain 'T' and resid 74 through 78 Processing helix chain 'T' and resid 99 through 117 removed outlier: 3.837A pdb=" N ASP T 104 " --> pdb=" O ALA T 100 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG T 108 " --> pdb=" O ASP T 104 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU T 114 " --> pdb=" O ASP T 110 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE T 117 " --> pdb=" O ARG T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 5 through 9 removed outlier: 3.528A pdb=" N ASP U 8 " --> pdb=" O THR U 5 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL U 9 " --> pdb=" O VAL U 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 5 through 9' Processing helix chain 'U' and resid 10 through 25 removed outlier: 3.724A pdb=" N VAL U 15 " --> pdb=" O GLN U 11 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS U 23 " --> pdb=" O ALA U 19 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 67 removed outlier: 3.617A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU U 66 " --> pdb=" O ARG U 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 79 Processing helix chain 'U' and resid 96 through 107 removed outlier: 3.614A pdb=" N LEU U 104 " --> pdb=" O ALA U 100 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 140 removed outlier: 3.643A pdb=" N LEU U 131 " --> pdb=" O GLY U 127 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP U 132 " --> pdb=" O GLN U 128 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 46 removed outlier: 3.540A pdb=" N LEU V 32 " --> pdb=" O ASN V 28 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS V 46 " --> pdb=" O GLY V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 105 removed outlier: 4.032A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS V 99 " --> pdb=" O SER V 95 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN V 100 " --> pdb=" O GLU V 96 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE V 101 " --> pdb=" O ILE V 97 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR V 102 " --> pdb=" O VAL V 98 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER V 103 " --> pdb=" O LYS V 99 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE V 104 " --> pdb=" O GLN V 100 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER V 105 " --> pdb=" O ILE V 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 94 through 105' Processing helix chain 'W' and resid 5 through 20 Processing helix chain 'W' and resid 31 through 44 removed outlier: 3.524A pdb=" N VAL W 40 " --> pdb=" O ARG W 36 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 84 No H-bonds generated for 'chain 'W' and resid 82 through 84' Processing helix chain 'W' and resid 85 through 94 Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'X' and resid 9 through 21 Processing helix chain 'X' and resid 24 through 32 removed outlier: 3.541A pdb=" N LEU X 32 " --> pdb=" O LYS X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 39 removed outlier: 3.547A pdb=" N ALA X 38 " --> pdb=" O THR X 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 89 through 94 Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 36 through 48 removed outlier: 3.557A pdb=" N LYS Y 43 " --> pdb=" O GLU Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 93 Processing helix chain 'Y' and resid 103 through 114 removed outlier: 3.551A pdb=" N ARG Y 107 " --> pdb=" O SER Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 118 through 123 removed outlier: 3.584A pdb=" N ALA Y 121 " --> pdb=" O ARG Y 118 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS Y 122 " --> pdb=" O GLY Y 119 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA Y 123 " --> pdb=" O THR Y 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 118 through 123' Processing helix chain 'Z' and resid 56 through 62 Processing helix chain 'Z' and resid 64 through 76 removed outlier: 3.656A pdb=" N ALA Z 75 " --> pdb=" O ARG Z 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 61 removed outlier: 3.533A pdb=" N LEU a 58 " --> pdb=" O THR a 54 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS a 59 " --> pdb=" O TYR a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 65 Processing helix chain 'a' and resid 69 through 78 removed outlier: 3.747A pdb=" N GLU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 82 through 95 removed outlier: 3.650A pdb=" N LEU a 88 " --> pdb=" O ALA a 84 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN a 89 " --> pdb=" O ARG a 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 18 Processing helix chain 'c' and resid 49 through 56 removed outlier: 3.594A pdb=" N ILE c 53 " --> pdb=" O ALA c 49 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA c 56 " --> pdb=" O ASP c 52 " (cutoff:3.500A) Processing helix chain 'c' and resid 74 through 81 Processing helix chain 'e' and resid 10 through 16 Processing helix chain 'e' and resid 30 through 43 removed outlier: 3.580A pdb=" N ARG e 41 " --> pdb=" O GLN e 37 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 19 removed outlier: 3.522A pdb=" N SER f 18 " --> pdb=" O GLY f 15 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG f 19 " --> pdb=" O GLN f 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 15 through 19' Processing helix chain 'f' and resid 32 through 36 Processing helix chain 'f' and resid 40 through 51 removed outlier: 3.632A pdb=" N GLN f 45 " --> pdb=" O GLN f 41 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS f 48 " --> pdb=" O ARG f 44 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASP f 49 " --> pdb=" O GLN f 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 104 removed outlier: 3.715A pdb=" N LEU g 103 " --> pdb=" O LEU g 100 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 15 Processing helix chain 'i' and resid 152 through 161 Processing helix chain 'i' and resid 165 through 179 Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.927A pdb=" N LYS B 40 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.074A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL B 124 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 50 removed outlier: 6.745A pdb=" N VAL C 33 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS C 46 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TYR C 31 " --> pdb=" O LYS C 46 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU C 48 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP C 29 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASN C 95 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL C 91 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU C 97 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS C 85 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N MET C 103 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS C 83 " --> pdb=" O MET C 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 120 through 127 removed outlier: 6.771A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 140 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL C 212 " --> pdb=" O VAL C 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 103 through 115 removed outlier: 6.709A pdb=" N PHE D 127 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE D 109 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS D 125 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG D 123 " --> pdb=" O PRO D 111 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN D 113 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG D 121 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 137 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 184 through 188 Processing sheet with id=AA7, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AA8, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.623A pdb=" N ILE E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.397A pdb=" N ILE E 136 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL E 131 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS E 138 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE E 129 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR E 159 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE E 172 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN E 161 " --> pdb=" O THR E 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.365A pdb=" N LYS E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS E 230 " --> pdb=" O LYS E 233 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS E 233 " --> pdb=" O LYS E 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 34 through 40 removed outlier: 6.690A pdb=" N LEU F 51 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL F 37 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE F 49 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL F 39 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU F 47 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 148 through 155 removed outlier: 3.759A pdb=" N GLY F 133 " --> pdb=" O MET F 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 223 through 226 removed outlier: 6.624A pdb=" N VAL j 176 " --> pdb=" O LYS j 185 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE j 165 " --> pdb=" O TRP j 177 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS j 153 " --> pdb=" O CYS j 168 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 13 through 17 removed outlier: 6.929A pdb=" N ASN G 56 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU G 109 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY G 54 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU G 111 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ILE G 52 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE G 113 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL G 50 " --> pdb=" O ILE G 113 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AB7, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AB8, first strand: chain 'H' and resid 47 through 53 removed outlier: 3.960A pdb=" N HIS H 91 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 185 through 188 Processing sheet with id=AC1, first strand: chain 'I' and resid 3 through 4 removed outlier: 4.378A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.462A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 62 through 67 removed outlier: 5.367A pdb=" N ARG I 77 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU I 103 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL I 81 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE I 101 " --> pdb=" O VAL I 81 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 140 through 141 Processing sheet with id=AC5, first strand: chain 'K' and resid 123 through 125 removed outlier: 8.060A pdb=" N ALA K 138 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LYS d 47 " --> pdb=" O ALA K 138 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP K 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG d 31 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL d 17 " --> pdb=" O ARG d 31 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 72 through 79 removed outlier: 17.883A pdb=" N ILE L 72 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.444A pdb=" N LEU L 93 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N SER L 74 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP L 91 " --> pdb=" O SER L 74 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL L 87 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 10.113A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 20 through 23 Processing sheet with id=AC8, first strand: chain 'O' and resid 31 through 32 removed outlier: 3.531A pdb=" N LEU O 49 " --> pdb=" O VAL O 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 52 through 57 removed outlier: 6.827A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N THR P 57 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR P 40 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU P 93 " --> pdb=" O ILE P 126 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG P 128 " --> pdb=" O LEU P 93 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 16 through 17 Processing sheet with id=AD2, first strand: chain 'Q' and resid 76 through 78 removed outlier: 6.458A pdb=" N VAL Q 76 " --> pdb=" O GLY Q 95 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N TYR Q 97 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N THR Q 78 " --> pdb=" O TYR Q 97 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 9 through 15 removed outlier: 6.186A pdb=" N LEU R 31 " --> pdb=" O ILE R 68 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL R 70 " --> pdb=" O LEU R 31 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS R 33 " --> pdb=" O VAL R 70 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL R 72 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 96 through 98 removed outlier: 6.214A pdb=" N ILE S 96 " --> pdb=" O GLN S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'T' and resid 12 through 14 Processing sheet with id=AD6, first strand: chain 'U' and resid 81 through 85 removed outlier: 4.454A pdb=" N ASN U 85 " --> pdb=" O PRO U 89 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AD8, first strand: chain 'V' and resid 49 through 55 removed outlier: 6.689A pdb=" N VAL V 50 " --> pdb=" O HIS V 92 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N HIS V 92 " --> pdb=" O VAL V 50 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLY V 52 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASP V 90 " --> pdb=" O GLY V 52 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V' and resid 59 through 66 removed outlier: 3.508A pdb=" N THR V 65 " --> pdb=" O ASP V 78 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AE2, first strand: chain 'W' and resid 71 through 74 removed outlier: 6.784A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE W 128 " --> pdb=" O PHE W 101 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 128 through 129 removed outlier: 6.433A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG X 71 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LYS X 54 " --> pdb=" O CYS X 69 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N CYS X 69 " --> pdb=" O LYS X 54 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY X 56 " --> pdb=" O ARG X 67 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ARG X 67 " --> pdb=" O GLY X 56 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE X 120 " --> pdb=" O THR X 82 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Y' and resid 6 through 15 removed outlier: 6.222A pdb=" N VAL Y 24 " --> pdb=" O ARG Y 10 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE Y 12 " --> pdb=" O GLN Y 22 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLN Y 22 " --> pdb=" O PHE Y 12 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR Y 14 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG Y 20 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Z' and resid 32 through 39 removed outlier: 4.905A pdb=" N GLN Z 49 " --> pdb=" O GLU Z 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'a' and resid 97 through 101 removed outlier: 6.804A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'b' and resid 43 through 47 removed outlier: 3.595A pdb=" N THR b 44 " --> pdb=" O VAL b 35 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE b 32 " --> pdb=" O LYS b 82 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER b 78 " --> pdb=" O LYS b 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'b' and resid 54 through 55 removed outlier: 7.002A pdb=" N VAL b 54 " --> pdb=" O LEU b 63 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'c' and resid 20 through 22 Processing sheet with id=AF1, first strand: chain 'c' and resid 36 through 43 Processing sheet with id=AF2, first strand: chain 'd' and resid 10 through 11 Processing sheet with id=AF3, first strand: chain 'f' and resid 30 through 31 Processing sheet with id=AF4, first strand: chain 'g' and resid 106 through 108 Processing sheet with id=AF5, first strand: chain 'g' and resid 139 through 140 Processing sheet with id=AF6, first strand: chain 'j' and resid 4 through 12 removed outlier: 6.414A pdb=" N MET j 5 " --> pdb=" O THR j 313 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR j 313 " --> pdb=" O MET j 5 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU j 7 " --> pdb=" O GLN j 311 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN j 311 " --> pdb=" O LEU j 7 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY j 9 " --> pdb=" O VAL j 309 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU j 306 " --> pdb=" O TYR j 302 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'j' and resid 18 through 23 removed outlier: 4.066A pdb=" N GLN j 20 " --> pdb=" O ALA j 34 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE j 31 " --> pdb=" O TRP j 43 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR j 39 " --> pdb=" O SER j 35 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE j 40 " --> pdb=" O ALA j 58 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA j 58 " --> pdb=" O ILE j 40 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N MET j 42 " --> pdb=" O GLN j 56 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'j' and resid 66 through 71 removed outlier: 3.855A pdb=" N ASP j 68 " --> pdb=" O GLY j 81 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER j 82 " --> pdb=" O THR j 86 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR j 86 " --> pdb=" O SER j 82 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU j 87 " --> pdb=" O ARG j 100 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG j 100 " --> pdb=" O LEU j 87 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU j 89 " --> pdb=" O THR j 98 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR j 96 " --> pdb=" O ASP j 91 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'j' and resid 108 through 113 removed outlier: 6.691A pdb=" N GLY j 123 " --> pdb=" O LEU j 109 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL j 111 " --> pdb=" O VAL j 121 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL j 121 " --> pdb=" O VAL j 111 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE j 129 " --> pdb=" O THR j 141 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR j 141 " --> pdb=" O ILE j 129 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU j 131 " --> pdb=" O LYS j 139 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'j' and resid 195 through 200 removed outlier: 6.680A pdb=" N LEU j 218 " --> pdb=" O LEU j 227 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS j 225 " --> pdb=" O ASP j 220 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'j' and resid 239 through 241 removed outlier: 5.902A pdb=" N ASP j 260 " --> pdb=" O ILE j 266 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE j 266 " --> pdb=" O ASP j 260 " (cutoff:3.500A) 1370 hydrogen bonds defined for protein. 3855 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1277 hydrogen bonds 2006 hydrogen bond angles 0 basepair planarities 515 basepair parallelities 914 stacking parallelities Total time for adding SS restraints: 54.86 Time building geometry restraints manager: 27.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 9575 1.32 - 1.44: 29925 1.44 - 1.57: 36334 1.57 - 1.69: 3317 1.69 - 1.82: 278 Bond restraints: 79429 Sorted by residual: bond pdb=" C GLN b 26 " pdb=" N SER b 27 " ideal model delta sigma weight residual 1.332 1.222 0.110 1.46e-02 4.69e+03 5.64e+01 bond pdb=" C GLY I 30 " pdb=" N ARG I 31 " ideal model delta sigma weight residual 1.327 1.247 0.080 1.39e-02 5.18e+03 3.33e+01 bond pdb=" C ASP F 162 " pdb=" N PRO F 163 " ideal model delta sigma weight residual 1.337 1.379 -0.042 9.80e-03 1.04e+04 1.88e+01 bond pdb=" C MET F 150 " pdb=" O MET F 150 " ideal model delta sigma weight residual 1.236 1.194 0.042 1.14e-02 7.69e+03 1.36e+01 bond pdb=" CB ARG K 159 " pdb=" CG ARG K 159 " ideal model delta sigma weight residual 1.520 1.421 0.099 3.00e-02 1.11e+03 1.09e+01 ... (remaining 79424 not shown) Histogram of bond angle deviations from ideal: 97.35 - 105.30: 8589 105.30 - 113.24: 46297 113.24 - 121.19: 38521 121.19 - 129.14: 20256 129.14 - 137.08: 1514 Bond angle restraints: 115177 Sorted by residual: angle pdb=" C THR g 87 " pdb=" N PRO g 88 " pdb=" CA PRO g 88 " ideal model delta sigma weight residual 118.85 133.41 -14.56 1.09e+00 8.42e-01 1.79e+02 angle pdb=" C VAL J 137 " pdb=" N ARG J 138 " pdb=" CA ARG J 138 " ideal model delta sigma weight residual 121.54 135.77 -14.23 1.91e+00 2.74e-01 5.55e+01 angle pdb=" C ASP d 36 " pdb=" N ASP d 37 " pdb=" CA ASP d 37 " ideal model delta sigma weight residual 121.54 134.59 -13.05 1.91e+00 2.74e-01 4.67e+01 angle pdb=" O3' U 21137 " pdb=" C3' U 21137 " pdb=" C2' U 21137 " ideal model delta sigma weight residual 113.70 122.82 -9.12 1.50e+00 4.44e-01 3.69e+01 angle pdb=" C4' C 21558 " pdb=" C3' C 21558 " pdb=" O3' C 21558 " ideal model delta sigma weight residual 109.40 117.94 -8.54 1.50e+00 4.44e-01 3.24e+01 ... (remaining 115172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 45769 35.98 - 71.97: 4280 71.97 - 107.95: 443 107.95 - 143.94: 29 143.94 - 179.92: 33 Dihedral angle restraints: 50554 sinusoidal: 36510 harmonic: 14044 Sorted by residual: dihedral pdb=" C4' A 21824 " pdb=" C3' A 21824 " pdb=" C2' A 21824 " pdb=" C1' A 21824 " ideal model delta sinusoidal sigma weight residual -35.00 33.85 -68.85 1 8.00e+00 1.56e-02 9.59e+01 dihedral pdb=" CA ALA K 40 " pdb=" C ALA K 40 " pdb=" N VAL K 41 " pdb=" CA VAL K 41 " ideal model delta harmonic sigma weight residual -180.00 -131.45 -48.55 0 5.00e+00 4.00e-02 9.43e+01 dihedral pdb=" C5' A 21824 " pdb=" C4' A 21824 " pdb=" C3' A 21824 " pdb=" O3' A 21824 " ideal model delta sinusoidal sigma weight residual 147.00 79.98 67.02 1 8.00e+00 1.56e-02 9.14e+01 ... (remaining 50551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 13209 0.103 - 0.206: 901 0.206 - 0.309: 74 0.309 - 0.412: 25 0.412 - 0.515: 8 Chirality restraints: 14217 Sorted by residual: chirality pdb=" C3' C 21373 " pdb=" C4' C 21373 " pdb=" O3' C 21373 " pdb=" C2' C 21373 " both_signs ideal model delta sigma weight residual False -2.48 -1.96 -0.52 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" C3' C 21231 " pdb=" C4' C 21231 " pdb=" O3' C 21231 " pdb=" C2' C 21231 " both_signs ideal model delta sigma weight residual False -2.48 -1.97 -0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" C3' A 21832 " pdb=" C4' A 21832 " pdb=" O3' A 21832 " pdb=" C2' A 21832 " both_signs ideal model delta sigma weight residual False -2.48 -1.98 -0.50 2.00e-01 2.50e+01 6.24e+00 ... (remaining 14214 not shown) Planarity restraints: 8432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 21606 " -0.077 2.00e-02 2.50e+03 3.09e-02 2.87e+01 pdb=" N9 G 21606 " 0.063 2.00e-02 2.50e+03 pdb=" C8 G 21606 " 0.011 2.00e-02 2.50e+03 pdb=" N7 G 21606 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 21606 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G 21606 " -0.016 2.00e-02 2.50e+03 pdb=" O6 G 21606 " -0.020 2.00e-02 2.50e+03 pdb=" N1 G 21606 " -0.009 2.00e-02 2.50e+03 pdb=" C2 G 21606 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G 21606 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G 21606 " 0.015 2.00e-02 2.50e+03 pdb=" C4 G 21606 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 236 " -0.037 2.00e-02 2.50e+03 3.20e-02 1.79e+01 pdb=" CG PHE D 236 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE D 236 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE D 236 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE D 236 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE D 236 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE D 236 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN K 165 " -0.020 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C ASN K 165 " 0.067 2.00e-02 2.50e+03 pdb=" O ASN K 165 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE K 166 " -0.023 2.00e-02 2.50e+03 ... (remaining 8429 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 243 2.47 - 3.08: 41617 3.08 - 3.68: 129124 3.68 - 4.29: 203845 4.29 - 4.90: 285264 Nonbonded interactions: 660093 Sorted by model distance: nonbonded pdb=" O THR g 87 " pdb=" N2 G 21507 " model vdw 1.859 2.520 nonbonded pdb=" O PRO g 88 " pdb=" CG LYS g 89 " model vdw 2.145 3.440 nonbonded pdb=" OG1 THR T 136 " pdb=" OP2 C 21521 " model vdw 2.199 2.440 nonbonded pdb=" OG SER K 142 " pdb=" O PRO d 49 " model vdw 2.256 2.440 nonbonded pdb=" O2' G 21324 " pdb=" O2' G 21510 " model vdw 2.261 2.440 ... (remaining 660088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 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: 0.060 Extract box with map and model: 14.840 Check model and map are aligned: 0.840 Set scattering table: 0.540 Process input model: 197.220 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 228.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.008 0.110 79429 Z= 0.511 Angle : 1.090 15.612 115177 Z= 0.578 Chirality : 0.059 0.515 14217 Planarity : 0.007 0.075 8432 Dihedral : 22.364 179.921 41496 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.70 % Favored : 96.05 % Rotamer: Outliers : 0.48 % Allowed : 6.30 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.10), residues: 4815 helix: -3.83 (0.08), residues: 1444 sheet: -1.36 (0.15), residues: 923 loop : -1.74 (0.10), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP U 52 HIS 0.022 0.002 HIS T 135 PHE 0.070 0.004 PHE D 236 TYR 0.033 0.003 TYR K 38 ARG 0.019 0.001 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1085 time to evaluate : 4.196 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: B 117 ARG cc_start: 0.7699 (ptp-170) cc_final: 0.7334 (ptm160) REVERT: C 159 GLN cc_start: 0.8932 (mm110) cc_final: 0.8641 (mp10) REVERT: D 89 LYS cc_start: 0.8174 (mmtp) cc_final: 0.7750 (mmmt) REVERT: D 152 ARG cc_start: 0.7726 (ttp-110) cc_final: 0.7439 (mtm-85) REVERT: E 67 GLN cc_start: 0.9077 (mt0) cc_final: 0.8761 (mt0) REVERT: E 199 GLU cc_start: 0.7775 (pt0) cc_final: 0.7482 (pt0) REVERT: G 149 LYS cc_start: 0.7310 (mmtt) cc_final: 0.7055 (mmtt) REVERT: J 75 ASN cc_start: 0.8272 (t0) cc_final: 0.8050 (t0) REVERT: J 156 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7265 (p-80) REVERT: K 195 GLU cc_start: 0.6847 (tp30) cc_final: 0.6043 (tp30) REVERT: L 103 GLU cc_start: 0.8707 (pt0) cc_final: 0.8388 (pt0) REVERT: N 127 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7734 (ttm110) REVERT: T 47 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8224 (mmtm) REVERT: X 14 ARG cc_start: 0.8001 (ptm160) cc_final: 0.7794 (ttp-170) REVERT: X 19 ASP cc_start: 0.7886 (p0) cc_final: 0.7641 (p0) REVERT: Y 72 PHE cc_start: 0.8033 (m-80) cc_final: 0.7775 (t80) REVERT: Y 86 GLU cc_start: 0.7918 (tp30) cc_final: 0.7677 (tp30) REVERT: Z 64 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7622 (mm-30) REVERT: h 20 MET cc_start: 0.6552 (mtp) cc_final: 0.5847 (mtp) REVERT: j 77 PHE cc_start: 0.8258 (m-80) cc_final: 0.7976 (m-80) REVERT: i 176 GLU cc_start: 0.8059 (tp30) cc_final: 0.7828 (tp30) outliers start: 20 outliers final: 6 residues processed: 1099 average time/residue: 1.9606 time to fit residues: 2701.8707 Evaluate side-chains 789 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 782 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 87 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 542 optimal weight: 10.0000 chunk 486 optimal weight: 8.9990 chunk 270 optimal weight: 0.6980 chunk 166 optimal weight: 7.9990 chunk 328 optimal weight: 0.9980 chunk 259 optimal weight: 0.1980 chunk 503 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 305 optimal weight: 8.9990 chunk 374 optimal weight: 0.7980 chunk 583 optimal weight: 6.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN B 131 HIS B 132 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN C 53 GLN C 186 ASN D 272 HIS E 8 HIS E 50 ASN E 98 ASN E 179 ASN E 197 ASN E 214 ASN F 101 GLN F 145 GLN F 174 HIS G 56 ASN G 81 HIS G 197 GLN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS ** H 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 HIS I 168 GLN J 113 GLN J 125 HIS J 156 HIS K 31 ASN K 79 HIS K 83 ASN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN L 112 HIS M 28 HIS M 32 HIS M 44 HIS M 61 GLN M 77 GLN N 13 GLN N 49 GLN O 72 HIS Q 41 GLN Q 79 HIS R 11 GLN R 48 GLN R 142 GLN S 83 ASN U 91 HIS U 126 GLN W 92 ASN X 46 HIS X 110 HIS X 127 ASN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 HIS Z 2 GLN a 103 HIS c 25 ASN c 72 HIS c 86 ASN j 4 GLN j 14 HIS j 64 HIS j 188 HIS j 191 HIS j 311 GLN i 158 GLN i 160 ASN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 79429 Z= 0.209 Angle : 0.660 10.519 115177 Z= 0.346 Chirality : 0.041 0.304 14217 Planarity : 0.005 0.066 8432 Dihedral : 23.669 179.501 31415 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.28 % Favored : 96.55 % Rotamer: Outliers : 3.80 % Allowed : 15.73 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.07 (0.11), residues: 4815 helix: -1.70 (0.12), residues: 1494 sheet: -0.82 (0.16), residues: 908 loop : -1.27 (0.11), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP j 259 HIS 0.007 0.001 HIS T 135 PHE 0.028 0.002 PHE D 236 TYR 0.017 0.001 TYR U 79 ARG 0.009 0.001 ARG G 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 861 time to evaluate : 4.351 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: B 117 ARG cc_start: 0.7675 (ptp-170) cc_final: 0.7304 (ptm160) REVERT: C 38 MET cc_start: 0.8392 (mpp) cc_final: 0.8177 (mpp) REVERT: C 120 MET cc_start: 0.8785 (ttp) cc_final: 0.8570 (ttp) REVERT: C 159 GLN cc_start: 0.8937 (mm110) cc_final: 0.8548 (mp-120) REVERT: D 89 LYS cc_start: 0.8153 (mmtp) cc_final: 0.7756 (mmmt) REVERT: D 121 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7403 (ttp-170) REVERT: D 123 ARG cc_start: 0.8428 (mtp180) cc_final: 0.8210 (mtm180) REVERT: D 152 ARG cc_start: 0.7616 (ttp-110) cc_final: 0.7402 (mtm-85) REVERT: E 16 LYS cc_start: 0.8573 (tttm) cc_final: 0.7980 (tptp) REVERT: E 67 GLN cc_start: 0.9018 (mt0) cc_final: 0.8699 (mt0) REVERT: E 220 THR cc_start: 0.8795 (p) cc_final: 0.8496 (m) REVERT: G 35 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: G 149 LYS cc_start: 0.7215 (mmtt) cc_final: 0.7013 (mmtt) REVERT: J 47 LYS cc_start: 0.8135 (ptmt) cc_final: 0.7900 (ptmm) REVERT: J 156 HIS cc_start: 0.8239 (OUTLIER) cc_final: 0.7357 (p90) REVERT: L 103 GLU cc_start: 0.8793 (pt0) cc_final: 0.8431 (pt0) REVERT: N 127 ARG cc_start: 0.8159 (ttp-110) cc_final: 0.7925 (ttp80) REVERT: Q 40 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7033 (tpm170) REVERT: Q 64 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7422 (ttmt) REVERT: R 27 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7577 (ptp90) REVERT: T 104 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: X 88 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.6629 (p0) REVERT: Y 42 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7439 (mm-30) REVERT: Y 72 PHE cc_start: 0.8256 (m-80) cc_final: 0.7897 (t80) REVERT: c 15 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.5920 (mpp-170) REVERT: c 85 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7491 (ptp-170) REVERT: h 20 MET cc_start: 0.6415 (mtp) cc_final: 0.5790 (mtp) REVERT: j 217 MET cc_start: 0.8236 (mtt) cc_final: 0.8010 (mtt) REVERT: i 155 GLU cc_start: 0.7078 (tt0) cc_final: 0.6868 (tt0) outliers start: 160 outliers final: 53 residues processed: 945 average time/residue: 1.8041 time to fit residues: 2187.3320 Evaluate side-chains 850 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 787 time to evaluate : 4.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 154 LYS Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 64 LYS Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 27 ARG Chi-restraints excluded: chain R residue 45 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain T residue 83 PHE Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 104 ASP Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain V residue 50 VAL Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 32 LYS Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain c residue 15 ARG Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 85 ARG Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 32 VAL Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain j residue 249 CYS Chi-restraints excluded: chain j residue 288 SER Chi-restraints excluded: chain i residue 167 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 324 optimal weight: 0.9980 chunk 180 optimal weight: 8.9990 chunk 485 optimal weight: 7.9990 chunk 396 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 584 optimal weight: 7.9990 chunk 630 optimal weight: 50.0000 chunk 520 optimal weight: 9.9990 chunk 579 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 468 optimal weight: 2.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN E 197 ASN E 201 HIS E 214 ASN F 145 GLN G 197 GLN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN K 83 ASN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN L 39 ASN L 83 GLN M 7 ASN P 26 ASN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN S 29 HIS U 126 GLN ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN W 92 ASN X 110 HIS X 127 ASN Y 63 HIS b 19 HIS b 83 GLN c 72 HIS c 86 ASN f 28 HIS j 4 GLN ** j 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 285 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.173 79429 Z= 0.391 Angle : 0.758 10.919 115177 Z= 0.391 Chirality : 0.048 0.342 14217 Planarity : 0.006 0.067 8432 Dihedral : 23.593 179.788 31413 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.82 % Favored : 95.99 % Rotamer: Outliers : 5.16 % Allowed : 16.85 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.43 (0.11), residues: 4815 helix: -0.89 (0.13), residues: 1500 sheet: -0.56 (0.16), residues: 917 loop : -1.04 (0.12), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP j 132 HIS 0.010 0.002 HIS b 49 PHE 0.028 0.002 PHE J 147 TYR 0.020 0.002 TYR K 38 ARG 0.009 0.001 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 771 time to evaluate : 4.299 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: B 52 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8070 (mtpp) REVERT: B 117 ARG cc_start: 0.7718 (ptp-170) cc_final: 0.7353 (ptm160) REVERT: B 181 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7899 (tp30) REVERT: C 120 MET cc_start: 0.8834 (ttp) cc_final: 0.8628 (ttp) REVERT: C 159 GLN cc_start: 0.8966 (mm110) cc_final: 0.8523 (mp-120) REVERT: D 89 LYS cc_start: 0.8128 (mmtp) cc_final: 0.7745 (mmmt) REVERT: D 121 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7541 (ttp-170) REVERT: D 152 ARG cc_start: 0.7660 (ttp-110) cc_final: 0.7447 (mtm-85) REVERT: D 227 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8334 (ttt180) REVERT: D 248 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8072 (m-80) REVERT: E 67 GLN cc_start: 0.9054 (mt0) cc_final: 0.8854 (mt0) REVERT: E 220 THR cc_start: 0.8793 (p) cc_final: 0.8543 (m) REVERT: F 79 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.7210 (p90) REVERT: F 123 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8559 (mp) REVERT: G 35 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7324 (mt-10) REVERT: J 47 LYS cc_start: 0.8204 (ptmt) cc_final: 0.7900 (ptmm) REVERT: J 156 HIS cc_start: 0.8508 (OUTLIER) cc_final: 0.7036 (p90) REVERT: K 177 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8558 (mp) REVERT: L 103 GLU cc_start: 0.8731 (pt0) cc_final: 0.8385 (pt0) REVERT: M 5 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6838 (tppt) REVERT: N 13 GLN cc_start: 0.8500 (pt0) cc_final: 0.8215 (pt0) REVERT: N 127 ARG cc_start: 0.8151 (ttp-110) cc_final: 0.7863 (ttp80) REVERT: Q 40 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7277 (tpm170) REVERT: R 126 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7709 (mtt180) REVERT: U 112 MET cc_start: 0.8235 (mtp) cc_final: 0.8010 (ttm) REVERT: X 138 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8754 (mttm) REVERT: Y 42 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7374 (mm-30) REVERT: Y 61 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7102 (mtp180) REVERT: Y 72 PHE cc_start: 0.8347 (m-80) cc_final: 0.7812 (t80) REVERT: Z 64 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7711 (mm-30) REVERT: a 44 LEU cc_start: 0.7567 (tp) cc_final: 0.7227 (mp) REVERT: c 15 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.5845 (mpp-170) REVERT: c 85 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7633 (ptp-170) REVERT: f 6 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7176 (tp) REVERT: h 20 MET cc_start: 0.6404 (mtp) cc_final: 0.5732 (mtp) outliers start: 217 outliers final: 105 residues processed: 898 average time/residue: 1.7807 time to fit residues: 2053.0800 Evaluate side-chains 875 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 752 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 154 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain K residue 198 ARG Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 69 SER Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 140 THR Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 126 ARG Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 10 GLN Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain V residue 50 VAL Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 138 LYS Chi-restraints excluded: chain Y residue 61 ARG Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 101 SER Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain c residue 15 ARG Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 85 ARG Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 42 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain j residue 197 THR Chi-restraints excluded: chain j residue 198 VAL Chi-restraints excluded: chain j residue 203 ASP Chi-restraints excluded: chain j residue 249 CYS Chi-restraints excluded: chain j residue 288 SER Chi-restraints excluded: chain i residue 166 SER Chi-restraints excluded: chain i residue 167 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 577 optimal weight: 3.9990 chunk 439 optimal weight: 9.9990 chunk 303 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 278 optimal weight: 0.9980 chunk 392 optimal weight: 0.7980 chunk 586 optimal weight: 6.9990 chunk 620 optimal weight: 1.9990 chunk 306 optimal weight: 20.0000 chunk 555 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN B 131 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN E 197 ASN E 214 ASN F 145 GLN G 177 GLN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 HIS K 83 ASN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN L 39 ASN L 83 GLN M 7 ASN M 77 GLN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 110 HIS X 127 ASN Y 94 HIS c 72 HIS c 86 ASN ** j 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 143 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 79429 Z= 0.196 Angle : 0.619 10.334 115177 Z= 0.323 Chirality : 0.040 0.297 14217 Planarity : 0.005 0.062 8432 Dihedral : 23.483 179.212 31413 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.36 % Favored : 96.51 % Rotamer: Outliers : 4.09 % Allowed : 18.80 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.93 (0.12), residues: 4815 helix: -0.25 (0.13), residues: 1518 sheet: -0.37 (0.16), residues: 912 loop : -0.87 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP f 8 HIS 0.006 0.001 HIS V 18 PHE 0.019 0.001 PHE M 67 TYR 0.015 0.001 TYR U 79 ARG 0.008 0.000 ARG M 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 798 time to evaluate : 4.289 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: B 181 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: C 120 MET cc_start: 0.8786 (ttp) cc_final: 0.8549 (ttp) REVERT: C 159 GLN cc_start: 0.8973 (mm110) cc_final: 0.8562 (mp-120) REVERT: D 89 LYS cc_start: 0.8211 (mmtp) cc_final: 0.7811 (mmmt) REVERT: D 121 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7581 (ttp-170) REVERT: D 227 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8278 (ttt180) REVERT: D 248 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: E 16 LYS cc_start: 0.8631 (tttm) cc_final: 0.8213 (tptm) REVERT: E 67 GLN cc_start: 0.9016 (mt0) cc_final: 0.8803 (mt0) REVERT: F 79 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.6943 (p90) REVERT: F 153 VAL cc_start: 0.8685 (m) cc_final: 0.8451 (m) REVERT: G 35 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: I 7 ASN cc_start: 0.6738 (OUTLIER) cc_final: 0.6519 (m-40) REVERT: I 64 ASN cc_start: 0.7626 (p0) cc_final: 0.7392 (p0) REVERT: J 47 LYS cc_start: 0.8129 (ptmt) cc_final: 0.7828 (ptmm) REVERT: J 155 LYS cc_start: 0.8315 (mmtt) cc_final: 0.8087 (mmtt) REVERT: J 156 HIS cc_start: 0.8444 (OUTLIER) cc_final: 0.6586 (p90) REVERT: K 177 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8528 (mp) REVERT: L 103 GLU cc_start: 0.8765 (pt0) cc_final: 0.8421 (pt0) REVERT: M 5 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6751 (tppt) REVERT: N 13 GLN cc_start: 0.8459 (pt0) cc_final: 0.8188 (pt0) REVERT: N 127 ARG cc_start: 0.8186 (ttp-110) cc_final: 0.7965 (ttp80) REVERT: Q 40 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.6912 (tpm170) REVERT: U 112 MET cc_start: 0.8172 (mtp) cc_final: 0.7923 (ttt) REVERT: W 4 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.6132 (mpp) REVERT: W 43 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8169 (mptm) REVERT: X 63 ASN cc_start: 0.7544 (p0) cc_final: 0.6979 (p0) REVERT: X 114 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6885 (t0) REVERT: Y 42 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7302 (mm-30) REVERT: Y 61 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7239 (mtp180) REVERT: Y 72 PHE cc_start: 0.8332 (m-80) cc_final: 0.7844 (t80) REVERT: a 44 LEU cc_start: 0.7528 (tp) cc_final: 0.7193 (mp) REVERT: c 15 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.5904 (mpp-170) REVERT: c 85 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7529 (ptp-170) REVERT: f 30 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7902 (tt) REVERT: h 20 MET cc_start: 0.6364 (mtp) cc_final: 0.5735 (mtp) REVERT: j 88 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7184 (ttt-90) outliers start: 172 outliers final: 76 residues processed: 899 average time/residue: 1.7916 time to fit residues: 2063.6613 Evaluate side-chains 844 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 749 time to evaluate : 4.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 171 GLU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 69 SER Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 45 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 10 GLN Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain V residue 50 VAL Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 43 LYS Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 114 ASP Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 61 ARG Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 101 SER Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain c residue 2 THR Chi-restraints excluded: chain c residue 15 ARG Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 85 ARG Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 30 LEU Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain j residue 27 PHE Chi-restraints excluded: chain j residue 88 ARG Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain j residue 288 SER Chi-restraints excluded: chain i residue 166 SER Chi-restraints excluded: chain i residue 167 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 516 optimal weight: 5.9990 chunk 352 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 462 optimal weight: 10.0000 chunk 256 optimal weight: 20.0000 chunk 529 optimal weight: 6.9990 chunk 428 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 316 optimal weight: 0.7980 chunk 557 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN B 36 GLN B 131 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN E 214 ASN F 145 GLN G 70 HIS G 197 GLN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 ASN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN L 83 GLN M 7 ASN O 72 HIS ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN ** U 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 ASN Y 22 GLN Y 63 HIS c 72 HIS c 86 ASN j 4 GLN ** j 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 143 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.205 79429 Z= 0.469 Angle : 0.800 11.147 115177 Z= 0.408 Chirality : 0.050 0.372 14217 Planarity : 0.007 0.082 8432 Dihedral : 23.521 179.415 31413 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.22 % Favored : 95.60 % Rotamer: Outliers : 5.30 % Allowed : 18.63 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.94 (0.11), residues: 4815 helix: -0.26 (0.13), residues: 1511 sheet: -0.33 (0.16), residues: 916 loop : -0.89 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP U 33 HIS 0.009 0.002 HIS b 49 PHE 0.030 0.003 PHE W 50 TYR 0.020 0.002 TYR K 38 ARG 0.012 0.001 ARG U 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 747 time to evaluate : 4.259 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: B 53 ARG cc_start: 0.7074 (mmm160) cc_final: 0.6780 (mmm160) REVERT: B 117 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7544 (ptm160) REVERT: B 181 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7968 (tp30) REVERT: C 120 MET cc_start: 0.8850 (ttp) cc_final: 0.8610 (ttp) REVERT: C 159 GLN cc_start: 0.8989 (mm110) cc_final: 0.8563 (mp-120) REVERT: D 89 LYS cc_start: 0.8264 (mmtp) cc_final: 0.7865 (mmmt) REVERT: D 121 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7589 (ttp-170) REVERT: D 227 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8374 (ttt180) REVERT: D 248 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: E 16 LYS cc_start: 0.8658 (tttm) cc_final: 0.8211 (tptm) REVERT: F 64 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7605 (ttm-80) REVERT: F 79 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.6973 (p90) REVERT: F 123 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8603 (mp) REVERT: F 153 VAL cc_start: 0.8741 (m) cc_final: 0.8485 (m) REVERT: G 35 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: I 7 ASN cc_start: 0.7007 (OUTLIER) cc_final: 0.6745 (m-40) REVERT: I 163 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6845 (tt0) REVERT: J 47 LYS cc_start: 0.8208 (ptmt) cc_final: 0.7883 (ptmm) REVERT: J 155 LYS cc_start: 0.8363 (mmtt) cc_final: 0.8142 (mmtt) REVERT: K 55 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7848 (mtp180) REVERT: K 177 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8561 (mp) REVERT: L 103 GLU cc_start: 0.8751 (pt0) cc_final: 0.8394 (pt0) REVERT: M 5 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6834 (tppt) REVERT: P 104 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7809 (mtm180) REVERT: Q 40 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7313 (tpm170) REVERT: U 112 MET cc_start: 0.8250 (mtp) cc_final: 0.8018 (ttt) REVERT: U 123 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8675 (mp) REVERT: W 19 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8170 (mtpt) REVERT: W 43 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8341 (mptm) REVERT: X 114 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7241 (t0) REVERT: X 138 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8750 (mttm) REVERT: Y 15 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8411 (t0) REVERT: Y 42 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7369 (mm-30) REVERT: Y 61 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7148 (mtp180) REVERT: Z 1 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7051 (tmm) REVERT: Z 64 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7727 (mm-30) REVERT: Z 74 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8686 (mtmm) REVERT: a 44 LEU cc_start: 0.7601 (tp) cc_final: 0.7291 (mp) REVERT: c 15 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.5817 (mpp-170) REVERT: h 20 MET cc_start: 0.6365 (mtp) cc_final: 0.5712 (mtp) REVERT: j 88 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7442 (ttt-90) REVERT: j 143 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6956 (mm-40) outliers start: 223 outliers final: 126 residues processed: 881 average time/residue: 1.8111 time to fit residues: 2051.3652 Evaluate side-chains 884 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 730 time to evaluate : 4.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain K residue 36 GLN Chi-restraints excluded: chain K residue 55 ARG Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 171 GLU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 198 ARG Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 69 SER Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain P residue 104 ARG Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 140 THR Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 64 LYS Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 97 GLN Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 10 GLN Chi-restraints excluded: chain T residue 17 ASN Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain V residue 50 VAL Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 43 LYS Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 18 ARG Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 114 ASP Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain X residue 138 LYS Chi-restraints excluded: chain Y residue 13 MET Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 61 ARG Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 74 LYS Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 101 SER Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain c residue 2 THR Chi-restraints excluded: chain c residue 15 ARG Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 42 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain g residue 100 LEU Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 27 PHE Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 88 ARG Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain j residue 143 GLN Chi-restraints excluded: chain j residue 164 ILE Chi-restraints excluded: chain j residue 203 ASP Chi-restraints excluded: chain j residue 249 CYS Chi-restraints excluded: chain j residue 288 SER Chi-restraints excluded: chain i residue 166 SER Chi-restraints excluded: chain i residue 167 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 208 optimal weight: 4.9990 chunk 558 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 364 optimal weight: 1.9990 chunk 153 optimal weight: 0.0670 chunk 621 optimal weight: 2.9990 chunk 515 optimal weight: 4.9990 chunk 287 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 205 optimal weight: 0.6980 chunk 326 optimal weight: 0.4980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN B 131 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN E 197 ASN F 145 GLN G 197 GLN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN K 36 GLN K 83 ASN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN L 83 GLN M 77 GLN N 58 HIS ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 HIS W 70 ASN W 91 ASN X 127 ASN c 72 HIS c 86 ASN f 26 ASN ** j 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 79429 Z= 0.155 Angle : 0.598 10.142 115177 Z= 0.311 Chirality : 0.039 0.287 14217 Planarity : 0.004 0.061 8432 Dihedral : 23.401 179.763 31413 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.57 % Rotamer: Outliers : 3.87 % Allowed : 20.84 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.12), residues: 4815 helix: 0.33 (0.13), residues: 1519 sheet: -0.14 (0.16), residues: 910 loop : -0.73 (0.12), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP j 259 HIS 0.004 0.001 HIS V 18 PHE 0.019 0.001 PHE M 67 TYR 0.014 0.001 TYR U 79 ARG 0.009 0.000 ARG M 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 781 time to evaluate : 4.295 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: B 177 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7908 (mtt) REVERT: B 181 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7852 (tp30) REVERT: C 120 MET cc_start: 0.8760 (ttp) cc_final: 0.8524 (ttp) REVERT: C 159 GLN cc_start: 0.8980 (mm110) cc_final: 0.8537 (mp-120) REVERT: D 89 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7801 (mmmt) REVERT: D 121 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7410 (ttp-170) REVERT: D 227 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8277 (ttt180) REVERT: D 248 TYR cc_start: 0.9030 (OUTLIER) cc_final: 0.8015 (m-80) REVERT: E 16 LYS cc_start: 0.8631 (tttm) cc_final: 0.7994 (tptp) REVERT: F 79 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.6825 (p90) REVERT: F 153 VAL cc_start: 0.8671 (m) cc_final: 0.8426 (m) REVERT: I 41 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7816 (ttm170) REVERT: I 64 ASN cc_start: 0.7605 (p0) cc_final: 0.7050 (p0) REVERT: I 102 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8597 (m) REVERT: J 47 LYS cc_start: 0.8131 (ptmt) cc_final: 0.7790 (ttpp) REVERT: J 155 LYS cc_start: 0.8338 (mmtt) cc_final: 0.8126 (mmtt) REVERT: L 103 GLU cc_start: 0.8765 (pt0) cc_final: 0.8385 (pt0) REVERT: M 5 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6719 (tppt) REVERT: N 13 GLN cc_start: 0.8422 (pt0) cc_final: 0.8182 (pt0) REVERT: P 66 ARG cc_start: 0.7994 (ptp90) cc_final: 0.7779 (ptp90) REVERT: P 104 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7649 (mtm180) REVERT: Q 40 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.6802 (tpm170) REVERT: T 113 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7622 (ttm110) REVERT: U 75 MET cc_start: 0.7844 (mmt) cc_final: 0.7300 (mmt) REVERT: V 51 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6729 (mmtm) REVERT: W 43 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8124 (mptm) REVERT: X 114 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.7056 (t0) REVERT: Y 61 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7213 (mtp180) REVERT: Z 74 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8643 (mtmm) REVERT: a 44 LEU cc_start: 0.7542 (tp) cc_final: 0.7226 (mp) REVERT: c 15 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.5903 (mpp-170) REVERT: g 104 LYS cc_start: 0.7313 (pttt) cc_final: 0.6977 (pttt) REVERT: h 20 MET cc_start: 0.6339 (mtp) cc_final: 0.5689 (mtp) REVERT: j 5 MET cc_start: 0.7664 (mmm) cc_final: 0.7404 (mmt) REVERT: j 88 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7247 (ttt-90) outliers start: 163 outliers final: 83 residues processed: 876 average time/residue: 1.7755 time to fit residues: 2015.1210 Evaluate side-chains 852 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 751 time to evaluate : 4.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 154 LYS Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 36 GLN Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 34 GLU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 69 SER Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain P residue 104 ARG Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 97 GLN Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 10 GLN Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain V residue 51 LYS Chi-restraints excluded: chain W residue 43 LYS Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 18 ARG Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 114 ASP Chi-restraints excluded: chain Y residue 61 ARG Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 74 LYS Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 101 SER Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain c residue 2 THR Chi-restraints excluded: chain c residue 15 ARG Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain j residue 88 ARG Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain j residue 141 THR Chi-restraints excluded: chain j residue 203 ASP Chi-restraints excluded: chain j residue 288 SER Chi-restraints excluded: chain j residue 311 GLN Chi-restraints excluded: chain i residue 166 SER Chi-restraints excluded: chain i residue 167 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 598 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 353 optimal weight: 0.8980 chunk 453 optimal weight: 0.0970 chunk 351 optimal weight: 10.0000 chunk 522 optimal weight: 7.9990 chunk 346 optimal weight: 7.9990 chunk 618 optimal weight: 3.9990 chunk 387 optimal weight: 0.9990 chunk 377 optimal weight: 0.9990 chunk 285 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN B 131 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN C 202 GLN F 145 GLN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN K 83 ASN K 118 ASN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN L 83 GLN M 7 ASN M 77 GLN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 83 ASN T 17 ASN ** U 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 HIS W 70 ASN X 127 ASN a 112 ASN c 72 HIS c 86 ASN j 4 GLN ** j 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 79429 Z= 0.154 Angle : 0.569 9.670 115177 Z= 0.296 Chirality : 0.038 0.278 14217 Planarity : 0.004 0.057 8432 Dihedral : 23.252 179.780 31412 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 3.56 % Allowed : 21.51 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.12), residues: 4815 helix: 0.64 (0.14), residues: 1518 sheet: -0.03 (0.17), residues: 908 loop : -0.58 (0.12), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP j 259 HIS 0.004 0.001 HIS U 42 PHE 0.033 0.001 PHE j 27 TYR 0.011 0.001 TYR J 35 ARG 0.020 0.000 ARG U 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 767 time to evaluate : 4.543 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: B 55 TRP cc_start: 0.8911 (t-100) cc_final: 0.8690 (t-100) REVERT: B 181 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7845 (tp30) REVERT: C 120 MET cc_start: 0.8760 (ttp) cc_final: 0.8551 (ttp) REVERT: C 159 GLN cc_start: 0.8979 (mm110) cc_final: 0.8558 (mp-120) REVERT: D 89 LYS cc_start: 0.8104 (mmtp) cc_final: 0.7624 (mmmt) REVERT: D 121 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7640 (ttp-170) REVERT: D 123 ARG cc_start: 0.8432 (mtm180) cc_final: 0.8190 (mtm110) REVERT: D 227 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8239 (ttt180) REVERT: D 248 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.8028 (m-80) REVERT: F 79 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.6885 (p90) REVERT: F 123 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8497 (mp) REVERT: F 153 VAL cc_start: 0.8671 (m) cc_final: 0.8447 (m) REVERT: I 41 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7563 (ttm170) REVERT: I 64 ASN cc_start: 0.7343 (p0) cc_final: 0.6861 (p0) REVERT: I 102 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8613 (m) REVERT: I 133 GLU cc_start: 0.6562 (pm20) cc_final: 0.6340 (pm20) REVERT: J 47 LYS cc_start: 0.8137 (ptmt) cc_final: 0.7783 (ptmm) REVERT: J 155 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8122 (mmtt) REVERT: L 19 ASN cc_start: 0.8892 (m-40) cc_final: 0.8612 (m-40) REVERT: L 103 GLU cc_start: 0.8744 (pt0) cc_final: 0.8415 (pt0) REVERT: N 4 MET cc_start: 0.8631 (ttm) cc_final: 0.8021 (ttm) REVERT: N 13 GLN cc_start: 0.8406 (pt0) cc_final: 0.8171 (pt0) REVERT: P 104 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7615 (mtm180) REVERT: Q 40 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.6818 (tpm170) REVERT: T 113 ARG cc_start: 0.7901 (ttp80) cc_final: 0.7616 (ttm110) REVERT: U 75 MET cc_start: 0.7828 (mmt) cc_final: 0.7293 (mmt) REVERT: V 51 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6658 (mmtm) REVERT: W 4 MET cc_start: 0.6537 (OUTLIER) cc_final: 0.6110 (mpp) REVERT: X 114 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.7051 (t0) REVERT: Y 61 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7222 (mtp180) REVERT: Y 72 PHE cc_start: 0.8215 (m-80) cc_final: 0.7779 (t80) REVERT: Z 74 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8623 (mtmm) REVERT: a 44 LEU cc_start: 0.7557 (tp) cc_final: 0.7278 (mp) REVERT: a 69 THR cc_start: 0.8700 (m) cc_final: 0.8484 (m) REVERT: c 15 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.5775 (mpp-170) REVERT: c 45 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8643 (t) REVERT: c 85 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7371 (mtt180) REVERT: d 60 GLU cc_start: 0.5515 (OUTLIER) cc_final: 0.4699 (pt0) REVERT: f 30 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8038 (tt) REVERT: g 104 LYS cc_start: 0.7263 (pttt) cc_final: 0.6971 (pttt) REVERT: h 20 MET cc_start: 0.6290 (mtp) cc_final: 0.5670 (mtp) REVERT: j 88 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7290 (ttt-90) outliers start: 150 outliers final: 89 residues processed: 850 average time/residue: 1.8115 time to fit residues: 1995.0820 Evaluate side-chains 855 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 745 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 171 GLU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 104 ARG Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 45 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 97 GLN Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 10 GLN Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain V residue 51 LYS Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 18 ARG Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 114 ASP Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 61 ARG Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 74 LYS Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 101 SER Chi-restraints excluded: chain a residue 112 ASN Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain c residue 2 THR Chi-restraints excluded: chain c residue 15 ARG Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 85 ARG Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 60 GLU Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 30 LEU Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 88 ARG Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain j residue 141 THR Chi-restraints excluded: chain j residue 203 ASP Chi-restraints excluded: chain j residue 288 SER Chi-restraints excluded: chain i residue 166 SER Chi-restraints excluded: chain i residue 167 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 382 optimal weight: 6.9990 chunk 247 optimal weight: 4.9990 chunk 369 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 393 optimal weight: 0.5980 chunk 421 optimal weight: 0.0060 chunk 305 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 486 optimal weight: 10.0000 overall best weight: 2.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN B 131 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN C 202 GLN F 145 GLN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 ASN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN L 83 GLN M 7 ASN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 70 ASN X 127 ASN a 112 ASN c 72 HIS c 86 ASN e 37 GLN j 4 GLN ** j 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 143 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 79429 Z= 0.280 Angle : 0.656 10.418 115177 Z= 0.338 Chirality : 0.042 0.301 14217 Planarity : 0.005 0.063 8432 Dihedral : 23.263 179.825 31412 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.12 % Rotamer: Outliers : 3.97 % Allowed : 21.44 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.26 (0.12), residues: 4815 helix: 0.54 (0.13), residues: 1517 sheet: -0.03 (0.17), residues: 898 loop : -0.62 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP U 33 HIS 0.006 0.001 HIS U 42 PHE 0.026 0.002 PHE j 27 TYR 0.015 0.002 TYR U 79 ARG 0.017 0.001 ARG M 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 744 time to evaluate : 4.324 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: B 181 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7911 (tp30) REVERT: C 120 MET cc_start: 0.8809 (ttp) cc_final: 0.8607 (ttp) REVERT: C 159 GLN cc_start: 0.8979 (mm110) cc_final: 0.8514 (mp-120) REVERT: D 121 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7631 (ttp-170) REVERT: D 123 ARG cc_start: 0.8585 (mtm180) cc_final: 0.8251 (mtm110) REVERT: D 227 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8322 (ttt180) REVERT: D 248 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: E 16 LYS cc_start: 0.8652 (tttm) cc_final: 0.8157 (tptm) REVERT: F 79 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.6824 (p90) REVERT: F 153 VAL cc_start: 0.8698 (m) cc_final: 0.8455 (m) REVERT: G 197 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7097 (mt0) REVERT: I 41 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7789 (ttm170) REVERT: J 47 LYS cc_start: 0.8158 (ptmt) cc_final: 0.7800 (ttpp) REVERT: J 79 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7997 (ttt180) REVERT: L 103 GLU cc_start: 0.8768 (pt0) cc_final: 0.8411 (pt0) REVERT: N 4 MET cc_start: 0.8670 (ttm) cc_final: 0.8188 (ttm) REVERT: N 13 GLN cc_start: 0.8469 (pt0) cc_final: 0.8205 (pt0) REVERT: O 27 ILE cc_start: 0.6513 (OUTLIER) cc_final: 0.6077 (pp) REVERT: P 104 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7720 (mtm180) REVERT: Q 40 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7095 (tpm170) REVERT: U 123 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8663 (mp) REVERT: V 51 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6676 (mmtm) REVERT: W 19 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8160 (mtpt) REVERT: X 114 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7106 (t0) REVERT: Y 61 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7155 (mtp180) REVERT: Y 72 PHE cc_start: 0.8333 (m-80) cc_final: 0.7827 (t80) REVERT: Z 74 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8626 (mtmm) REVERT: a 44 LEU cc_start: 0.7605 (tp) cc_final: 0.7321 (mp) REVERT: c 15 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.5891 (mpp-170) REVERT: c 85 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7435 (mtt180) REVERT: g 104 LYS cc_start: 0.7322 (pttt) cc_final: 0.7008 (pttt) REVERT: h 20 MET cc_start: 0.6267 (mtp) cc_final: 0.5626 (mtp) REVERT: j 88 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7319 (ttt-90) REVERT: j 118 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6450 (mtp-110) outliers start: 167 outliers final: 105 residues processed: 841 average time/residue: 1.7666 time to fit residues: 1912.0808 Evaluate side-chains 859 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 733 time to evaluate : 4.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 154 LYS Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 171 GLU Chi-restraints excluded: chain K residue 198 ARG Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain O residue 27 ILE Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain O residue 75 ASN Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 104 ARG Chi-restraints excluded: chain Q residue 32 GLN Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 64 LYS Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 97 GLN Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 10 GLN Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain V residue 51 LYS Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 18 ARG Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 114 ASP Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 61 ARG Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 74 LYS Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 101 SER Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain c residue 2 THR Chi-restraints excluded: chain c residue 15 ARG Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 85 ARG Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 88 ARG Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain j residue 118 ARG Chi-restraints excluded: chain j residue 141 THR Chi-restraints excluded: chain j residue 203 ASP Chi-restraints excluded: chain j residue 288 SER Chi-restraints excluded: chain j residue 311 GLN Chi-restraints excluded: chain i residue 166 SER Chi-restraints excluded: chain i residue 167 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 562 optimal weight: 8.9990 chunk 592 optimal weight: 3.9990 chunk 540 optimal weight: 7.9990 chunk 576 optimal weight: 5.9990 chunk 347 optimal weight: 8.9990 chunk 251 optimal weight: 10.0000 chunk 452 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 521 optimal weight: 7.9990 chunk 545 optimal weight: 50.0000 chunk 574 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN B 131 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN C 202 GLN E 214 ASN F 145 GLN G 197 GLN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN I 22 HIS K 83 ASN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN L 83 GLN O 48 HIS ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 70 ASN X 127 ASN Y 63 HIS c 72 HIS c 86 ASN j 4 GLN ** j 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.235 79429 Z= 0.581 Angle : 0.888 11.597 115177 Z= 0.448 Chirality : 0.055 0.453 14217 Planarity : 0.008 0.092 8432 Dihedral : 23.478 178.868 31411 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.40 % Favored : 95.41 % Rotamer: Outliers : 4.37 % Allowed : 21.20 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.70 (0.12), residues: 4815 helix: 0.05 (0.13), residues: 1506 sheet: -0.26 (0.16), residues: 910 loop : -0.79 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP U 33 HIS 0.014 0.002 HIS H 91 PHE 0.033 0.003 PHE W 50 TYR 0.019 0.003 TYR L 36 ARG 0.013 0.001 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 748 time to evaluate : 4.288 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: B 53 ARG cc_start: 0.7084 (mmm160) cc_final: 0.6738 (mmm160) REVERT: B 181 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7965 (tp30) REVERT: C 120 MET cc_start: 0.8864 (ttp) cc_final: 0.8623 (ttp) REVERT: C 131 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7901 (p0) REVERT: C 159 GLN cc_start: 0.9010 (mm110) cc_final: 0.8584 (mp-120) REVERT: D 89 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7856 (mmmt) REVERT: D 121 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7525 (ttp-170) REVERT: D 227 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8398 (ttt180) REVERT: D 248 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: E 16 LYS cc_start: 0.8684 (tttm) cc_final: 0.8203 (tptm) REVERT: F 64 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7707 (ttm-80) REVERT: F 79 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.6804 (p90) REVERT: F 153 VAL cc_start: 0.8749 (m) cc_final: 0.8493 (m) REVERT: I 41 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7865 (ttm170) REVERT: J 47 LYS cc_start: 0.8235 (ptmt) cc_final: 0.7871 (ptmm) REVERT: J 79 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8030 (ttt180) REVERT: J 117 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8846 (mp) REVERT: K 55 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7911 (mtp180) REVERT: K 177 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8569 (mp) REVERT: K 195 GLU cc_start: 0.6750 (tp30) cc_final: 0.5918 (tp30) REVERT: L 103 GLU cc_start: 0.8753 (pt0) cc_final: 0.8392 (pt0) REVERT: M 60 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: N 4 MET cc_start: 0.8729 (ttm) cc_final: 0.8346 (ttm) REVERT: N 13 GLN cc_start: 0.8543 (pt0) cc_final: 0.8261 (pt0) REVERT: Q 40 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7341 (tpm170) REVERT: U 123 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8743 (mp) REVERT: V 51 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.6914 (mmtm) REVERT: W 19 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8140 (mtpt) REVERT: W 84 LYS cc_start: 0.8387 (pttp) cc_final: 0.8182 (pttp) REVERT: Y 61 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7195 (mtp180) REVERT: Z 1 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7057 (tmm) REVERT: Z 74 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8631 (mtmm) REVERT: a 44 LEU cc_start: 0.7589 (tp) cc_final: 0.7332 (mp) REVERT: c 15 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.5842 (mpp-170) REVERT: c 36 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8860 (mt) REVERT: g 104 LYS cc_start: 0.7335 (pttt) cc_final: 0.7021 (pttt) REVERT: h 20 MET cc_start: 0.6238 (mtp) cc_final: 0.5598 (mtp) REVERT: j 88 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7436 (ttt-90) REVERT: j 118 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6535 (mtp-110) outliers start: 184 outliers final: 113 residues processed: 858 average time/residue: 1.7912 time to fit residues: 1980.7259 Evaluate side-chains 871 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 734 time to evaluate : 4.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 154 LYS Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain K residue 55 ARG Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 171 GLU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 117 ARG Chi-restraints excluded: chain P residue 140 THR Chi-restraints excluded: chain Q residue 32 GLN Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 70 MET Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 97 GLN Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 10 GLN Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 129 LEU Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain V residue 51 LYS Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 18 ARG Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 61 ARG Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 74 LYS Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 101 SER Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain c residue 2 THR Chi-restraints excluded: chain c residue 15 ARG Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain g residue 100 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 88 ARG Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain j residue 118 ARG Chi-restraints excluded: chain j residue 203 ASP Chi-restraints excluded: chain j residue 288 SER Chi-restraints excluded: chain j residue 311 GLN Chi-restraints excluded: chain i residue 166 SER Chi-restraints excluded: chain i residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 378 optimal weight: 0.6980 chunk 609 optimal weight: 0.5980 chunk 372 optimal weight: 0.9990 chunk 289 optimal weight: 0.7980 chunk 423 optimal weight: 7.9990 chunk 639 optimal weight: 2.9990 chunk 588 optimal weight: 0.5980 chunk 509 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 393 optimal weight: 0.6980 chunk 312 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN B 131 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN C 202 GLN E 197 ASN F 145 GLN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN I 167 GLN J 143 ASN K 83 ASN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN L 83 GLN O 28 HIS ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 142 GLN V 92 HIS W 70 ASN X 127 ASN a 112 ASN c 72 HIS c 86 ASN j 4 GLN ** j 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 143 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 79429 Z= 0.163 Angle : 0.610 10.135 115177 Z= 0.316 Chirality : 0.039 0.282 14217 Planarity : 0.005 0.074 8432 Dihedral : 23.329 179.317 31409 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 3.07 % Allowed : 22.67 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.24 (0.12), residues: 4815 helix: 0.60 (0.14), residues: 1511 sheet: -0.09 (0.17), residues: 905 loop : -0.61 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP j 259 HIS 0.014 0.001 HIS H 91 PHE 0.024 0.001 PHE M 67 TYR 0.011 0.001 TYR R 141 ARG 0.018 0.001 ARG M 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 749 time to evaluate : 4.307 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: B 181 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: C 120 MET cc_start: 0.8740 (ttp) cc_final: 0.8526 (ttp) REVERT: C 131 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7736 (p0) REVERT: C 159 GLN cc_start: 0.8961 (mm110) cc_final: 0.8500 (mp-120) REVERT: D 89 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7884 (mmmt) REVERT: D 121 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7589 (ttp-170) REVERT: D 123 ARG cc_start: 0.8408 (mtm180) cc_final: 0.8191 (mtm110) REVERT: D 227 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8266 (ttt180) REVERT: D 248 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: E 16 LYS cc_start: 0.8660 (tttm) cc_final: 0.8183 (tptm) REVERT: F 79 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.6834 (p90) REVERT: F 153 VAL cc_start: 0.8670 (m) cc_final: 0.8421 (m) REVERT: I 41 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7799 (ttm170) REVERT: J 47 LYS cc_start: 0.8178 (ptmt) cc_final: 0.7790 (ttpp) REVERT: L 103 GLU cc_start: 0.8715 (pt0) cc_final: 0.8360 (pt0) REVERT: N 4 MET cc_start: 0.8659 (ttm) cc_final: 0.8263 (ttm) REVERT: N 13 GLN cc_start: 0.8437 (pt0) cc_final: 0.8188 (pt0) REVERT: P 104 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7700 (mtm180) REVERT: Q 40 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.6827 (tpm170) REVERT: Q 106 GLU cc_start: 0.7191 (tp30) cc_final: 0.6510 (tp30) REVERT: T 113 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7604 (ttm110) REVERT: U 75 MET cc_start: 0.7869 (mmt) cc_final: 0.7324 (mmt) REVERT: U 129 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7429 (ptp90) REVERT: W 19 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8078 (mtpt) REVERT: X 63 ASN cc_start: 0.7537 (p0) cc_final: 0.7054 (p0) REVERT: Y 61 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7226 (mtp180) REVERT: Y 72 PHE cc_start: 0.8330 (m-80) cc_final: 0.7840 (t80) REVERT: a 44 LEU cc_start: 0.7608 (tp) cc_final: 0.7344 (mp) REVERT: c 15 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.5846 (mpp-170) REVERT: c 36 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8771 (mt) REVERT: h 20 MET cc_start: 0.6232 (mtp) cc_final: 0.5604 (mtp) REVERT: j 88 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7193 (ttt-90) REVERT: j 118 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6481 (mtp-110) outliers start: 129 outliers final: 82 residues processed: 820 average time/residue: 1.7838 time to fit residues: 1884.2894 Evaluate side-chains 840 residues out of total 4217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 743 time to evaluate : 4.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 154 LYS Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 171 GLU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 104 ARG Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain Q residue 32 GLN Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 45 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 97 GLN Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 10 GLN Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 18 ARG Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 61 ARG Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 112 ASN Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain c residue 2 THR Chi-restraints excluded: chain c residue 15 ARG Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain j residue 88 ARG Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain j residue 118 ARG Chi-restraints excluded: chain j residue 288 SER Chi-restraints excluded: chain j residue 311 GLN Chi-restraints excluded: chain i residue 166 SER Chi-restraints excluded: chain i residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 404 optimal weight: 0.6980 chunk 542 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 469 optimal weight: 20.0000 chunk 75 optimal weight: 0.0030 chunk 141 optimal weight: 9.9990 chunk 510 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 523 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 overall best weight: 2.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN B 131 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN C 202 GLN F 145 GLN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 ASN K 83 ASN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN L 83 GLN M 7 ASN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN W 70 ASN X 127 ASN a 112 ASN c 72 HIS c 86 ASN j 4 GLN ** j 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 143 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.170952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144939 restraints weight = 77767.516| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 0.79 r_work: 0.3455 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 79429 Z= 0.268 Angle : 0.687 59.200 115177 Z= 0.375 Chirality : 0.042 0.288 14217 Planarity : 0.005 0.101 8432 Dihedral : 23.320 179.273 31409 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 2.80 % Allowed : 23.17 % Favored : 74.03 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.22 (0.12), residues: 4815 helix: 0.62 (0.13), residues: 1512 sheet: -0.09 (0.17), residues: 905 loop : -0.60 (0.13), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP j 259 HIS 0.029 0.001 HIS H 91 PHE 0.023 0.002 PHE M 67 TYR 0.027 0.001 TYR g 148 ARG 0.042 0.001 ARG K 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27792.95 seconds wall clock time: 482 minutes 52.31 seconds (28972.31 seconds total)