Starting phenix.real_space_refine on Fri Mar 15 05:39:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v91_2599/03_2024/4v91_2599.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v91_2599/03_2024/4v91_2599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v91_2599/03_2024/4v91_2599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v91_2599/03_2024/4v91_2599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v91_2599/03_2024/4v91_2599.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v91_2599/03_2024/4v91_2599.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3482 5.49 5 S 105 5.16 5 C 65657 2.51 5 N 23215 2.21 5 O 33206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 125665 Number of models: 1 Model: "" Number of chains: 45 Chain: "1" Number of atoms: 68514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3203, 68514 Classifications: {'RNA': 3203} Modifications used: {'rna2p_pur': 381, 'rna2p_pyr': 255, 'rna3p_pur': 1395, 'rna3p_pyr': 1172} Link IDs: {'rna2p': 636, 'rna3p': 2566} Chain breaks: 211 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 52} Link IDs: {'rna2p': 13, 'rna3p': 107} Chain breaks: 10 Chain: "4" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 14, 'rna3p_pur': 58, 'rna3p_pyr': 66} Link IDs: {'rna2p': 34, 'rna3p': 123} Chain breaks: 3 Chain: "A" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1914 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 240} Chain breaks: 7 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 14, 'TRANS': 371} Chain breaks: 24 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 17, 'TRANS': 343} Chain breaks: 17 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2375 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain breaks: 29 Chain: "E" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1239 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 8, 'TRANS': 147} Chain breaks: 18 Chain: "F" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 11 Chain: "G" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1804 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain breaks: 23 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 10 Chain: "I" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1705 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain breaks: 14 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 3} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain breaks: 15 Chain: "L" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 8 Chain: "M" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain breaks: 5 Chain: "N" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 194} Chain breaks: 7 Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 2 Chain: "P" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1420 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 9 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 9 Chain: "R" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1521 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 16 Chain: "S" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1445 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain breaks: 10 Chain: "T" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1276 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 7 Chain: "U" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 796 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain breaks: 10 Chain: "V" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain breaks: 9 Chain: "W" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 500 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 2 Chain: "X" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Y" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain breaks: 3 Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain breaks: 7 Chain: "a" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1173 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain breaks: 10 Chain: "b" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain breaks: 9 Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain breaks: 6 Chain: "d" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 7 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "e" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 4 Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain breaks: 3 Chain: "g" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain breaks: 6 Chain: "i" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 771 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain breaks: 12 Chain: "j" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 681 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain breaks: 4 Chain: "k" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain breaks: 9 Chain: "l" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain breaks: 3 Chain: "m" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain breaks: 5 Chain: "n" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 233 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain breaks: 2 Chain: "o" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 847 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain breaks: 6 Chain: "p" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain breaks: 5 Chain: "t" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1718 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 46 Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N VAL O 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 13 " occ=0.50 residue: pdb=" N HIS O 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2 HIS O 14 " occ=0.50 ... (remaining 185 not shown) Time building chain proxies: 45.54, per 1000 atoms: 0.36 Number of scatterers: 125665 At special positions: 0 Unit cell: (206.36, 242.54, 262.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 3482 15.00 O 33206 8.00 N 23215 7.00 C 65657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS j 19 " - pdb=" SG CYS j 37 " distance=2.95 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: 45.74 Conformation dependent library (CDL) restraints added in 7.2 seconds 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB PRO C 21 " pdb=" CB LEU P 52 " pdb=" CB LYS P 89 " pdb=" CB GLN T 49 " pdb=" CB GLU Z 47 " pdb=" CB TYR g 76 " pdb=" CB LEU t 93 " Number of C-beta restraints generated: 12020 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 64 sheets defined 18.9% alpha, 6.6% beta 933 base pairs and 1757 stacking pairs defined. Time for finding SS restraints: 37.51 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 removed outlier: 3.531A pdb=" N GLY A 13 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 107 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.840A pdb=" N LYS A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.622A pdb=" N LEU A 191 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.585A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.504A pdb=" N HIS B 377 " --> pdb=" O PRO B 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 34 through 44 removed outlier: 3.690A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 119 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 174 through 184 removed outlier: 3.567A pdb=" N VAL C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 320 through 325 removed outlier: 3.514A pdb=" N LEU C 324 " --> pdb=" O ASN C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 337 removed outlier: 4.124A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'D' and resid 9 through 15 removed outlier: 3.671A pdb=" N SER D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 44 Processing helix chain 'D' and resid 82 through 87 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 162 through 169 Processing helix chain 'D' and resid 194 through 200 removed outlier: 3.625A pdb=" N TYR D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 222 removed outlier: 3.938A pdb=" N PHE D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 removed outlier: 3.805A pdb=" N ALA D 228 " --> pdb=" O LYS D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 237 through 244 removed outlier: 3.597A pdb=" N THR D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 272 Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'E' and resid 132 through 140 removed outlier: 3.573A pdb=" N LYS E 139 " --> pdb=" O VAL E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 147 removed outlier: 3.526A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'F' and resid 31 through 40 removed outlier: 3.513A pdb=" N LYS F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 54 Processing helix chain 'F' and resid 66 through 72 Processing helix chain 'F' and resid 96 through 104 removed outlier: 3.720A pdb=" N LYS F 101 " --> pdb=" O PRO F 97 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 131 removed outlier: 3.880A pdb=" N LEU F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 130 " --> pdb=" O LEU F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 152 removed outlier: 4.310A pdb=" N LEU F 147 " --> pdb=" O THR F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 174 removed outlier: 4.195A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 186 Processing helix chain 'F' and resid 197 through 202 Processing helix chain 'G' and resid 46 through 50 removed outlier: 3.848A pdb=" N VAL G 50 " --> pdb=" O SER G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 59 removed outlier: 3.542A pdb=" N ARG G 57 " --> pdb=" O PRO G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 69 removed outlier: 3.681A pdb=" N LEU G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 165 removed outlier: 4.494A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 208 removed outlier: 3.534A pdb=" N ASP G 207 " --> pdb=" O ARG G 204 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU G 208 " --> pdb=" O ALA G 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 204 through 208' Processing helix chain 'G' and resid 239 through 244 Processing helix chain 'H' and resid 61 through 67 removed outlier: 3.735A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 77 Processing helix chain 'H' and resid 160 through 164 Processing helix chain 'I' and resid 5 through 10 removed outlier: 3.878A pdb=" N TYR I 9 " --> pdb=" O PRO I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 81 removed outlier: 5.905A pdb=" N TYR I 75 " --> pdb=" O CYS I 71 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR I 77 " --> pdb=" O ASN I 73 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR I 78 " --> pdb=" O LYS I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 148 Processing helix chain 'I' and resid 149 through 156 Processing helix chain 'I' and resid 178 through 185 Processing helix chain 'J' and resid 72 through 76 removed outlier: 4.167A pdb=" N LYS J 75 " --> pdb=" O ARG J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 84 removed outlier: 3.561A pdb=" N GLY J 83 " --> pdb=" O ILE J 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 47 removed outlier: 3.585A pdb=" N ARG L 39 " --> pdb=" O ARG L 35 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG L 42 " --> pdb=" O ALA L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 122 Processing helix chain 'L' and resid 170 through 180 removed outlier: 3.649A pdb=" N PHE L 179 " --> pdb=" O SER L 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 94 removed outlier: 3.853A pdb=" N LYS M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 107 Processing helix chain 'M' and resid 108 through 112 removed outlier: 3.510A pdb=" N LEU M 112 " --> pdb=" O ARG M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 120 removed outlier: 3.562A pdb=" N PHE M 118 " --> pdb=" O ASP M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 138 removed outlier: 4.036A pdb=" N LYS M 137 " --> pdb=" O LYS M 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 13 removed outlier: 3.746A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 28 removed outlier: 4.091A pdb=" N ARG N 24 " --> pdb=" O ARG N 20 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 107 removed outlier: 3.596A pdb=" N ARG N 105 " --> pdb=" O THR N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 152 removed outlier: 3.825A pdb=" N ILE N 151 " --> pdb=" O TYR N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 181 removed outlier: 3.508A pdb=" N PHE N 180 " --> pdb=" O GLY N 177 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 196 Processing helix chain 'O' and resid 25 through 30 Processing helix chain 'O' and resid 50 through 57 removed outlier: 3.746A pdb=" N PHE O 57 " --> pdb=" O LYS O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'O' and resid 120 through 124 Processing helix chain 'O' and resid 138 through 144 removed outlier: 3.527A pdb=" N THR O 143 " --> pdb=" O GLY O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 160 removed outlier: 3.865A pdb=" N ALA O 158 " --> pdb=" O ALA O 154 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG O 160 " --> pdb=" O LEU O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 169 removed outlier: 3.670A pdb=" N TYR O 168 " --> pdb=" O SER O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 195 removed outlier: 3.746A pdb=" N GLN O 193 " --> pdb=" O ASP O 189 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU O 194 " --> pdb=" O VAL O 190 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA O 195 " --> pdb=" O ALA O 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 189 through 195' Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.913A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 52 removed outlier: 3.519A pdb=" N LYS P 46 " --> pdb=" O THR P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 97 Processing helix chain 'P' and resid 169 through 174 Processing helix chain 'P' and resid 178 through 183 Processing helix chain 'Q' and resid 24 through 34 removed outlier: 3.552A pdb=" N LEU Q 29 " --> pdb=" O TYR Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 52 removed outlier: 4.311A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL Q 47 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 59 Processing helix chain 'Q' and resid 64 through 68 removed outlier: 3.592A pdb=" N ALA Q 68 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 64 through 68' Processing helix chain 'Q' and resid 111 through 116 Processing helix chain 'Q' and resid 123 through 131 removed outlier: 3.585A pdb=" N LEU Q 127 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL Q 129 " --> pdb=" O ASP Q 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 151 Processing helix chain 'R' and resid 9 through 16 Processing helix chain 'R' and resid 18 through 22 Processing helix chain 'R' and resid 29 through 34 Processing helix chain 'R' and resid 62 through 70 Processing helix chain 'R' and resid 91 through 96 removed outlier: 3.777A pdb=" N TRP R 95 " --> pdb=" O SER R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 103 Processing helix chain 'R' and resid 116 through 125 removed outlier: 3.873A pdb=" N TYR R 120 " --> pdb=" O ASP R 116 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL R 122 " --> pdb=" O HIS R 118 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 143 Processing helix chain 'R' and resid 143 through 148 removed outlier: 3.545A pdb=" N ALA R 147 " --> pdb=" O ILE R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 163 removed outlier: 3.513A pdb=" N ARG R 162 " --> pdb=" O GLU R 158 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 49 removed outlier: 3.521A pdb=" N LEU S 45 " --> pdb=" O TYR S 41 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 111 Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'T' and resid 54 through 58 Processing helix chain 'T' and resid 100 through 109 removed outlier: 3.703A pdb=" N GLU T 104 " --> pdb=" O LYS T 100 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE T 105 " --> pdb=" O CYS T 101 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 24 removed outlier: 3.542A pdb=" N THR U 23 " --> pdb=" O VAL U 19 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 41 Processing helix chain 'U' and resid 72 through 79 Processing helix chain 'V' and resid 126 through 132 removed outlier: 3.644A pdb=" N ALA V 130 " --> pdb=" O TRP V 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 43 Processing helix chain 'W' and resid 45 through 49 Processing helix chain 'W' and resid 52 through 57 Processing helix chain 'X' and resid 72 through 78 removed outlier: 4.101A pdb=" N VAL X 76 " --> pdb=" O ALA X 72 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP X 78 " --> pdb=" O LYS X 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 72 through 78' Processing helix chain 'X' and resid 91 through 99 Processing helix chain 'Y' and resid 12 through 18 Processing helix chain 'Y' and resid 25 through 30 removed outlier: 4.001A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 38 through 44 Processing helix chain 'Y' and resid 112 through 117 Processing helix chain 'Z' and resid 61 through 66 Processing helix chain 'Z' and resid 78 through 80 No H-bonds generated for 'chain 'Z' and resid 78 through 80' Processing helix chain 'Z' and resid 89 through 93 Processing helix chain 'Z' and resid 118 through 123 Processing helix chain 'Z' and resid 128 through 132 Processing helix chain 'a' and resid 6 through 11 removed outlier: 4.171A pdb=" N LYS a 10 " --> pdb=" O THR a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 91 removed outlier: 3.517A pdb=" N TYR a 90 " --> pdb=" O LYS a 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 108 Processing helix chain 'b' and resid 36 through 41 Processing helix chain 'b' and resid 43 through 50 removed outlier: 3.722A pdb=" N LEU b 47 " --> pdb=" O HIS b 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 21 Processing helix chain 'c' and resid 49 through 63 Processing helix chain 'd' and resid 33 through 45 Processing helix chain 'd' and resid 59 through 63 removed outlier: 4.221A pdb=" N ARG d 62 " --> pdb=" O ILE d 59 " (cutoff:3.500A) Processing helix chain 'e' and resid 78 through 83 removed outlier: 3.633A pdb=" N GLU e 83 " --> pdb=" O VAL e 79 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 114 removed outlier: 3.638A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE e 108 " --> pdb=" O ASN e 104 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU e 109 " --> pdb=" O ARG e 105 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS e 113 " --> pdb=" O LEU e 109 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) Processing helix chain 'g' and resid 94 through 101 removed outlier: 3.516A pdb=" N GLN g 98 " --> pdb=" O LEU g 94 " (cutoff:3.500A) Processing helix chain 'g' and resid 104 through 112 removed outlier: 3.741A pdb=" N THR g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU g 110 " --> pdb=" O LYS g 106 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA g 111 " --> pdb=" O GLU g 107 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 12 removed outlier: 3.785A pdb=" N THR h 11 " --> pdb=" O GLU h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 17 through 27 removed outlier: 3.614A pdb=" N LEU h 24 " --> pdb=" O GLN h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 41 through 45 Processing helix chain 'h' and resid 47 through 63 Processing helix chain 'h' and resid 94 through 99 Processing helix chain 'i' and resid 40 through 45 Processing helix chain 'i' and resid 69 through 76 Processing helix chain 'i' and resid 84 through 97 removed outlier: 3.908A pdb=" N ASN i 92 " --> pdb=" O GLU i 88 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 10 removed outlier: 3.970A pdb=" N LYS j 10 " --> pdb=" O PRO j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 52 through 58 removed outlier: 3.782A pdb=" N ARG j 56 " --> pdb=" O LYS j 52 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 75 removed outlier: 4.338A pdb=" N VAL j 70 " --> pdb=" O TYR j 66 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 13 Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'l' and resid 6 through 18 removed outlier: 3.990A pdb=" N LYS l 12 " --> pdb=" O ARG l 8 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS l 15 " --> pdb=" O GLN l 11 " (cutoff:3.500A) Processing helix chain 'n' and resid 19 through 24 removed outlier: 3.536A pdb=" N ARG n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER n 24 " --> pdb=" O VAL n 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 19 through 24' Processing helix chain 'o' and resid 37 through 46 Processing helix chain 'p' and resid 8 through 14 removed outlier: 3.518A pdb=" N THR p 11 " --> pdb=" O VAL p 8 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 24 through 29 removed outlier: 3.666A pdb=" N LYS p 28 " --> pdb=" O ARG p 24 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU p 29 " --> pdb=" O GLN p 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 24 through 29' Processing helix chain 'p' and resid 77 through 87 Processing helix chain 't' and resid 71 through 76 Processing helix chain 't' and resid 115 through 120 removed outlier: 3.902A pdb=" N GLN t 119 " --> pdb=" O VAL t 115 " (cutoff:3.500A) Processing helix chain 't' and resid 176 through 182 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 149 Processing sheet with id=AA3, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA4, first strand: chain 'B' and resid 285 through 286 removed outlier: 3.586A pdb=" N PHE B 321 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 50 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 71 through 74 removed outlier: 6.566A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 106 removed outlier: 5.535A pdb=" N LEU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR B 95 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AA8, first strand: chain 'B' and resid 219 through 220 removed outlier: 3.644A pdb=" N ALA B 219 " --> pdb=" O ARG B 275 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 225 through 226 removed outlier: 3.515A pdb=" N GLY B 225 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 6 through 9 removed outlier: 7.119A pdb=" N VAL C 6 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASN C 18 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL C 8 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 63 through 64 Processing sheet with id=AB3, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB4, first strand: chain 'C' and resid 228 through 229 Processing sheet with id=AB5, first strand: chain 'D' and resid 74 through 76 removed outlier: 6.903A pdb=" N ILE D 64 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 77 through 80 removed outlier: 7.065A pdb=" N THR E 62 " --> pdb=" O HIS E 57 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N HIS E 57 " --> pdb=" O THR E 62 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU E 64 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER E 66 " --> pdb=" O VAL E 53 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 74 through 76 Processing sheet with id=AB8, first strand: chain 'F' and resid 115 through 118 Processing sheet with id=AB9, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AC1, first strand: chain 'G' and resid 70 through 71 Processing sheet with id=AC2, first strand: chain 'G' and resid 133 through 134 removed outlier: 3.738A pdb=" N LEU G 150 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AC4, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AC5, first strand: chain 'H' and resid 47 through 49 removed outlier: 6.512A pdb=" N LEU H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 92 through 93 Processing sheet with id=AC7, first strand: chain 'H' and resid 113 through 114 Processing sheet with id=AC8, first strand: chain 'H' and resid 136 through 137 removed outlier: 4.056A pdb=" N GLU H 143 " --> pdb=" O SER H 137 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 86 through 88 removed outlier: 6.189A pdb=" N ILE I 134 " --> pdb=" O SER I 54 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N SER I 54 " --> pdb=" O ILE I 134 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE I 136 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 97 through 99 removed outlier: 6.643A pdb=" N LEU I 97 " --> pdb=" O HIS I 123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 46 through 48 removed outlier: 3.674A pdb=" N ALA J 66 " --> pdb=" O SER J 48 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET J 125 " --> pdb=" O ILE J 106 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE J 106 " --> pdb=" O MET J 125 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE J 104 " --> pdb=" O PHE J 127 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AD4, first strand: chain 'M' and resid 15 through 16 Processing sheet with id=AD5, first strand: chain 'M' and resid 43 through 45 Processing sheet with id=AD6, first strand: chain 'N' and resid 36 through 37 removed outlier: 7.590A pdb=" N TYR N 129 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TRP N 120 " --> pdb=" O TYR N 129 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLU N 131 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N SER N 118 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 33 through 36 removed outlier: 4.188A pdb=" N VAL O 35 " --> pdb=" O LYS O 103 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 14 through 15 removed outlier: 6.292A pdb=" N HIS P 145 " --> pdb=" O VAL P 119 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL P 119 " --> pdb=" O HIS P 145 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU P 147 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE P 117 " --> pdb=" O GLU P 147 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL P 149 " --> pdb=" O SER P 115 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 128 through 131 Processing sheet with id=AE1, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AE2, first strand: chain 'Q' and resid 100 through 101 Processing sheet with id=AE3, first strand: chain 'S' and resid 61 through 63 Processing sheet with id=AE4, first strand: chain 'S' and resid 87 through 96 removed outlier: 3.628A pdb=" N TYR S 81 " --> pdb=" O HIS S 88 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE S 75 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP S 96 " --> pdb=" O LYS S 73 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY S 76 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N VAL S 126 " --> pdb=" O GLY S 76 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 63 through 67 removed outlier: 3.646A pdb=" N VAL T 63 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY T 73 " --> pdb=" O TYR T 65 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL T 67 " --> pdb=" O SER T 71 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N SER T 71 " --> pdb=" O VAL T 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 15 through 17 Processing sheet with id=AE7, first strand: chain 'V' and resid 34 through 39 removed outlier: 5.788A pdb=" N ILE V 36 " --> pdb=" O THR V 61 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR V 61 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA V 38 " --> pdb=" O MET V 59 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 85 through 86 Processing sheet with id=AE9, first strand: chain 'W' and resid 4 through 5 Processing sheet with id=AF1, first strand: chain 'X' and resid 63 through 66 removed outlier: 7.457A pdb=" N GLN X 85 " --> pdb=" O GLU X 64 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL X 83 " --> pdb=" O PRO X 66 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS X 121 " --> pdb=" O THR X 112 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR X 112 " --> pdb=" O LYS X 121 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR X 123 " --> pdb=" O VAL X 110 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL X 110 " --> pdb=" O TYR X 123 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG X 125 " --> pdb=" O LEU X 108 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 32 through 33 Processing sheet with id=AF3, first strand: chain 'Y' and resid 56 through 58 removed outlier: 3.521A pdb=" N LEU Y 57 " --> pdb=" O VAL Y 105 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 70 through 73 removed outlier: 7.615A pdb=" N GLN Y 81 " --> pdb=" O SER Y 71 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 10 through 11 Processing sheet with id=AF6, first strand: chain 'Z' and resid 27 through 29 removed outlier: 4.103A pdb=" N LYS Z 27 " --> pdb=" O LEU Z 42 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'a' and resid 102 through 103 Processing sheet with id=AF8, first strand: chain 'c' and resid 43 through 44 Processing sheet with id=AF9, first strand: chain 'd' and resid 13 through 15 removed outlier: 3.720A pdb=" N ILE d 14 " --> pdb=" O LEU d 71 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'd' and resid 49 through 51 Processing sheet with id=AG2, first strand: chain 'e' and resid 75 through 76 Processing sheet with id=AG3, first strand: chain 'f' and resid 11 through 13 Processing sheet with id=AG4, first strand: chain 'g' and resid 19 through 20 removed outlier: 4.395A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 23 through 25 Processing sheet with id=AG6, first strand: chain 'j' and resid 16 through 17 removed outlier: 3.515A pdb=" N PHE j 27 " --> pdb=" O THR j 17 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'k' and resid 44 through 46 Processing sheet with id=AG8, first strand: chain 'm' and resid 94 through 95 Processing sheet with id=AG9, first strand: chain 'o' and resid 23 through 27 Processing sheet with id=AH1, first strand: chain 't' and resid 83 through 84 730 hydrogen bonds defined for protein. 1881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2241 hydrogen bonds 3706 hydrogen bond angles 0 basepair planarities 933 basepair parallelities 1757 stacking parallelities Total time for adding SS restraints: 157.99 Time building geometry restraints manager: 49.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.46 - 0.97: 4 0.97 - 1.48: 82352 1.48 - 1.98: 50931 1.98 - 2.49: 448 2.49 - 3.00: 1079 Warning: very small bond lengths. Bond restraints: 134814 Sorted by residual: bond pdb=" C THR L 152 " pdb=" N ASP L 153 " ideal model delta sigma weight residual 1.332 2.921 -1.589 8.30e-03 1.45e+04 3.66e+04 bond pdb=" C LYS J 35 " pdb=" N VAL J 36 " ideal model delta sigma weight residual 1.329 2.847 -1.517 9.40e-03 1.13e+04 2.61e+04 bond pdb=" C ASP k 19 " pdb=" N VAL k 20 " ideal model delta sigma weight residual 1.331 2.986 -1.655 1.05e-02 9.07e+03 2.49e+04 bond pdb=" C ALA Z 19 " pdb=" N GLY Z 20 " ideal model delta sigma weight residual 1.329 2.874 -1.545 1.00e-02 1.00e+04 2.39e+04 bond pdb=" C GLU J 78 " pdb=" N ILE J 79 " ideal model delta sigma weight residual 1.335 2.994 -1.659 1.10e-02 8.26e+03 2.27e+04 ... (remaining 134809 not shown) Histogram of bond angle deviations from ideal: 20.84 - 51.90: 26 51.90 - 82.97: 950 82.97 - 114.03: 99362 114.03 - 145.09: 97243 145.09 - 176.15: 131 Bond angle restraints: 197712 Sorted by residual: angle pdb=" O VAL O 153 " pdb=" C VAL O 153 " pdb=" N ALA O 154 " ideal model delta sigma weight residual 122.23 39.27 82.96 9.80e-01 1.04e+00 7.17e+03 angle pdb=" O ALA O 186 " pdb=" C ALA O 186 " pdb=" N GLU O 187 " ideal model delta sigma weight residual 122.11 23.53 98.58 1.18e+00 7.18e-01 6.98e+03 angle pdb=" O HIS O 72 " pdb=" C HIS O 72 " pdb=" N PHE O 73 " ideal model delta sigma weight residual 122.87 21.26 101.61 1.23e+00 6.61e-01 6.82e+03 angle pdb=" O ARG n 12 " pdb=" C ARG n 12 " pdb=" N LEU n 13 " ideal model delta sigma weight residual 122.07 44.94 77.13 1.03e+00 9.43e-01 5.61e+03 angle pdb=" O PHE O 64 " pdb=" C PHE O 64 " pdb=" N ASN O 65 " ideal model delta sigma weight residual 122.42 26.36 96.06 1.31e+00 5.83e-01 5.38e+03 ... (remaining 197707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 72821 35.85 - 71.69: 10981 71.69 - 107.54: 1026 107.54 - 143.39: 75 143.39 - 179.23: 66 Dihedral angle restraints: 84969 sinusoidal: 66743 harmonic: 18226 Sorted by residual: dihedral pdb=" CA ILE Q 93 " pdb=" C ILE Q 93 " pdb=" N PHE Q 94 " pdb=" CA PHE Q 94 " ideal model delta harmonic sigma weight residual -180.00 -45.88 -134.12 0 5.00e+00 4.00e-02 7.20e+02 dihedral pdb=" CA VAL f 59 " pdb=" C VAL f 59 " pdb=" N ARG f 60 " pdb=" CA ARG f 60 " ideal model delta harmonic sigma weight residual 180.00 51.04 128.96 0 5.00e+00 4.00e-02 6.65e+02 dihedral pdb=" CA TYR g 76 " pdb=" C TYR g 76 " pdb=" N GLY g 77 " pdb=" CA GLY g 77 " ideal model delta harmonic sigma weight residual -180.00 -60.62 -119.38 0 5.00e+00 4.00e-02 5.70e+02 ... (remaining 84966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.749: 23504 0.749 - 1.498: 559 1.498 - 2.247: 991 2.247 - 2.997: 42 2.997 - 3.746: 6 Chirality restraints: 25102 Sorted by residual: chirality pdb=" C3' U 11056 " pdb=" C4' U 11056 " pdb=" O3' U 11056 " pdb=" C2' U 11056 " both_signs ideal model delta sigma weight residual False -2.48 1.27 -3.75 2.00e-01 2.50e+01 3.51e+02 chirality pdb=" C3' U 11888 " pdb=" C4' U 11888 " pdb=" O3' U 11888 " pdb=" C2' U 11888 " both_signs ideal model delta sigma weight residual False -2.48 0.97 -3.45 2.00e-01 2.50e+01 2.97e+02 chirality pdb=" CA PRO C 21 " pdb=" N PRO C 21 " pdb=" C PRO C 21 " pdb=" CB PRO C 21 " both_signs ideal model delta sigma weight residual False 2.72 -0.65 3.37 2.00e-01 2.50e+01 2.84e+02 ... (remaining 25099 not shown) Planarity restraints: 11954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE I 33 " 0.193 2.00e-02 2.50e+03 2.81e-01 7.91e+02 pdb=" C ILE I 33 " -0.461 2.00e-02 2.50e+03 pdb=" O ILE I 33 " 0.259 2.00e-02 2.50e+03 pdb=" N TYR I 34 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR g 76 " 0.190 2.00e-02 2.50e+03 2.80e-01 7.84e+02 pdb=" C TYR g 76 " -0.454 2.00e-02 2.50e+03 pdb=" O TYR g 76 " 0.267 2.00e-02 2.50e+03 pdb=" N GLY g 77 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU J 108 " -0.195 2.00e-02 2.50e+03 2.78e-01 7.74e+02 pdb=" C GLU J 108 " 0.446 2.00e-02 2.50e+03 pdb=" O GLU J 108 " -0.269 2.00e-02 2.50e+03 pdb=" N HIS J 109 " 0.018 2.00e-02 2.50e+03 ... (remaining 11951 not shown) Histogram of nonbonded interaction distances: 0.69 - 1.54: 11 1.54 - 2.38: 374 2.38 - 3.22: 110306 3.22 - 4.06: 396148 4.06 - 4.90: 616198 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1123037 Sorted by model distance: nonbonded pdb=" O VAL O 162 " pdb=" N SER O 164 " model vdw 0.695 2.520 nonbonded pdb=" O LEU O 129 " pdb=" CA LYS O 130 " model vdw 0.835 2.776 nonbonded pdb=" O ARG O 125 " pdb=" CA VAL O 126 " model vdw 0.897 2.776 nonbonded pdb=" O VAL O 16 " pdb=" CA GLY O 17 " model vdw 1.043 2.752 nonbonded pdb=" O ASP O 56 " pdb=" N LEU O 58 " model vdw 1.069 2.520 ... (remaining 1123032 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 11.230 Check model and map are aligned: 1.300 Set scattering table: 0.810 Process input model: 370.070 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 389.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3606 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 : 0.133 1.666 134814 Z= 8.262 Angle : 4.765 102.156 197712 Z= 3.214 Chirality : 0.426 3.746 25102 Planarity : 0.067 0.281 11954 Dihedral : 25.544 179.234 72946 Min Nonbonded Distance : 0.695 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 7.75 % Allowed : 14.09 % Favored : 78.16 % Rotamer: Outliers : 12.79 % Allowed : 13.82 % Favored : 73.39 % Cbeta Deviations : 8.73 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.07 % 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: -5.39 (0.10), residues: 3740 helix: -4.21 (0.09), residues: 989 sheet: -3.30 (0.23), residues: 334 loop : -3.54 (0.10), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 255 HIS 0.008 0.002 HIS B 13 PHE 0.029 0.002 PHE F 229 TYR 0.026 0.002 TYR f 103 ARG 0.014 0.001 ARG n 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1501 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 688 poor density : 813 time to evaluate : 5.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 199 THR cc_start: 0.7125 (OUTLIER) cc_final: 0.6888 (p) REVERT: A 247 ARG cc_start: 0.5335 (mmt-90) cc_final: 0.4546 (ttt180) REVERT: B 78 VAL cc_start: 0.6401 (t) cc_final: 0.6200 (t) REVERT: B 211 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7591 (mm-40) REVERT: B 238 LEU cc_start: 0.4334 (OUTLIER) cc_final: 0.4117 (mm) REVERT: B 279 ASN cc_start: 0.5208 (OUTLIER) cc_final: 0.4598 (m110) REVERT: B 285 VAL cc_start: 0.3222 (OUTLIER) cc_final: 0.2709 (t) REVERT: B 290 ASP cc_start: 0.6288 (t0) cc_final: 0.6029 (m-30) REVERT: B 319 ASN cc_start: 0.4577 (OUTLIER) cc_final: 0.4235 (p0) REVERT: C 149 PRO cc_start: 0.4149 (Cg_exo) cc_final: 0.3333 (Cg_exo) REVERT: C 186 LYS cc_start: 0.3409 (mmtt) cc_final: 0.3157 (mtmt) REVERT: C 193 LYS cc_start: 0.4388 (OUTLIER) cc_final: 0.4023 (mtpp) REVERT: C 299 ILE cc_start: 0.5824 (mm) cc_final: 0.5554 (mt) REVERT: D 36 LEU cc_start: 0.4787 (mt) cc_final: 0.4099 (mp) REVERT: D 41 LYS cc_start: 0.5367 (OUTLIER) cc_final: 0.4332 (mttt) REVERT: D 145 PHE cc_start: 0.1104 (OUTLIER) cc_final: 0.0701 (p90) REVERT: D 209 GLU cc_start: 0.6176 (tp30) cc_final: 0.5874 (tt0) REVERT: D 219 PHE cc_start: 0.5539 (t80) cc_final: 0.5109 (t80) REVERT: D 234 ASP cc_start: 0.6397 (p0) cc_final: 0.5426 (t0) REVERT: D 254 LYS cc_start: 0.6832 (OUTLIER) cc_final: 0.6303 (mttm) REVERT: D 277 LEU cc_start: 0.3282 (OUTLIER) cc_final: 0.2116 (tt) REVERT: F 77 VAL cc_start: -0.1341 (OUTLIER) cc_final: -0.1580 (m) REVERT: G 69 LEU cc_start: 0.2757 (OUTLIER) cc_final: 0.2280 (mp) REVERT: H 70 THR cc_start: 0.4543 (OUTLIER) cc_final: 0.4311 (t) REVERT: H 172 ILE cc_start: 0.3258 (OUTLIER) cc_final: 0.2890 (tp) REVERT: I 76 MET cc_start: 0.2340 (mtp) cc_final: 0.2112 (mtp) REVERT: J 17 LEU cc_start: 0.4946 (tp) cc_final: 0.4724 (tp) REVERT: J 39 GLN cc_start: 0.6344 (pt0) cc_final: 0.5887 (pm20) REVERT: J 62 ASN cc_start: 0.3640 (OUTLIER) cc_final: 0.2799 (t0) REVERT: J 102 PHE cc_start: 0.3347 (p90) cc_final: 0.2904 (p90) REVERT: J 130 VAL cc_start: 0.6769 (p) cc_final: 0.6320 (p) REVERT: L 67 ARG cc_start: 0.3367 (OUTLIER) cc_final: 0.0498 (tpm170) REVERT: M 107 GLU cc_start: 0.4198 (mp0) cc_final: 0.3361 (tp30) REVERT: N 22 LEU cc_start: 0.2814 (OUTLIER) cc_final: 0.2163 (mp) REVERT: O 84 LEU cc_start: 0.4245 (OUTLIER) cc_final: 0.4037 (mm) REVERT: O 87 MET cc_start: 0.4812 (mtt) cc_final: 0.4527 (tpp) REVERT: P 59 PRO cc_start: 0.4195 (Cg_endo) cc_final: 0.3487 (Cg_exo) REVERT: P 76 PHE cc_start: 0.4983 (m-80) cc_final: 0.4624 (m-80) REVERT: Q 148 GLU cc_start: 0.3821 (OUTLIER) cc_final: 0.3417 (mp0) REVERT: Q 164 ARG cc_start: 0.2896 (OUTLIER) cc_final: 0.2538 (mtt-85) REVERT: R 10 LEU cc_start: 0.5132 (OUTLIER) cc_final: 0.4685 (mp) REVERT: R 166 ASN cc_start: 0.0748 (OUTLIER) cc_final: -0.0721 (t0) REVERT: R 170 ARG cc_start: -0.2041 (OUTLIER) cc_final: -0.2387 (tpt90) REVERT: S 48 LEU cc_start: 0.4526 (OUTLIER) cc_final: 0.4017 (tp) REVERT: T 11 THR cc_start: 0.3370 (p) cc_final: 0.2890 (p) REVERT: T 71 SER cc_start: 0.1654 (OUTLIER) cc_final: 0.0598 (p) REVERT: U 76 LEU cc_start: 0.6126 (tp) cc_final: 0.5898 (tp) REVERT: U 100 THR cc_start: 0.6406 (OUTLIER) cc_final: 0.6090 (m) REVERT: V 66 LYS cc_start: 0.6142 (mttp) cc_final: 0.5816 (mmmt) REVERT: W 1 MET cc_start: 0.2277 (OUTLIER) cc_final: 0.1344 (ttt) REVERT: X 33 ARG cc_start: 0.5922 (OUTLIER) cc_final: 0.5109 (mtt90) REVERT: X 131 ASP cc_start: 0.5877 (t0) cc_final: 0.5473 (t0) REVERT: Z 34 LYS cc_start: 0.5383 (OUTLIER) cc_final: 0.4799 (mptt) REVERT: b 59 LYS cc_start: 0.1621 (OUTLIER) cc_final: 0.1306 (ttpp) REVERT: c 101 LEU cc_start: 0.1004 (OUTLIER) cc_final: 0.0398 (mt) REVERT: d 68 GLU cc_start: 0.6038 (OUTLIER) cc_final: 0.5718 (pt0) REVERT: e 18 LYS cc_start: 0.3039 (OUTLIER) cc_final: 0.2826 (mmtt) REVERT: e 81 ASP cc_start: 0.3701 (OUTLIER) cc_final: 0.3293 (t0) REVERT: f 20 LYS cc_start: 0.1484 (OUTLIER) cc_final: 0.1137 (ptpp) REVERT: g 31 ARG cc_start: 0.5181 (tpp80) cc_final: 0.4583 (mmp-170) REVERT: g 44 CYS cc_start: 0.7764 (t) cc_final: 0.7303 (p) REVERT: g 76 TYR cc_start: 0.0727 (OUTLIER) cc_final: 0.0334 (t80) REVERT: g 81 CYS cc_start: 0.3679 (OUTLIER) cc_final: 0.3315 (t) REVERT: g 100 ILE cc_start: 0.2190 (OUTLIER) cc_final: 0.1658 (mp) REVERT: h 51 ILE cc_start: 0.3106 (mt) cc_final: 0.2798 (mt) REVERT: h 58 ILE cc_start: 0.2804 (mt) cc_final: 0.1886 (mt) REVERT: i 28 TYR cc_start: 0.2548 (m-80) cc_final: 0.2043 (m-10) REVERT: i 57 LEU cc_start: 0.5729 (OUTLIER) cc_final: 0.5396 (mm) REVERT: j 25 ARG cc_start: 0.5350 (OUTLIER) cc_final: 0.4884 (ptt90) REVERT: k 28 ASN cc_start: 0.4998 (OUTLIER) cc_final: 0.4354 (t0) REVERT: k 29 LYS cc_start: 0.5622 (OUTLIER) cc_final: 0.4187 (mmtm) REVERT: k 41 THR cc_start: 0.2501 (OUTLIER) cc_final: 0.2039 (t) REVERT: l 23 LEU cc_start: 0.2890 (OUTLIER) cc_final: 0.0955 (pt) REVERT: l 36 ARG cc_start: 0.4537 (OUTLIER) cc_final: 0.3670 (ttp80) REVERT: m 91 CYS cc_start: 0.2185 (OUTLIER) cc_final: 0.1666 (p) REVERT: n 5 TRP cc_start: 0.4644 (OUTLIER) cc_final: 0.4221 (m100) REVERT: o 100 LYS cc_start: 0.3666 (OUTLIER) cc_final: 0.2902 (mttt) REVERT: p 11 THR cc_start: 0.3991 (OUTLIER) cc_final: 0.3249 (t) REVERT: p 47 VAL cc_start: 0.4849 (t) cc_final: 0.3818 (t) REVERT: p 90 VAL cc_start: 0.2821 (OUTLIER) cc_final: 0.2229 (t) REVERT: t 5 THR cc_start: 0.2244 (OUTLIER) cc_final: 0.1909 (p) REVERT: t 128 LEU cc_start: 0.0247 (OUTLIER) cc_final: -0.0428 (tp) REVERT: t 129 SER cc_start: 0.5234 (OUTLIER) cc_final: 0.3964 (t) REVERT: t 192 SER cc_start: 0.0588 (OUTLIER) cc_final: -0.0215 (p) REVERT: t 198 TRP cc_start: 0.2933 (OUTLIER) cc_final: 0.1660 (t60) REVERT: t 206 VAL cc_start: 0.2284 (OUTLIER) cc_final: 0.0750 (p) outliers start: 688 outliers final: 166 residues processed: 1397 average time/residue: 1.2492 time to fit residues: 2856.9866 Evaluate side-chains 665 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 443 time to evaluate : 5.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ARG Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 207 GLU Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 62 ASN Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 163 PHE Chi-restraints excluded: chain J residue 166 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 131 LYS Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 164 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 65 ASN Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 85 ARG Chi-restraints excluded: chain O residue 91 LYS Chi-restraints excluded: chain O residue 106 GLU Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain P residue 26 PHE Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 150 VAL Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain P residue 172 GLN Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain Q residue 164 ARG Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 158 GLU Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 165 TYR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 32 LYS Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 58 HIS Chi-restraints excluded: chain X residue 33 ARG Chi-restraints excluded: chain X residue 34 LEU Chi-restraints excluded: chain X residue 39 LYS Chi-restraints excluded: chain X residue 40 LEU Chi-restraints excluded: chain X residue 45 LYS Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 93 TYR Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 34 LYS Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain b residue 59 LYS Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 101 LEU Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 86 LYS Chi-restraints excluded: chain e residue 18 LYS Chi-restraints excluded: chain e residue 25 TYR Chi-restraints excluded: chain e residue 46 PHE Chi-restraints excluded: chain e residue 81 ASP Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 70 LYS Chi-restraints excluded: chain f residue 78 SER Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 76 TYR Chi-restraints excluded: chain g residue 80 ARG Chi-restraints excluded: chain g residue 81 CYS Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain h residue 27 GLU Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 27 SER Chi-restraints excluded: chain i residue 57 LEU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 28 ASN Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain l residue 5 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 36 ARG Chi-restraints excluded: chain l residue 51 ILE Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 83 LYS Chi-restraints excluded: chain m residue 91 CYS Chi-restraints excluded: chain n residue 5 TRP Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 11 THR Chi-restraints excluded: chain p residue 22 LEU Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 110 PHE Chi-restraints excluded: chain t residue 128 LEU Chi-restraints excluded: chain t residue 129 SER Chi-restraints excluded: chain t residue 151 VAL Chi-restraints excluded: chain t residue 152 ARG Chi-restraints excluded: chain t residue 192 SER Chi-restraints excluded: chain t residue 194 LEU Chi-restraints excluded: chain t residue 198 TRP Chi-restraints excluded: chain t residue 206 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 820 optimal weight: 0.9980 chunk 736 optimal weight: 6.9990 chunk 408 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 496 optimal weight: 5.9990 chunk 393 optimal weight: 7.9990 chunk 761 optimal weight: 5.9990 chunk 294 optimal weight: 5.9990 chunk 463 optimal weight: 8.9990 chunk 567 optimal weight: 5.9990 chunk 882 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 132 ASN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 250 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN B 231 HIS ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS C 213 ASN C 296 GLN ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 90 HIS D 244 HIS D 264 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN F 80 GLN F 159 GLN ** F 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 GLN ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN I 12 GLN ** J 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 ASN L 13 HIS ** L 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN L 137 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 HIS N 175 ASN O 50 ASN O 90 HIS P 45 GLN ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN P 96 GLN ** P 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 GLN ** Q 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 HIS S 46 GLN ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 HIS T 26 HIS T 95 HIS T 98 HIS ** T 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 132 ASN ** X 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 111 ASN ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 78 ASN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 HIS ** a 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 67 HIS a 74 ASN b 6 ASN b 10 HIS ** b 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 11 ASN d 15 ASN ** e 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 17 GLN ** f 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 3 GLN g 52 GLN h 16 GLN ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 63 ASN j 13 ASN k 40 GLN l 4 GLN l 11 GLN ** l 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 32 ASN l 33 ASN l 50 ASN o 23 HIS o 59 HIS o 82 GLN o 90 HIS p 32 GLN t 94 ASN t 158 GLN t 188 ASN t 199 GLN t 200 ASN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4948 moved from start: 0.7583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.407 134814 Z= 0.540 Angle : 1.400 30.415 197712 Z= 0.684 Chirality : 0.066 0.926 25102 Planarity : 0.012 0.163 11954 Dihedral : 24.539 179.968 60433 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 28.84 Ramachandran Plot: Outliers : 3.64 % Allowed : 12.90 % Favored : 83.46 % Rotamer: Outliers : 9.67 % Allowed : 18.59 % Favored : 71.74 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 4.13 % Twisted General : 0.28 % 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: -5.06 (0.09), residues: 5611 helix: -3.87 (0.08), residues: 1641 sheet: -2.87 (0.18), residues: 634 loop : -3.31 (0.09), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP S 42 HIS 0.023 0.004 HIS Q 5 PHE 0.082 0.006 PHE I 213 TYR 0.041 0.005 TYR D 30 ARG 0.024 0.002 ARG B 4 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1436 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 520 poor density : 916 time to evaluate : 5.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.5993 (mtmm) cc_final: 0.5632 (mtmt) REVERT: A 15 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7145 (pp) REVERT: A 72 ARG cc_start: 0.5320 (OUTLIER) cc_final: 0.5010 (mtt90) REVERT: A 194 ASN cc_start: 0.7585 (t0) cc_final: 0.7249 (t0) REVERT: A 204 MET cc_start: 0.7392 (ptp) cc_final: 0.7100 (ptp) REVERT: A 247 ARG cc_start: 0.6023 (mmt-90) cc_final: 0.5123 (ttp80) REVERT: B 53 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.5781 (mmm) REVERT: B 73 VAL cc_start: 0.6954 (OUTLIER) cc_final: 0.6629 (m) REVERT: B 94 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6425 (pm20) REVERT: B 216 ASP cc_start: 0.5397 (OUTLIER) cc_final: 0.5167 (m-30) REVERT: C 20 LEU cc_start: 0.2941 (OUTLIER) cc_final: 0.1936 (pp) REVERT: C 38 VAL cc_start: 0.4224 (t) cc_final: 0.3922 (t) REVERT: C 99 MET cc_start: 0.7200 (ptm) cc_final: 0.6917 (ptp) REVERT: C 149 PRO cc_start: 0.4190 (Cg_exo) cc_final: 0.3948 (Cg_exo) REVERT: C 255 PHE cc_start: 0.6767 (t80) cc_final: 0.6449 (t80) REVERT: D 8 LYS cc_start: 0.5610 (OUTLIER) cc_final: 0.5203 (mmpt) REVERT: D 54 ARG cc_start: 0.6646 (mmt-90) cc_final: 0.6440 (mmt-90) REVERT: D 57 ASN cc_start: 0.5418 (m-40) cc_final: 0.4805 (t0) REVERT: D 58 LYS cc_start: 0.2692 (mmtm) cc_final: 0.2284 (pttt) REVERT: D 93 THR cc_start: 0.5950 (t) cc_final: 0.5599 (t) REVERT: D 115 LEU cc_start: 0.2904 (OUTLIER) cc_final: 0.2564 (tp) REVERT: D 187 THR cc_start: 0.2932 (OUTLIER) cc_final: 0.1583 (p) REVERT: D 190 ILE cc_start: 0.5027 (OUTLIER) cc_final: 0.4531 (tt) REVERT: D 193 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7228 (mp0) REVERT: D 234 ASP cc_start: 0.7075 (p0) cc_final: 0.6707 (t0) REVERT: D 254 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7109 (pptt) REVERT: E 102 ASN cc_start: 0.1511 (OUTLIER) cc_final: 0.0408 (t0) REVERT: E 133 GLU cc_start: 0.2159 (OUTLIER) cc_final: 0.1722 (pt0) REVERT: F 243 MET cc_start: 0.4681 (OUTLIER) cc_final: 0.4451 (mtt) REVERT: G 86 THR cc_start: 0.6848 (OUTLIER) cc_final: 0.6648 (p) REVERT: G 221 ASN cc_start: 0.4849 (m-40) cc_final: 0.3903 (p0) REVERT: G 237 ILE cc_start: 0.3402 (OUTLIER) cc_final: 0.2853 (mt) REVERT: G 238 LEU cc_start: 0.3741 (OUTLIER) cc_final: 0.3144 (mt) REVERT: H 7 GLU cc_start: 0.4900 (pm20) cc_final: 0.4044 (mp0) REVERT: H 100 ASN cc_start: 0.5584 (t0) cc_final: 0.4621 (p0) REVERT: H 139 ASN cc_start: 0.3242 (OUTLIER) cc_final: 0.0487 (t0) REVERT: H 179 ILE cc_start: 0.5508 (mt) cc_final: 0.5252 (mt) REVERT: I 10 ARG cc_start: 0.6416 (ttt180) cc_final: 0.5994 (ttp80) REVERT: J 101 ASN cc_start: 0.7464 (m-40) cc_final: 0.6566 (m-40) REVERT: J 128 TYR cc_start: 0.5682 (t80) cc_final: 0.5392 (t80) REVERT: J 130 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7437 (p) REVERT: L 131 LYS cc_start: 0.3277 (OUTLIER) cc_final: 0.2962 (ptmt) REVERT: L 164 GLU cc_start: 0.1781 (OUTLIER) cc_final: 0.1326 (mp0) REVERT: M 72 LEU cc_start: 0.0506 (OUTLIER) cc_final: 0.0283 (tp) REVERT: M 113 THR cc_start: 0.2147 (OUTLIER) cc_final: 0.1910 (t) REVERT: N 36 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7687 (mp) REVERT: N 114 ARG cc_start: 0.6485 (mmt90) cc_final: 0.5637 (mmt90) REVERT: N 151 ILE cc_start: 0.2200 (OUTLIER) cc_final: 0.1956 (tt) REVERT: P 40 GLU cc_start: 0.6602 (tt0) cc_final: 0.6208 (tm-30) REVERT: P 55 GLN cc_start: 0.5958 (tp40) cc_final: 0.5661 (mm110) REVERT: Q 111 ARG cc_start: 0.0694 (OUTLIER) cc_final: 0.0471 (ptt-90) REVERT: Q 172 PHE cc_start: 0.7198 (m-80) cc_final: 0.6668 (m-80) REVERT: R 14 VAL cc_start: 0.8015 (t) cc_final: 0.7796 (t) REVERT: R 52 LYS cc_start: 0.6363 (tmtt) cc_final: 0.6149 (ptmm) REVERT: R 110 ARG cc_start: 0.6347 (OUTLIER) cc_final: 0.6074 (mtm180) REVERT: R 141 HIS cc_start: 0.4531 (t70) cc_final: 0.4086 (t70) REVERT: T 131 GLN cc_start: 0.5990 (OUTLIER) cc_final: 0.5277 (tp40) REVERT: U 88 GLN cc_start: 0.7302 (mp10) cc_final: 0.7087 (mm110) REVERT: U 99 LYS cc_start: 0.5705 (ttmm) cc_final: 0.5333 (mmtm) REVERT: V 66 LYS cc_start: 0.6087 (mttp) cc_final: 0.5845 (mmmt) REVERT: W 23 ARG cc_start: 0.4216 (ttp-170) cc_final: 0.3918 (ttt90) REVERT: X 26 VAL cc_start: 0.0637 (OUTLIER) cc_final: -0.0297 (p) REVERT: X 33 ARG cc_start: 0.6599 (mpt180) cc_final: 0.5536 (mmm-85) REVERT: X 53 HIS cc_start: 0.6078 (OUTLIER) cc_final: 0.5825 (m90) REVERT: X 70 GLU cc_start: 0.7574 (pt0) cc_final: 0.7309 (mt-10) REVERT: Y 99 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7748 (tt) REVERT: Z 34 LYS cc_start: 0.5957 (OUTLIER) cc_final: 0.5750 (tptp) REVERT: Z 46 ILE cc_start: 0.3096 (OUTLIER) cc_final: 0.2726 (pp) REVERT: Z 65 ARG cc_start: 0.3869 (mmt90) cc_final: 0.3663 (mmp80) REVERT: Z 69 LYS cc_start: 0.6158 (tttt) cc_final: 0.5621 (tttp) REVERT: a 52 TYR cc_start: 0.6164 (t80) cc_final: 0.5946 (t80) REVERT: b 59 LYS cc_start: 0.0733 (OUTLIER) cc_final: 0.0405 (ttpp) REVERT: d 15 ASN cc_start: 0.7979 (t0) cc_final: 0.7215 (t0) REVERT: d 56 ASN cc_start: 0.6096 (t0) cc_final: 0.5890 (t0) REVERT: d 62 ARG cc_start: 0.6719 (ttm170) cc_final: 0.6004 (mtp-110) REVERT: e 18 LYS cc_start: 0.6079 (OUTLIER) cc_final: 0.5538 (mmtm) REVERT: g 80 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6709 (mtp85) REVERT: g 100 ILE cc_start: 0.3546 (OUTLIER) cc_final: 0.3181 (mp) REVERT: h 5 LYS cc_start: 0.5762 (mmtp) cc_final: 0.5561 (mmtt) REVERT: h 15 GLU cc_start: 0.5760 (pm20) cc_final: 0.5535 (mm-30) REVERT: j 25 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6834 (ptt90) REVERT: j 35 SER cc_start: 0.6914 (OUTLIER) cc_final: 0.6700 (p) REVERT: j 36 SER cc_start: 0.7388 (t) cc_final: 0.7109 (p) REVERT: j 57 HIS cc_start: 0.4209 (OUTLIER) cc_final: 0.3717 (t-170) REVERT: k 29 LYS cc_start: 0.5010 (OUTLIER) cc_final: 0.3366 (mmtm) REVERT: k 75 VAL cc_start: 0.2609 (OUTLIER) cc_final: 0.2185 (p) REVERT: l 25 GLN cc_start: 0.4580 (OUTLIER) cc_final: 0.4040 (pm20) REVERT: l 51 ILE cc_start: 0.5383 (OUTLIER) cc_final: 0.5080 (tt) REVERT: n 1 MET cc_start: 0.1802 (OUTLIER) cc_final: 0.1238 (mmt) REVERT: n 2 ARG cc_start: 0.3885 (ttp80) cc_final: -0.0953 (mmt180) REVERT: n 5 TRP cc_start: 0.4884 (OUTLIER) cc_final: 0.4469 (m100) REVERT: o 8 ARG cc_start: 0.6233 (mtp85) cc_final: 0.5766 (mtp-110) REVERT: o 29 LYS cc_start: 0.6398 (tppt) cc_final: 0.6040 (mtpt) REVERT: o 100 LYS cc_start: 0.3523 (OUTLIER) cc_final: 0.3063 (mttt) REVERT: t 16 LEU cc_start: -0.0093 (OUTLIER) cc_final: -0.0422 (mm) REVERT: t 47 LYS cc_start: 0.3624 (OUTLIER) cc_final: 0.2286 (mmtt) REVERT: t 63 MET cc_start: 0.5411 (ppp) cc_final: 0.4984 (ppp) REVERT: t 129 SER cc_start: 0.4041 (OUTLIER) cc_final: 0.3334 (t) outliers start: 520 outliers final: 166 residues processed: 1322 average time/residue: 1.1967 time to fit residues: 2652.7613 Evaluate side-chains 897 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 681 time to evaluate : 6.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 62 ASN Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 131 LYS Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 26 PHE Chi-restraints excluded: chain P residue 101 ASN Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 150 VAL Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 111 ARG Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain R residue 134 HIS Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 103 GLN Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 53 HIS Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 82 LEU Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 83 ASP Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 34 LYS Chi-restraints excluded: chain Z residue 36 HIS Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 114 VAL Chi-restraints excluded: chain b residue 48 HIS Chi-restraints excluded: chain b residue 59 LYS Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 101 LEU Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain d residue 79 ARG Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 18 LYS Chi-restraints excluded: chain e residue 33 ARG Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 51 LEU Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 80 ARG Chi-restraints excluded: chain g residue 81 CYS Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 27 GLU Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 27 SER Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 29 VAL Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain j residue 57 HIS Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 9 LYS Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain l residue 25 GLN Chi-restraints excluded: chain l residue 51 ILE Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 5 TRP Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 11 THR Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain t residue 16 LEU Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 55 LEU Chi-restraints excluded: chain t residue 110 PHE Chi-restraints excluded: chain t residue 129 SER Chi-restraints excluded: chain t residue 155 ILE Chi-restraints excluded: chain t residue 194 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 490 optimal weight: 0.9980 chunk 273 optimal weight: 8.9990 chunk 734 optimal weight: 7.9990 chunk 601 optimal weight: 0.7980 chunk 243 optimal weight: 8.9990 chunk 884 optimal weight: 0.0980 chunk 955 optimal weight: 7.9990 chunk 787 optimal weight: 4.9990 chunk 876 optimal weight: 2.9990 chunk 301 optimal weight: 10.0000 chunk 709 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN C 45 ASN C 114 ASN C 311 HIS ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 ASN F 194 HIS ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN G 192 GLN G 232 HIS ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 GLN ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 HIS ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 ASN J 7 ASN J 62 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 HIS L 103 ASN M 119 GLN N 15 GLN N 156 HIS O 31 GLN ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 HIS O 122 GLN P 28 ASN P 34 GLN P 45 GLN P 92 GLN ** P 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 126 GLN R 118 HIS S 46 GLN T 95 HIS T 149 GLN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 111 ASN ** Y 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 122 HIS a 62 HIS a 74 ASN ** b 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 71 GLN ** d 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 57 GLN e 49 ASN e 52 GLN e 104 ASN f 87 ASN g 52 GLN j 48 ASN k 40 GLN l 11 GLN o 3 ASN p 32 GLN t 27 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5149 moved from start: 0.8795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 134814 Z= 0.249 Angle : 0.768 19.302 197712 Z= 0.395 Chirality : 0.042 0.453 25102 Planarity : 0.007 0.148 11954 Dihedral : 23.820 179.599 60125 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 1.12 % Allowed : 8.43 % Favored : 90.45 % Rotamer: Outliers : 6.34 % Allowed : 20.70 % Favored : 72.96 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 3.72 % Twisted General : 0.10 % 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: -3.89 (0.09), residues: 5611 helix: -2.74 (0.10), residues: 1648 sheet: -2.31 (0.18), residues: 674 loop : -2.63 (0.09), residues: 3289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP S 42 HIS 0.021 0.002 HIS Z 29 PHE 0.035 0.003 PHE I 46 TYR 0.049 0.002 TYR I 17 ARG 0.040 0.001 ARG S 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 848 time to evaluate : 5.906 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: A 147 ARG cc_start: 0.6296 (tpp-160) cc_final: 0.6017 (ttp80) REVERT: A 194 ASN cc_start: 0.8186 (t0) cc_final: 0.7917 (t0) REVERT: B 53 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6399 (mmm) REVERT: B 59 ASP cc_start: 0.5071 (m-30) cc_final: 0.4672 (m-30) REVERT: B 70 ARG cc_start: 0.7269 (mtp-110) cc_final: 0.6857 (mtp-110) REVERT: B 94 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6394 (pm20) REVERT: B 193 ASP cc_start: 0.6258 (m-30) cc_final: 0.5680 (t0) REVERT: B 211 GLN cc_start: 0.6918 (mm-40) cc_final: 0.6717 (tp-100) REVERT: B 308 MET cc_start: 0.4493 (mtp) cc_final: 0.4130 (mtp) REVERT: B 313 HIS cc_start: 0.5181 (OUTLIER) cc_final: 0.4461 (m-70) REVERT: B 358 TRP cc_start: 0.6715 (t60) cc_final: 0.6334 (t60) REVERT: C 243 HIS cc_start: 0.4082 (m170) cc_final: 0.3563 (m170) REVERT: C 255 PHE cc_start: 0.6455 (t80) cc_final: 0.5944 (t80) REVERT: D 22 ARG cc_start: 0.6305 (tpp80) cc_final: 0.5776 (tpp80) REVERT: D 54 ARG cc_start: 0.7312 (mmt-90) cc_final: 0.6913 (mmm160) REVERT: D 93 THR cc_start: 0.6809 (t) cc_final: 0.6531 (t) REVERT: D 144 VAL cc_start: 0.6213 (OUTLIER) cc_final: 0.5916 (p) REVERT: D 151 GLN cc_start: 0.6384 (tt0) cc_final: 0.6170 (tm-30) REVERT: D 168 ASP cc_start: 0.6204 (m-30) cc_final: 0.5850 (m-30) REVERT: D 254 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6638 (mttm) REVERT: E 102 ASN cc_start: 0.0810 (OUTLIER) cc_final: 0.0310 (t0) REVERT: F 112 ASN cc_start: 0.7195 (m-40) cc_final: 0.6806 (t0) REVERT: G 221 ASN cc_start: 0.5420 (m-40) cc_final: 0.4272 (p0) REVERT: G 228 GLU cc_start: 0.7214 (tp30) cc_final: 0.6904 (tm-30) REVERT: G 252 ASN cc_start: 0.6172 (p0) cc_final: 0.5764 (m-40) REVERT: H 50 ASN cc_start: 0.2776 (OUTLIER) cc_final: 0.1852 (t0) REVERT: H 100 ASN cc_start: 0.5485 (t0) cc_final: 0.4494 (p0) REVERT: H 139 ASN cc_start: 0.3340 (OUTLIER) cc_final: 0.0477 (t0) REVERT: I 10 ARG cc_start: 0.6088 (ttt180) cc_final: 0.5681 (ttp80) REVERT: I 55 ASN cc_start: 0.6714 (OUTLIER) cc_final: 0.6354 (m-40) REVERT: I 190 VAL cc_start: 0.3383 (OUTLIER) cc_final: 0.3125 (m) REVERT: J 35 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7805 (ttmt) REVERT: J 82 ARG cc_start: 0.4459 (OUTLIER) cc_final: 0.3342 (ttp-170) REVERT: J 101 ASN cc_start: 0.7275 (m-40) cc_final: 0.6853 (m-40) REVERT: J 128 TYR cc_start: 0.5528 (t80) cc_final: 0.4630 (t80) REVERT: J 130 VAL cc_start: 0.7713 (OUTLIER) cc_final: 0.7340 (p) REVERT: L 131 LYS cc_start: 0.3105 (OUTLIER) cc_final: 0.2750 (ptmt) REVERT: L 184 GLU cc_start: 0.5598 (OUTLIER) cc_final: 0.4849 (tp30) REVERT: N 36 ILE cc_start: 0.7984 (mt) cc_final: 0.7728 (mt) REVERT: N 148 TYR cc_start: 0.5212 (m-80) cc_final: 0.4968 (m-80) REVERT: N 183 THR cc_start: 0.6035 (OUTLIER) cc_final: 0.5812 (t) REVERT: O 14 HIS cc_start: 0.6202 (OUTLIER) cc_final: 0.5614 (t-90) REVERT: O 82 LYS cc_start: 0.6454 (tptm) cc_final: 0.6077 (tmmt) REVERT: O 87 MET cc_start: 0.7705 (mtm) cc_final: 0.7285 (mtm) REVERT: P 4 TYR cc_start: 0.6275 (m-10) cc_final: 0.6007 (m-10) REVERT: P 59 PRO cc_start: 0.6935 (Cg_endo) cc_final: 0.6574 (Cg_exo) REVERT: P 105 LYS cc_start: 0.6650 (mmmt) cc_final: 0.6286 (mttt) REVERT: P 131 ARG cc_start: 0.5803 (mtp85) cc_final: 0.5535 (mtp85) REVERT: Q 46 LYS cc_start: 0.5214 (mttp) cc_final: 0.4933 (pptt) REVERT: R 128 LYS cc_start: 0.5459 (tmtp) cc_final: 0.5187 (tttp) REVERT: R 141 HIS cc_start: 0.4677 (t70) cc_final: 0.4447 (t-90) REVERT: R 173 ARG cc_start: 0.0695 (OUTLIER) cc_final: 0.0203 (pmt170) REVERT: S 1 MET cc_start: 0.5079 (ptt) cc_final: 0.3959 (tpp) REVERT: T 41 ASP cc_start: 0.5986 (m-30) cc_final: 0.5544 (m-30) REVERT: T 131 GLN cc_start: 0.5844 (OUTLIER) cc_final: 0.5079 (tp40) REVERT: U 99 LYS cc_start: 0.5637 (ttmm) cc_final: 0.5287 (mmtm) REVERT: V 66 LYS cc_start: 0.6096 (mttp) cc_final: 0.5829 (mmmt) REVERT: V 71 LYS cc_start: 0.5345 (mtpm) cc_final: 0.4953 (mtmm) REVERT: V 88 ARG cc_start: 0.5547 (mtp180) cc_final: 0.5280 (mtt180) REVERT: W 23 ARG cc_start: 0.4207 (ttp-170) cc_final: 0.3896 (ttm-80) REVERT: X 53 HIS cc_start: 0.6470 (OUTLIER) cc_final: 0.6199 (m-70) REVERT: Z 34 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.5864 (mptt) REVERT: Z 46 ILE cc_start: 0.3024 (OUTLIER) cc_final: 0.2658 (pp) REVERT: Z 69 LYS cc_start: 0.5734 (tttt) cc_final: 0.5354 (tttp) REVERT: a 16 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.7678 (p) REVERT: a 34 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.5780 (ptm) REVERT: a 52 TYR cc_start: 0.6265 (t80) cc_final: 0.5649 (t80) REVERT: a 133 LEU cc_start: 0.4156 (OUTLIER) cc_final: 0.3929 (tt) REVERT: c 74 ASN cc_start: 0.7462 (p0) cc_final: 0.7239 (p0) REVERT: e 17 PHE cc_start: 0.5861 (m-80) cc_final: 0.5494 (m-80) REVERT: e 18 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6302 (mptt) REVERT: f 67 MET cc_start: 0.2902 (tpt) cc_final: 0.2593 (tpp) REVERT: f 86 ARG cc_start: 0.6360 (tpm170) cc_final: 0.5932 (mmt180) REVERT: g 46 ASP cc_start: 0.4844 (OUTLIER) cc_final: 0.4638 (m-30) REVERT: g 52 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.5745 (mt0) REVERT: g 100 ILE cc_start: 0.3579 (OUTLIER) cc_final: 0.3175 (mp) REVERT: i 47 ILE cc_start: 0.6288 (OUTLIER) cc_final: 0.6047 (mm) REVERT: j 25 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.7016 (ptt90) REVERT: j 35 SER cc_start: 0.6846 (p) cc_final: 0.6492 (p) REVERT: j 57 HIS cc_start: 0.4284 (OUTLIER) cc_final: 0.3516 (t-170) REVERT: n 2 ARG cc_start: 0.4560 (ttp80) cc_final: -0.1228 (mmt180) REVERT: n 5 TRP cc_start: 0.4994 (OUTLIER) cc_final: 0.4788 (m100) REVERT: o 8 ARG cc_start: 0.6671 (mtp85) cc_final: 0.5927 (mtp180) REVERT: o 25 VAL cc_start: 0.6589 (t) cc_final: 0.6306 (t) REVERT: o 29 LYS cc_start: 0.6449 (tppt) cc_final: 0.6099 (mtpt) REVERT: o 93 LEU cc_start: 0.5014 (pt) cc_final: 0.4474 (tt) REVERT: o 100 LYS cc_start: 0.3529 (OUTLIER) cc_final: 0.2752 (mttt) REVERT: p 11 THR cc_start: 0.7081 (OUTLIER) cc_final: 0.6861 (m) REVERT: p 14 TYR cc_start: 0.6290 (m-80) cc_final: 0.5085 (m-80) REVERT: p 18 TYR cc_start: 0.6572 (m-80) cc_final: 0.4734 (m-80) REVERT: t 26 ARG cc_start: 0.4096 (OUTLIER) cc_final: 0.3763 (ttp80) REVERT: t 85 MET cc_start: 0.3536 (tmm) cc_final: 0.3336 (tmm) outliers start: 341 outliers final: 148 residues processed: 1093 average time/residue: 1.2226 time to fit residues: 2266.9434 Evaluate side-chains 883 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 701 time to evaluate : 5.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 172 HIS Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 55 ASN Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 82 ARG Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 131 LYS Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 14 HIS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 167 TYR Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 150 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 134 HIS Chi-restraints excluded: chain R residue 173 ARG Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 45 ASN Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 104 ASN Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain X residue 38 LEU Chi-restraints excluded: chain X residue 53 HIS Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 34 LYS Chi-restraints excluded: chain Z residue 36 HIS Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 34 MET Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain d residue 59 ILE Chi-restraints excluded: chain e residue 18 LYS Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 38 ILE Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 46 ASP Chi-restraints excluded: chain g residue 51 LEU Chi-restraints excluded: chain g residue 52 GLN Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain h residue 4 VAL Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 27 GLU Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 57 HIS Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain k residue 9 LYS Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain n residue 5 TRP Chi-restraints excluded: chain o residue 20 HIS Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 11 THR Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain t residue 26 ARG Chi-restraints excluded: chain t residue 55 LEU Chi-restraints excluded: chain t residue 72 PHE Chi-restraints excluded: chain t residue 110 PHE Chi-restraints excluded: chain t residue 115 VAL Chi-restraints excluded: chain t residue 190 PHE Chi-restraints excluded: chain t residue 194 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 873 optimal weight: 0.0980 chunk 664 optimal weight: 0.8980 chunk 458 optimal weight: 9.9990 chunk 97 optimal weight: 40.0000 chunk 422 optimal weight: 2.9990 chunk 593 optimal weight: 0.2980 chunk 887 optimal weight: 8.9990 chunk 939 optimal weight: 0.2980 chunk 463 optimal weight: 6.9990 chunk 841 optimal weight: 4.9990 chunk 253 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 HIS B 279 ASN C 48 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 HIS G 77 GLN ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN H 58 HIS ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 ASN J 62 ASN J 109 HIS L 66 ASN N 15 GLN ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 HIS ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN S 142 GLN X 65 GLN ** Y 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN c 71 GLN d 15 ASN ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 113 GLN ** i 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5215 moved from start: 0.9675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.187 134814 Z= 0.166 Angle : 0.645 19.208 197712 Z= 0.329 Chirality : 0.036 0.372 25102 Planarity : 0.006 0.162 11954 Dihedral : 23.509 179.044 60070 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 1.00 % Allowed : 7.24 % Favored : 91.77 % Rotamer: Outliers : 4.67 % Allowed : 23.28 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 3.31 % Twisted General : 0.05 % 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: -3.03 (0.10), residues: 5611 helix: -1.93 (0.11), residues: 1672 sheet: -1.75 (0.19), residues: 654 loop : -2.16 (0.10), residues: 3285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP S 42 HIS 0.011 0.001 HIS Z 29 PHE 0.023 0.002 PHE Z 38 TYR 0.018 0.002 TYR N 148 ARG 0.017 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 812 time to evaluate : 5.774 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: A 93 LYS cc_start: 0.7967 (tttp) cc_final: 0.7750 (mmtp) REVERT: A 147 ARG cc_start: 0.6383 (tpp-160) cc_final: 0.6141 (ttp80) REVERT: A 194 ASN cc_start: 0.8099 (t0) cc_final: 0.7844 (t0) REVERT: B 6 TYR cc_start: 0.6215 (m-80) cc_final: 0.5813 (m-80) REVERT: B 46 PHE cc_start: 0.5852 (OUTLIER) cc_final: 0.5593 (t80) REVERT: B 53 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6224 (mmm) REVERT: B 59 ASP cc_start: 0.5503 (m-30) cc_final: 0.5100 (m-30) REVERT: B 70 ARG cc_start: 0.6683 (mtp180) cc_final: 0.6350 (mtp-110) REVERT: B 94 GLU cc_start: 0.7557 (mt-10) cc_final: 0.6718 (pm20) REVERT: B 108 GLU cc_start: 0.6300 (tp30) cc_final: 0.5862 (tp30) REVERT: B 193 ASP cc_start: 0.5745 (m-30) cc_final: 0.5238 (t0) REVERT: B 308 MET cc_start: 0.4602 (mtp) cc_final: 0.4342 (mtp) REVERT: C 243 HIS cc_start: 0.3380 (m170) cc_final: 0.2720 (m170) REVERT: C 255 PHE cc_start: 0.6201 (t80) cc_final: 0.5921 (t80) REVERT: D 22 ARG cc_start: 0.6140 (tpp80) cc_final: 0.5752 (tpp80) REVERT: D 69 ILE cc_start: 0.2057 (OUTLIER) cc_final: 0.1853 (pp) REVERT: D 168 ASP cc_start: 0.6239 (m-30) cc_final: 0.5927 (m-30) REVERT: D 193 GLU cc_start: 0.7025 (mp0) cc_final: 0.6804 (tp30) REVERT: D 254 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.6941 (mttp) REVERT: E 101 PHE cc_start: 0.3849 (OUTLIER) cc_final: 0.2875 (m-80) REVERT: F 153 PHE cc_start: 0.6338 (m-80) cc_final: 0.6087 (m-80) REVERT: G 221 ASN cc_start: 0.5511 (m-40) cc_final: 0.4303 (p0) REVERT: G 228 GLU cc_start: 0.7137 (tp30) cc_final: 0.6896 (tm-30) REVERT: G 252 ASN cc_start: 0.6086 (p0) cc_final: 0.5699 (m-40) REVERT: H 5 GLN cc_start: 0.7607 (mp10) cc_final: 0.6908 (mt0) REVERT: H 7 GLU cc_start: 0.5865 (pm20) cc_final: 0.4816 (mt-10) REVERT: H 50 ASN cc_start: 0.2469 (OUTLIER) cc_final: 0.1813 (t0) REVERT: H 100 ASN cc_start: 0.5266 (t0) cc_final: 0.4219 (p0) REVERT: H 115 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5328 (mpp80) REVERT: H 139 ASN cc_start: 0.3009 (OUTLIER) cc_final: 0.0565 (t0) REVERT: I 10 ARG cc_start: 0.6077 (ttt180) cc_final: 0.5683 (ttp80) REVERT: I 115 MET cc_start: 0.6229 (tpt) cc_final: 0.5886 (mmm) REVERT: I 171 TRP cc_start: 0.6169 (t-100) cc_final: 0.5625 (t-100) REVERT: J 82 ARG cc_start: 0.4526 (OUTLIER) cc_final: 0.3388 (ttp-170) REVERT: J 101 ASN cc_start: 0.7423 (m-40) cc_final: 0.6966 (m-40) REVERT: J 128 TYR cc_start: 0.5669 (t80) cc_final: 0.4788 (t80) REVERT: J 130 VAL cc_start: 0.7660 (OUTLIER) cc_final: 0.7260 (p) REVERT: L 131 LYS cc_start: 0.2853 (OUTLIER) cc_final: 0.2211 (ptmt) REVERT: L 184 GLU cc_start: 0.5776 (pt0) cc_final: 0.5171 (tp30) REVERT: M 107 GLU cc_start: 0.4210 (OUTLIER) cc_final: 0.3848 (tp30) REVERT: N 62 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.6814 (m-80) REVERT: N 81 TYR cc_start: 0.6422 (m-80) cc_final: 0.6072 (m-80) REVERT: N 114 ARG cc_start: 0.5689 (mmt90) cc_final: 0.5166 (mmt90) REVERT: O 14 HIS cc_start: 0.7117 (OUTLIER) cc_final: 0.5937 (t-90) REVERT: O 82 LYS cc_start: 0.6330 (tptm) cc_final: 0.5802 (tmmt) REVERT: O 87 MET cc_start: 0.7520 (mtm) cc_final: 0.7206 (mtm) REVERT: O 89 SER cc_start: 0.7469 (t) cc_final: 0.7214 (p) REVERT: P 4 TYR cc_start: 0.6409 (m-10) cc_final: 0.5871 (m-10) REVERT: P 49 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: P 55 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.5645 (mm110) REVERT: P 80 LYS cc_start: 0.5403 (OUTLIER) cc_final: 0.5148 (ptpt) REVERT: P 105 LYS cc_start: 0.6572 (mmmt) cc_final: 0.6300 (mttt) REVERT: P 131 ARG cc_start: 0.5776 (mtp85) cc_final: 0.5541 (mtp85) REVERT: Q 12 ARG cc_start: 0.6066 (ttp-170) cc_final: 0.5455 (ttp-170) REVERT: R 128 LYS cc_start: 0.5560 (tmtp) cc_final: 0.5353 (tttp) REVERT: R 175 GLN cc_start: 0.0910 (OUTLIER) cc_final: 0.0188 (pm20) REVERT: T 41 ASP cc_start: 0.6432 (m-30) cc_final: 0.5996 (m-30) REVERT: T 57 TYR cc_start: 0.6957 (m-80) cc_final: 0.6736 (m-80) REVERT: U 99 LYS cc_start: 0.5805 (ttmm) cc_final: 0.5461 (mmtm) REVERT: V 66 LYS cc_start: 0.6094 (mttp) cc_final: 0.5742 (ptmt) REVERT: V 71 LYS cc_start: 0.5277 (mtpm) cc_final: 0.4873 (mtmm) REVERT: W 23 ARG cc_start: 0.4181 (ttp-170) cc_final: 0.3842 (ttm-80) REVERT: W 59 HIS cc_start: 0.7291 (m-70) cc_final: 0.7001 (m90) REVERT: X 53 HIS cc_start: 0.6618 (OUTLIER) cc_final: 0.6373 (m-70) REVERT: Z 34 LYS cc_start: 0.6275 (OUTLIER) cc_final: 0.5692 (mptt) REVERT: Z 69 LYS cc_start: 0.6551 (tttt) cc_final: 0.6332 (ttmt) REVERT: Z 101 PHE cc_start: 0.0941 (m-80) cc_final: 0.0670 (m-80) REVERT: a 16 SER cc_start: 0.7870 (t) cc_final: 0.6873 (p) REVERT: a 52 TYR cc_start: 0.6530 (t80) cc_final: 0.5973 (t80) REVERT: b 29 TYR cc_start: 0.5789 (m-80) cc_final: 0.5369 (m-80) REVERT: d 44 MET cc_start: 0.7480 (mmm) cc_final: 0.7167 (mmm) REVERT: d 62 ARG cc_start: 0.6084 (ttm170) cc_final: 0.5793 (mtp180) REVERT: e 17 PHE cc_start: 0.6341 (m-80) cc_final: 0.5970 (m-80) REVERT: e 18 LYS cc_start: 0.6917 (OUTLIER) cc_final: 0.6422 (mptt) REVERT: f 67 MET cc_start: 0.3097 (tpt) cc_final: 0.2396 (tpp) REVERT: f 86 ARG cc_start: 0.6680 (tpm170) cc_final: 0.6285 (mmt180) REVERT: g 31 ARG cc_start: 0.7251 (mtp85) cc_final: 0.6897 (mtp85) REVERT: g 52 GLN cc_start: 0.6560 (OUTLIER) cc_final: 0.6118 (pm20) REVERT: g 100 ILE cc_start: 0.3513 (OUTLIER) cc_final: 0.3171 (mp) REVERT: h 10 ARG cc_start: 0.5106 (tpp80) cc_final: 0.4566 (tpp80) REVERT: i 47 ILE cc_start: 0.5516 (OUTLIER) cc_final: 0.5221 (mm) REVERT: j 39 TYR cc_start: 0.5441 (t80) cc_final: 0.4888 (t80) REVERT: j 45 ARG cc_start: 0.4649 (OUTLIER) cc_final: 0.4384 (ttp-170) REVERT: k 31 LEU cc_start: 0.5244 (pt) cc_final: 0.4747 (mp) REVERT: n 2 ARG cc_start: 0.4466 (OUTLIER) cc_final: -0.1077 (mmt180) REVERT: o 8 ARG cc_start: 0.6604 (mtp85) cc_final: 0.5879 (mtp180) REVERT: o 25 VAL cc_start: 0.6767 (t) cc_final: 0.6508 (t) REVERT: o 27 GLN cc_start: 0.7453 (mp10) cc_final: 0.7157 (mt0) REVERT: o 29 LYS cc_start: 0.6669 (tppt) cc_final: 0.6174 (mtpt) REVERT: o 93 LEU cc_start: 0.5369 (pt) cc_final: 0.4997 (tt) REVERT: o 100 LYS cc_start: 0.3283 (OUTLIER) cc_final: 0.2716 (mttt) REVERT: p 13 LYS cc_start: 0.4553 (pttt) cc_final: 0.4273 (pttp) REVERT: p 28 LYS cc_start: 0.6089 (mmtm) cc_final: 0.5857 (mttt) REVERT: p 45 LYS cc_start: 0.6519 (ptpp) cc_final: 0.6217 (mtmm) REVERT: t 16 LEU cc_start: -0.1066 (OUTLIER) cc_final: -0.1418 (tp) REVERT: t 26 ARG cc_start: 0.3422 (OUTLIER) cc_final: 0.3038 (ttp80) REVERT: t 85 MET cc_start: 0.3967 (tmm) cc_final: 0.3743 (tmm) REVERT: t 110 PHE cc_start: 0.3112 (OUTLIER) cc_final: 0.2908 (t80) outliers start: 251 outliers final: 126 residues processed: 991 average time/residue: 1.1423 time to fit residues: 1919.7056 Evaluate side-chains 873 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 717 time to evaluate : 5.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 177 ASP Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 82 ARG Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 131 LYS Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 62 TYR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 14 HIS Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 55 GLN Chi-restraints excluded: chain P residue 80 LYS Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 150 VAL Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 92 GLN Chi-restraints excluded: chain R residue 134 HIS Chi-restraints excluded: chain R residue 173 ARG Chi-restraints excluded: chain R residue 175 GLN Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 45 ASN Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain X residue 53 HIS Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 34 LYS Chi-restraints excluded: chain Z residue 36 HIS Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 51 LEU Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain b residue 48 HIS Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain e residue 18 LYS Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 52 GLN Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain h residue 4 VAL Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 27 GLU Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 68 GLN Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain o residue 20 HIS Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain o residue 102 GLN Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain t residue 16 LEU Chi-restraints excluded: chain t residue 26 ARG Chi-restraints excluded: chain t residue 55 LEU Chi-restraints excluded: chain t residue 72 PHE Chi-restraints excluded: chain t residue 110 PHE Chi-restraints excluded: chain t residue 194 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 782 optimal weight: 0.5980 chunk 533 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 699 optimal weight: 0.8980 chunk 387 optimal weight: 4.9990 chunk 801 optimal weight: 9.9990 chunk 649 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 479 optimal weight: 10.0000 chunk 843 optimal weight: 6.9990 chunk 237 optimal weight: 20.0000 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 HIS ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 HIS C 307 GLN ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN F 112 ASN G 33 ASN G 77 GLN H 9 GLN H 77 ASN I 55 ASN I 92 HIS J 95 ASN L 25 HIS L 103 ASN ** N 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 GLN ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** R 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 132 ASN W 59 HIS ** Y 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 HIS a 62 HIS b 12 GLN b 42 ASN c 74 ASN d 105 GLN ** e 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 71 HIS ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 GLN j 48 ASN o 99 GLN t 44 GLN t 200 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5665 moved from start: 1.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.166 134814 Z= 0.303 Angle : 0.823 25.312 197712 Z= 0.415 Chirality : 0.042 0.448 25102 Planarity : 0.008 0.196 11954 Dihedral : 23.512 179.741 60046 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 1.02 % Allowed : 8.80 % Favored : 90.18 % Rotamer: Outliers : 6.27 % Allowed : 23.65 % Favored : 70.08 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 3.31 % 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: -3.05 (0.10), residues: 5611 helix: -2.05 (0.11), residues: 1606 sheet: -1.71 (0.19), residues: 676 loop : -2.13 (0.10), residues: 3329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.004 TRP S 42 HIS 0.083 0.003 HIS C 311 PHE 0.048 0.003 PHE p 41 TYR 0.026 0.003 TYR B 92 ARG 0.026 0.001 ARG i 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1350 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 1013 time to evaluate : 5.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.5506 (OUTLIER) cc_final: 0.5028 (mt-10) REVERT: B 18 PRO cc_start: 0.6726 (Cg_exo) cc_final: 0.6328 (Cg_endo) REVERT: B 37 ARG cc_start: 0.6425 (mtp85) cc_final: 0.5769 (ttm170) REVERT: B 53 MET cc_start: 0.7210 (mmp) cc_final: 0.6792 (mmm) REVERT: B 94 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7668 (pt0) REVERT: B 119 TYR cc_start: 0.6552 (m-80) cc_final: 0.6352 (m-80) REVERT: B 128 LYS cc_start: 0.5443 (OUTLIER) cc_final: 0.5112 (tttp) REVERT: B 193 ASP cc_start: 0.6402 (m-30) cc_final: 0.5606 (t0) REVERT: B 232 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.5812 (ttt180) REVERT: B 260 VAL cc_start: 0.8259 (t) cc_final: 0.7956 (m) REVERT: B 360 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.6166 (t0) REVERT: B 380 MET cc_start: 0.7235 (mpp) cc_final: 0.7003 (mtp) REVERT: C 255 PHE cc_start: 0.7190 (t80) cc_final: 0.6719 (t80) REVERT: D 208 MET cc_start: 0.4719 (OUTLIER) cc_final: 0.4172 (ttm) REVERT: D 254 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.7032 (mttp) REVERT: F 175 LYS cc_start: 0.6755 (tmmt) cc_final: 0.6451 (mtmm) REVERT: F 225 GLN cc_start: 0.6831 (mt0) cc_final: 0.6593 (mt0) REVERT: G 86 THR cc_start: 0.5878 (OUTLIER) cc_final: 0.5572 (p) REVERT: G 98 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7367 (ttt-90) REVERT: G 133 LYS cc_start: 0.5759 (mmtt) cc_final: 0.5554 (mmtm) REVERT: G 252 ASN cc_start: 0.6262 (p0) cc_final: 0.6014 (m-40) REVERT: H 5 GLN cc_start: 0.7407 (mp10) cc_final: 0.6995 (mt0) REVERT: H 7 GLU cc_start: 0.5759 (pm20) cc_final: 0.4877 (mt-10) REVERT: H 50 ASN cc_start: 0.3511 (OUTLIER) cc_final: 0.2868 (t0) REVERT: H 90 MET cc_start: 0.4704 (mmp) cc_final: 0.4501 (mmp) REVERT: H 100 ASN cc_start: 0.5786 (t0) cc_final: 0.4609 (p0) REVERT: H 139 ASN cc_start: 0.4750 (OUTLIER) cc_final: 0.2067 (t0) REVERT: I 10 ARG cc_start: 0.6249 (ttt180) cc_final: 0.6047 (ttt-90) REVERT: J 61 ARG cc_start: 0.5657 (ttp80) cc_final: 0.5160 (ttt90) REVERT: J 101 ASN cc_start: 0.7682 (m-40) cc_final: 0.7477 (m-40) REVERT: L 9 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7017 (mm) REVERT: L 103 ASN cc_start: 0.3718 (OUTLIER) cc_final: 0.3147 (m-40) REVERT: L 131 LYS cc_start: 0.2806 (OUTLIER) cc_final: 0.2149 (ptmt) REVERT: L 184 GLU cc_start: 0.5261 (pt0) cc_final: 0.4426 (tp30) REVERT: M 25 LYS cc_start: 0.5796 (OUTLIER) cc_final: 0.5346 (mttm) REVERT: N 62 TYR cc_start: 0.6362 (OUTLIER) cc_final: 0.4777 (m-80) REVERT: N 202 TYR cc_start: 0.7326 (m-80) cc_final: 0.6566 (m-80) REVERT: O 14 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.6394 (t-90) REVERT: O 58 LEU cc_start: 0.8128 (tp) cc_final: 0.7859 (mt) REVERT: O 87 MET cc_start: 0.5246 (mtm) cc_final: 0.5003 (mtm) REVERT: P 49 GLU cc_start: 0.7572 (tp30) cc_final: 0.7114 (tt0) REVERT: P 55 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.5553 (tp40) REVERT: Q 12 ARG cc_start: 0.7168 (ttp-170) cc_final: 0.6647 (ttp-170) REVERT: R 25 ASP cc_start: 0.7051 (t0) cc_final: 0.6463 (t70) REVERT: R 130 ASN cc_start: 0.5279 (m-40) cc_final: 0.4816 (m110) REVERT: R 173 ARG cc_start: 0.1872 (OUTLIER) cc_final: -0.1183 (pmt170) REVERT: R 175 GLN cc_start: 0.1793 (OUTLIER) cc_final: 0.1234 (pm20) REVERT: S 38 LYS cc_start: 0.6029 (ttpt) cc_final: 0.5623 (ttmm) REVERT: S 41 TYR cc_start: 0.7372 (t80) cc_final: 0.7054 (t80) REVERT: S 90 MET cc_start: 0.5455 (pmm) cc_final: 0.4980 (pmm) REVERT: S 154 HIS cc_start: 0.7834 (t70) cc_final: 0.7629 (t-90) REVERT: S 172 TYR cc_start: 0.4347 (OUTLIER) cc_final: 0.2176 (m-10) REVERT: T 136 ARG cc_start: 0.5541 (OUTLIER) cc_final: 0.5078 (ptp90) REVERT: U 49 ASN cc_start: 0.5082 (OUTLIER) cc_final: 0.4537 (t0) REVERT: V 27 ASP cc_start: 0.6723 (p0) cc_final: 0.6467 (p0) REVERT: V 66 LYS cc_start: 0.6484 (mttp) cc_final: 0.6051 (ptmt) REVERT: V 68 GLU cc_start: 0.7227 (tt0) cc_final: 0.7021 (tt0) REVERT: V 71 LYS cc_start: 0.5768 (mtpm) cc_final: 0.5171 (mtmm) REVERT: W 23 ARG cc_start: 0.4741 (ttp-170) cc_final: 0.4263 (ttm-80) REVERT: X 53 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.7252 (t-90) REVERT: X 96 LYS cc_start: 0.5707 (tttp) cc_final: 0.5505 (ttmt) REVERT: X 119 THR cc_start: 0.5951 (p) cc_final: 0.5676 (p) REVERT: Y 77 LYS cc_start: 0.7370 (mtmt) cc_final: 0.7149 (mtpt) REVERT: Z 29 HIS cc_start: 0.3769 (t-90) cc_final: 0.3537 (t70) REVERT: Z 34 LYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6385 (mptt) REVERT: Z 36 HIS cc_start: 0.4965 (OUTLIER) cc_final: 0.4599 (m90) REVERT: Z 46 ILE cc_start: 0.4521 (OUTLIER) cc_final: 0.4287 (pp) REVERT: Z 101 PHE cc_start: 0.3163 (m-80) cc_final: 0.2382 (m-10) REVERT: a 32 ARG cc_start: 0.5896 (ttm170) cc_final: 0.5611 (ttm170) REVERT: a 47 LYS cc_start: 0.5754 (OUTLIER) cc_final: 0.5536 (ptmm) REVERT: a 52 TYR cc_start: 0.6136 (t80) cc_final: 0.5325 (t80) REVERT: b 11 ASN cc_start: 0.7775 (t0) cc_final: 0.7289 (t0) REVERT: b 14 ARG cc_start: 0.6240 (ttp-170) cc_final: 0.5932 (ttt180) REVERT: c 74 ASN cc_start: 0.7539 (OUTLIER) cc_final: 0.7277 (p0) REVERT: d 62 ARG cc_start: 0.6124 (ttm170) cc_final: 0.5663 (mtp180) REVERT: d 74 ARG cc_start: 0.5999 (ttp80) cc_final: 0.5660 (mtp85) REVERT: e 9 ILE cc_start: 0.5470 (mt) cc_final: 0.5212 (tt) REVERT: e 95 GLU cc_start: 0.5853 (tt0) cc_final: 0.5631 (tt0) REVERT: e 103 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6456 (ttmm) REVERT: f 12 LYS cc_start: 0.3380 (mmtt) cc_final: 0.3004 (mmtm) REVERT: f 86 ARG cc_start: 0.7393 (tpm170) cc_final: 0.7082 (mmt180) REVERT: f 101 PHE cc_start: 0.6527 (m-80) cc_final: 0.6130 (m-10) REVERT: g 100 ILE cc_start: 0.5048 (OUTLIER) cc_final: 0.4768 (mp) REVERT: h 61 GLN cc_start: 0.7040 (pp30) cc_final: 0.6749 (pp30) REVERT: h 62 GLN cc_start: 0.7267 (tp-100) cc_final: 0.6979 (tt0) REVERT: i 77 LEU cc_start: 0.6146 (mt) cc_final: 0.5939 (mp) REVERT: j 57 HIS cc_start: 0.4919 (OUTLIER) cc_final: 0.4316 (t-170) REVERT: k 29 LYS cc_start: 0.6141 (OUTLIER) cc_final: 0.4131 (tppt) REVERT: l 31 THR cc_start: 0.7467 (t) cc_final: 0.7117 (m) REVERT: l 49 MET cc_start: 0.4588 (OUTLIER) cc_final: 0.4057 (tmm) REVERT: n 2 ARG cc_start: 0.3769 (OUTLIER) cc_final: -0.1890 (mmt180) REVERT: o 47 GLN cc_start: 0.6264 (tt0) cc_final: 0.5855 (tt0) REVERT: o 93 LEU cc_start: 0.6004 (pt) cc_final: 0.5638 (tt) REVERT: o 98 LYS cc_start: 0.5899 (mttt) cc_final: 0.5308 (mttm) REVERT: o 100 LYS cc_start: 0.3384 (OUTLIER) cc_final: 0.2656 (mttt) REVERT: t 26 ARG cc_start: 0.2590 (OUTLIER) cc_final: 0.2302 (ttt90) REVERT: t 76 ARG cc_start: 0.4932 (OUTLIER) cc_final: 0.3813 (mtt180) REVERT: t 85 MET cc_start: 0.3784 (tmm) cc_final: 0.3389 (tmm) outliers start: 337 outliers final: 151 residues processed: 1250 average time/residue: 1.1831 time to fit residues: 2466.8096 Evaluate side-chains 1024 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 836 time to evaluate : 5.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 TRP Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 131 LYS Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 62 TYR Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 164 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 14 HIS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 116 LYS Chi-restraints excluded: chain O residue 167 TYR Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 55 GLN Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 150 VAL Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain R residue 134 HIS Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 173 ARG Chi-restraints excluded: chain R residue 175 GLN Chi-restraints excluded: chain S residue 121 ILE Chi-restraints excluded: chain S residue 149 LYS Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 38 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 45 ASN Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain X residue 53 HIS Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 60 ARG Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 34 LYS Chi-restraints excluded: chain Z residue 36 HIS Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 135 ARG Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain e residue 103 LYS Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain h residue 27 GLU Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 15 LYS Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 26 ILE Chi-restraints excluded: chain i residue 29 LYS Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 87 VAL Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 57 HIS Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 51 LEU Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 54 THR Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain t residue 26 ARG Chi-restraints excluded: chain t residue 55 LEU Chi-restraints excluded: chain t residue 63 MET Chi-restraints excluded: chain t residue 72 PHE Chi-restraints excluded: chain t residue 76 ARG Chi-restraints excluded: chain t residue 88 ASP Chi-restraints excluded: chain t residue 99 LEU Chi-restraints excluded: chain t residue 153 SER Chi-restraints excluded: chain t residue 190 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 316 optimal weight: 10.0000 chunk 846 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 551 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 940 optimal weight: 3.9990 chunk 780 optimal weight: 2.9990 chunk 435 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 311 optimal weight: 9.9990 chunk 493 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 HIS ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS C 307 GLN E 138 GLN F 112 ASN F 166 ASN ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 ASN J 39 GLN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN L 103 ASN N 15 GLN ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN ** R 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 4 GLN Z 36 HIS b 42 ASN d 87 ASN ** e 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 GLN g 3 GLN g 61 GLN h 59 ASN j 48 ASN j 79 GLN m 90 ASN ** t 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 moved from start: 1.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 134814 Z= 0.249 Angle : 0.699 28.117 197712 Z= 0.352 Chirality : 0.038 0.346 25102 Planarity : 0.007 0.168 11954 Dihedral : 23.331 179.105 60029 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.88 % Favored : 92.28 % Rotamer: Outliers : 5.26 % Allowed : 25.33 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.89 % Twisted General : 0.07 % 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: -2.84 (0.10), residues: 5611 helix: -1.87 (0.12), residues: 1625 sheet: -1.78 (0.19), residues: 692 loop : -1.94 (0.10), residues: 3294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP S 42 HIS 0.023 0.002 HIS C 311 PHE 0.041 0.002 PHE R 132 TYR 0.028 0.002 TYR B 92 ARG 0.018 0.001 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 981 time to evaluate : 5.858 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: A 70 ARG cc_start: 0.5480 (ptt180) cc_final: 0.5247 (ptm-80) REVERT: A 160 SER cc_start: 0.6619 (t) cc_final: 0.5727 (m) REVERT: B 18 PRO cc_start: 0.7295 (Cg_exo) cc_final: 0.7087 (Cg_endo) REVERT: B 39 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7541 (mtpp) REVERT: B 46 PHE cc_start: 0.5444 (OUTLIER) cc_final: 0.5091 (t80) REVERT: B 53 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6297 (mmm) REVERT: B 81 THR cc_start: 0.7310 (m) cc_final: 0.7074 (p) REVERT: B 133 TYR cc_start: 0.7533 (t80) cc_final: 0.6779 (t80) REVERT: B 137 TYR cc_start: 0.5708 (OUTLIER) cc_final: 0.5082 (m-80) REVERT: B 167 ARG cc_start: 0.7597 (ptt-90) cc_final: 0.7126 (mtm-85) REVERT: B 360 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.6007 (t0) REVERT: C 150 LEU cc_start: 0.4303 (OUTLIER) cc_final: 0.4023 (tt) REVERT: D 41 LYS cc_start: 0.5575 (OUTLIER) cc_final: 0.5359 (mmtt) REVERT: D 54 ARG cc_start: 0.7663 (mmt-90) cc_final: 0.7052 (mmt180) REVERT: D 151 GLN cc_start: 0.7219 (tm-30) cc_final: 0.6804 (tm-30) REVERT: D 193 GLU cc_start: 0.7345 (tp30) cc_final: 0.6812 (mp0) REVERT: D 208 MET cc_start: 0.4797 (mtm) cc_final: 0.4403 (ttm) REVERT: D 254 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6859 (mttp) REVERT: F 225 GLN cc_start: 0.6465 (mt0) cc_final: 0.6253 (mt0) REVERT: F 237 ASN cc_start: 0.6381 (m-40) cc_final: 0.6139 (m110) REVERT: G 78 PHE cc_start: 0.5468 (m-80) cc_final: 0.5241 (m-80) REVERT: G 79 GLN cc_start: 0.5930 (OUTLIER) cc_final: 0.5548 (pt0) REVERT: G 185 ARG cc_start: 0.5494 (mtm180) cc_final: 0.5007 (ttt180) REVERT: G 252 ASN cc_start: 0.6223 (p0) cc_final: 0.5973 (m-40) REVERT: H 5 GLN cc_start: 0.8120 (mp10) cc_final: 0.7698 (mt0) REVERT: H 100 ASN cc_start: 0.6766 (t0) cc_final: 0.5426 (p0) REVERT: H 139 ASN cc_start: 0.5545 (OUTLIER) cc_final: 0.3165 (t0) REVERT: I 10 ARG cc_start: 0.6359 (ttt180) cc_final: 0.6099 (ttt-90) REVERT: I 55 ASN cc_start: 0.6511 (OUTLIER) cc_final: 0.6046 (m110) REVERT: I 134 ILE cc_start: 0.6553 (mp) cc_final: 0.5838 (mt) REVERT: I 181 TYR cc_start: 0.4765 (t80) cc_final: 0.3742 (t80) REVERT: I 203 LYS cc_start: 0.7190 (tptm) cc_final: 0.6734 (tttm) REVERT: J 61 ARG cc_start: 0.5386 (ttp80) cc_final: 0.4889 (ttt90) REVERT: L 77 LEU cc_start: 0.4635 (OUTLIER) cc_final: 0.4422 (pp) REVERT: L 131 LYS cc_start: 0.3312 (OUTLIER) cc_final: 0.2648 (ptmt) REVERT: L 184 GLU cc_start: 0.5913 (pt0) cc_final: 0.5357 (tp30) REVERT: M 27 GLN cc_start: 0.5253 (mm-40) cc_final: 0.4885 (mm-40) REVERT: M 41 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6963 (tm-30) REVERT: N 62 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.5532 (m-80) REVERT: N 202 TYR cc_start: 0.7167 (m-80) cc_final: 0.6837 (m-80) REVERT: O 82 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.6148 (tmmt) REVERT: P 49 GLU cc_start: 0.7593 (tp30) cc_final: 0.7138 (tt0) REVERT: P 53 ASP cc_start: 0.7204 (t0) cc_final: 0.6785 (t70) REVERT: P 75 GLU cc_start: 0.7805 (tt0) cc_final: 0.7604 (mm-30) REVERT: P 118 GLN cc_start: 0.7549 (tt0) cc_final: 0.7190 (tt0) REVERT: P 126 ARG cc_start: 0.7299 (tpt170) cc_final: 0.6941 (mmt90) REVERT: Q 113 LYS cc_start: 0.5827 (mmtm) cc_final: 0.5562 (mttt) REVERT: Q 147 ARG cc_start: 0.3592 (OUTLIER) cc_final: 0.3318 (ptm160) REVERT: R 175 GLN cc_start: 0.1275 (OUTLIER) cc_final: 0.0767 (pm20) REVERT: S 1 MET cc_start: 0.6102 (ptt) cc_final: 0.4891 (tpt) REVERT: S 172 TYR cc_start: 0.5185 (OUTLIER) cc_final: 0.3582 (m-10) REVERT: T 57 TYR cc_start: 0.6843 (m-80) cc_final: 0.5903 (m-80) REVERT: T 124 VAL cc_start: 0.4338 (OUTLIER) cc_final: 0.4137 (p) REVERT: V 66 LYS cc_start: 0.6968 (mttp) cc_final: 0.6549 (ptmt) REVERT: V 71 LYS cc_start: 0.5806 (mtpm) cc_final: 0.5194 (mtmm) REVERT: W 23 ARG cc_start: 0.4850 (ttp-170) cc_final: 0.4175 (ttt90) REVERT: X 38 LEU cc_start: 0.7269 (tt) cc_final: 0.7036 (mp) REVERT: X 53 HIS cc_start: 0.7611 (OUTLIER) cc_final: 0.7018 (t-90) REVERT: X 119 THR cc_start: 0.6109 (p) cc_final: 0.5828 (p) REVERT: Y 4 GLN cc_start: 0.5894 (OUTLIER) cc_final: 0.5678 (mm-40) REVERT: Y 7 ASP cc_start: 0.6183 (m-30) cc_final: 0.5594 (p0) REVERT: Y 77 LYS cc_start: 0.7502 (mtmt) cc_final: 0.7177 (mtpt) REVERT: Y 98 ASN cc_start: 0.7784 (m-40) cc_final: 0.7501 (m-40) REVERT: Z 29 HIS cc_start: 0.4512 (t-90) cc_final: 0.4294 (t-90) REVERT: Z 31 GLU cc_start: 0.6413 (tp30) cc_final: 0.5473 (tt0) REVERT: Z 69 LYS cc_start: 0.6802 (ttmt) cc_final: 0.6165 (tttt) REVERT: Z 127 ASN cc_start: 0.6255 (OUTLIER) cc_final: 0.6052 (t0) REVERT: a 47 LYS cc_start: 0.5991 (OUTLIER) cc_final: 0.5742 (ptmm) REVERT: a 52 TYR cc_start: 0.5906 (t80) cc_final: 0.5349 (t80) REVERT: a 130 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.8013 (m) REVERT: b 11 ASN cc_start: 0.7589 (t0) cc_final: 0.7093 (t0) REVERT: b 14 ARG cc_start: 0.6777 (ttp-170) cc_final: 0.6440 (ttt180) REVERT: c 24 THR cc_start: 0.6889 (t) cc_final: 0.6638 (p) REVERT: c 69 TYR cc_start: 0.7027 (m-10) cc_final: 0.6804 (m-10) REVERT: c 75 ASN cc_start: 0.8396 (t0) cc_final: 0.7823 (p0) REVERT: c 76 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7516 (mp0) REVERT: e 9 ILE cc_start: 0.5932 (mt) cc_final: 0.5597 (tp) REVERT: e 103 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7151 (ttmm) REVERT: f 101 PHE cc_start: 0.8125 (m-80) cc_final: 0.7056 (m-80) REVERT: g 91 ARG cc_start: 0.5662 (ttm110) cc_final: 0.5327 (ttm-80) REVERT: g 100 ILE cc_start: 0.5550 (OUTLIER) cc_final: 0.5317 (mp) REVERT: i 62 ARG cc_start: 0.4025 (tpp80) cc_final: 0.3718 (tpp80) REVERT: j 57 HIS cc_start: 0.5362 (OUTLIER) cc_final: 0.4389 (t-170) REVERT: k 31 LEU cc_start: 0.5503 (pt) cc_final: 0.4937 (mp) REVERT: l 31 THR cc_start: 0.7304 (t) cc_final: 0.6822 (m) REVERT: n 2 ARG cc_start: 0.4694 (OUTLIER) cc_final: -0.1099 (mmt180) REVERT: o 8 ARG cc_start: 0.6399 (mtp85) cc_final: 0.5839 (ttm-80) REVERT: o 93 LEU cc_start: 0.6531 (pt) cc_final: 0.5843 (tt) REVERT: o 100 LYS cc_start: 0.3541 (OUTLIER) cc_final: 0.2974 (mttt) REVERT: p 45 LYS cc_start: 0.7445 (mtmm) cc_final: 0.7031 (mtpt) REVERT: t 1 MET cc_start: 0.2269 (mmm) cc_final: 0.1950 (mmm) REVERT: t 76 ARG cc_start: 0.4941 (OUTLIER) cc_final: 0.4054 (mmt180) REVERT: t 210 MET cc_start: -0.1302 (mmm) cc_final: -0.1830 (mpp) outliers start: 283 outliers final: 157 residues processed: 1171 average time/residue: 1.1923 time to fit residues: 2350.6254 Evaluate side-chains 1037 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 849 time to evaluate : 5.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 55 ASN Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 199 PHE Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 131 LYS Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 62 TYR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 14 HIS Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 82 LYS Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 150 VAL Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 147 ARG Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 175 GLN Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 38 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 45 ASN Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain V residue 59 MET Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain X residue 53 HIS Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain Y residue 4 GLN Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 83 ASP Chi-restraints excluded: chain Z residue 51 LEU Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 127 ASN Chi-restraints excluded: chain Z residue 135 ARG Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 25 LYS Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain e residue 103 LYS Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain h residue 27 GLU Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 68 GLN Chi-restraints excluded: chain i residue 26 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain j residue 57 HIS Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 20 HIS Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain t residue 55 LEU Chi-restraints excluded: chain t residue 72 PHE Chi-restraints excluded: chain t residue 76 ARG Chi-restraints excluded: chain t residue 88 ASP Chi-restraints excluded: chain t residue 99 LEU Chi-restraints excluded: chain t residue 113 SER Chi-restraints excluded: chain t residue 155 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 906 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 535 optimal weight: 8.9990 chunk 686 optimal weight: 0.9980 chunk 532 optimal weight: 8.9990 chunk 791 optimal weight: 0.0050 chunk 525 optimal weight: 0.8980 chunk 936 optimal weight: 8.9990 chunk 586 optimal weight: 1.9990 chunk 571 optimal weight: 4.9990 chunk 432 optimal weight: 3.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 HIS B 121 ASN B 184 ASN C 9 HIS E 97 ASN F 166 ASN F 200 ASN ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 ASN ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 GLN Q 58 ASN R 27 ASN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 132 ASN Y 4 GLN ** f 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 3 GLN g 52 GLN h 76 GLN ** t 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 40 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5788 moved from start: 1.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 134814 Z= 0.176 Angle : 0.615 21.133 197712 Z= 0.311 Chirality : 0.034 0.425 25102 Planarity : 0.006 0.161 11954 Dihedral : 23.203 179.906 60022 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.54 % Favored : 92.62 % Rotamer: Outliers : 4.30 % Allowed : 27.13 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.89 % Twisted General : 0.03 % 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: -2.53 (0.10), residues: 5611 helix: -1.58 (0.12), residues: 1637 sheet: -1.56 (0.19), residues: 695 loop : -1.77 (0.10), residues: 3279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP W 51 HIS 0.009 0.001 HIS B 259 PHE 0.026 0.002 PHE D 223 TYR 0.033 0.001 TYR L 65 ARG 0.010 0.001 ARG L 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 940 time to evaluate : 5.866 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: A 147 ARG cc_start: 0.6862 (ttp-170) cc_final: 0.6640 (ttp80) REVERT: B 18 PRO cc_start: 0.7310 (Cg_exo) cc_final: 0.7099 (Cg_endo) REVERT: B 37 ARG cc_start: 0.6393 (mtp85) cc_final: 0.5757 (ttm170) REVERT: B 39 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7614 (mtpp) REVERT: B 53 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6470 (mmm) REVERT: B 77 THR cc_start: 0.6593 (p) cc_final: 0.6383 (p) REVERT: B 81 THR cc_start: 0.7555 (m) cc_final: 0.7296 (p) REVERT: B 92 TYR cc_start: 0.7105 (m-80) cc_final: 0.6588 (m-80) REVERT: B 94 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7102 (pt0) REVERT: B 100 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.5558 (ptt90) REVERT: B 133 TYR cc_start: 0.7633 (t80) cc_final: 0.6960 (t80) REVERT: B 137 TYR cc_start: 0.5378 (OUTLIER) cc_final: 0.5077 (m-80) REVERT: B 206 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7726 (p0) REVERT: B 214 MET cc_start: 0.6107 (ttm) cc_final: 0.5859 (tpp) REVERT: D 54 ARG cc_start: 0.7680 (mmt-90) cc_final: 0.7338 (mmt180) REVERT: D 64 ILE cc_start: 0.5000 (mp) cc_final: 0.4684 (mt) REVERT: D 105 ILE cc_start: 0.3701 (tt) cc_final: 0.3460 (tp) REVERT: D 193 GLU cc_start: 0.7517 (tp30) cc_final: 0.7011 (mp0) REVERT: D 254 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6918 (mttp) REVERT: D 268 GLU cc_start: 0.6308 (tm-30) cc_final: 0.5873 (tp30) REVERT: E 99 GLU cc_start: 0.5883 (tp30) cc_final: 0.5168 (mm-30) REVERT: F 24 GLU cc_start: 0.4551 (pp20) cc_final: 0.3708 (mp0) REVERT: F 219 LYS cc_start: 0.5941 (OUTLIER) cc_final: 0.5324 (ttpt) REVERT: F 233 GLU cc_start: 0.5603 (mm-30) cc_final: 0.5357 (mm-30) REVERT: G 185 ARG cc_start: 0.6386 (mtm180) cc_final: 0.6044 (ttt180) REVERT: H 5 GLN cc_start: 0.7870 (mp10) cc_final: 0.7655 (mt0) REVERT: H 7 GLU cc_start: 0.5801 (pm20) cc_final: 0.4923 (mp0) REVERT: H 50 ASN cc_start: 0.3465 (OUTLIER) cc_final: 0.2127 (t0) REVERT: H 90 MET cc_start: 0.5672 (mmp) cc_final: 0.5418 (mmp) REVERT: H 100 ASN cc_start: 0.6710 (t0) cc_final: 0.5285 (p0) REVERT: H 116 ASN cc_start: 0.6098 (t0) cc_final: 0.5489 (t0) REVERT: H 139 ASN cc_start: 0.5595 (OUTLIER) cc_final: 0.3183 (t0) REVERT: I 10 ARG cc_start: 0.6288 (ttt180) cc_final: 0.5981 (ttt-90) REVERT: I 134 ILE cc_start: 0.6275 (mp) cc_final: 0.5503 (mt) REVERT: I 181 TYR cc_start: 0.4954 (t80) cc_final: 0.4037 (t80) REVERT: I 203 LYS cc_start: 0.7198 (tptm) cc_final: 0.6759 (tttm) REVERT: J 61 ARG cc_start: 0.5692 (ttp80) cc_final: 0.5217 (ttt90) REVERT: L 5 LYS cc_start: 0.6658 (mmtp) cc_final: 0.6252 (mppt) REVERT: L 45 LYS cc_start: 0.6919 (tttp) cc_final: 0.6394 (ttmm) REVERT: L 79 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7207 (pt0) REVERT: L 131 LYS cc_start: 0.3183 (OUTLIER) cc_final: 0.2583 (ptmt) REVERT: L 184 GLU cc_start: 0.5731 (pt0) cc_final: 0.5433 (tp30) REVERT: M 27 GLN cc_start: 0.5012 (mm-40) cc_final: 0.4635 (mm-40) REVERT: M 41 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6472 (mt0) REVERT: M 102 LYS cc_start: 0.6206 (tppp) cc_final: 0.5504 (mtmm) REVERT: N 62 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.5639 (m-80) REVERT: N 202 TYR cc_start: 0.7585 (m-80) cc_final: 0.6964 (m-80) REVERT: O 82 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.6109 (tmmt) REVERT: P 55 GLN cc_start: 0.6143 (OUTLIER) cc_final: 0.4658 (tp-100) REVERT: P 126 ARG cc_start: 0.7334 (tpt170) cc_final: 0.6958 (mmt90) REVERT: P 147 GLU cc_start: 0.7241 (pt0) cc_final: 0.6718 (pt0) REVERT: Q 12 ARG cc_start: 0.7148 (ttp-170) cc_final: 0.6732 (ttp-170) REVERT: Q 147 ARG cc_start: 0.4118 (OUTLIER) cc_final: 0.3843 (ptm160) REVERT: R 173 ARG cc_start: 0.2953 (OUTLIER) cc_final: 0.2343 (ptt180) REVERT: R 175 GLN cc_start: 0.1452 (OUTLIER) cc_final: 0.0948 (pm20) REVERT: S 1 MET cc_start: 0.6520 (ptt) cc_final: 0.5580 (tpt) REVERT: S 13 ARG cc_start: 0.6476 (tpt90) cc_final: 0.6240 (tpt90) REVERT: S 90 MET cc_start: 0.6015 (ptp) cc_final: 0.5597 (ptp) REVERT: S 143 PHE cc_start: 0.6864 (m-80) cc_final: 0.6624 (m-80) REVERT: S 172 TYR cc_start: 0.5406 (OUTLIER) cc_final: 0.3381 (m-10) REVERT: T 38 ASP cc_start: 0.6488 (OUTLIER) cc_final: 0.6275 (t0) REVERT: T 47 SER cc_start: 0.8228 (p) cc_final: 0.7685 (m) REVERT: U 49 ASN cc_start: 0.4758 (m110) cc_final: 0.4558 (m-40) REVERT: U 70 LYS cc_start: 0.6001 (tttp) cc_final: 0.4573 (mmtm) REVERT: U 88 GLN cc_start: 0.7169 (mp10) cc_final: 0.6939 (mt0) REVERT: V 56 ASP cc_start: 0.8155 (m-30) cc_final: 0.7886 (m-30) REVERT: V 66 LYS cc_start: 0.6871 (mttp) cc_final: 0.6446 (ptmt) REVERT: W 23 ARG cc_start: 0.4785 (ttp-170) cc_final: 0.4293 (ttt90) REVERT: X 53 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.6805 (t-90) REVERT: X 103 TYR cc_start: 0.7178 (m-80) cc_final: 0.6926 (m-80) REVERT: X 133 LEU cc_start: 0.6466 (mt) cc_final: 0.6104 (pp) REVERT: Y 7 ASP cc_start: 0.6282 (m-30) cc_final: 0.5916 (p0) REVERT: Y 98 ASN cc_start: 0.7749 (m-40) cc_final: 0.7450 (m-40) REVERT: Z 31 GLU cc_start: 0.6371 (tp30) cc_final: 0.5541 (tt0) REVERT: Z 93 LYS cc_start: 0.7711 (tptp) cc_final: 0.7489 (tptm) REVERT: a 47 LYS cc_start: 0.6060 (OUTLIER) cc_final: 0.5796 (ptmm) REVERT: a 52 TYR cc_start: 0.6318 (t80) cc_final: 0.5539 (t80) REVERT: b 11 ASN cc_start: 0.7578 (t0) cc_final: 0.7123 (t0) REVERT: c 24 THR cc_start: 0.7213 (t) cc_final: 0.6788 (p) REVERT: c 75 ASN cc_start: 0.8284 (t0) cc_final: 0.7955 (p0) REVERT: d 62 ARG cc_start: 0.6109 (ttm170) cc_final: 0.5741 (mtp180) REVERT: e 9 ILE cc_start: 0.6154 (mt) cc_final: 0.5898 (tp) REVERT: e 103 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7355 (ttmm) REVERT: f 101 PHE cc_start: 0.8171 (m-80) cc_final: 0.7708 (m-80) REVERT: f 103 TYR cc_start: 0.6809 (p90) cc_final: 0.6589 (p90) REVERT: g 3 GLN cc_start: 0.7116 (tt0) cc_final: 0.6892 (tt0) REVERT: g 100 ILE cc_start: 0.5796 (OUTLIER) cc_final: 0.5565 (mp) REVERT: h 75 TYR cc_start: 0.7390 (m-10) cc_final: 0.7075 (m-10) REVERT: i 20 MET cc_start: 0.7735 (tmm) cc_final: 0.7341 (ttt) REVERT: i 47 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6559 (mm) REVERT: j 57 HIS cc_start: 0.5434 (OUTLIER) cc_final: 0.4692 (t-170) REVERT: k 29 LYS cc_start: 0.6502 (OUTLIER) cc_final: 0.4586 (tppt) REVERT: l 30 ARG cc_start: 0.4900 (mtm180) cc_final: 0.4558 (mtt90) REVERT: l 31 THR cc_start: 0.7504 (t) cc_final: 0.7231 (m) REVERT: n 2 ARG cc_start: 0.4723 (OUTLIER) cc_final: -0.0967 (mmt180) REVERT: o 8 ARG cc_start: 0.6435 (mtp85) cc_final: 0.5970 (ttm-80) REVERT: o 21 THR cc_start: 0.5453 (OUTLIER) cc_final: 0.5109 (t) REVERT: o 93 LEU cc_start: 0.6340 (pt) cc_final: 0.5688 (tt) REVERT: o 98 LYS cc_start: 0.5646 (mttt) cc_final: 0.5296 (mttm) REVERT: o 100 LYS cc_start: 0.3267 (OUTLIER) cc_final: 0.2579 (mttt) REVERT: t 1 MET cc_start: 0.2334 (mmm) cc_final: 0.2116 (mmm) REVERT: t 72 PHE cc_start: 0.4187 (OUTLIER) cc_final: 0.3501 (t80) REVERT: t 76 ARG cc_start: 0.4976 (OUTLIER) cc_final: 0.3678 (mmt180) REVERT: t 210 MET cc_start: -0.1138 (mmm) cc_final: -0.1483 (mpp) outliers start: 231 outliers final: 129 residues processed: 1093 average time/residue: 1.1555 time to fit residues: 2127.3669 Evaluate side-chains 1011 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 850 time to evaluate : 5.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 131 LYS Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 62 TYR Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 164 LEU Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 14 HIS Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 82 LYS Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 55 GLN Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 147 ARG Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 173 ARG Chi-restraints excluded: chain R residue 175 GLN Chi-restraints excluded: chain S residue 149 LYS Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 38 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 45 ASN Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 146 ASN Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain V residue 106 LYS Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain X residue 53 HIS Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Z residue 51 LEU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 135 ARG Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 25 LYS Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain e residue 103 LYS Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 27 GLU Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain i residue 26 ILE Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain j residue 57 HIS Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 27 ILE Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 41 PHE Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain t residue 19 TYR Chi-restraints excluded: chain t residue 55 LEU Chi-restraints excluded: chain t residue 72 PHE Chi-restraints excluded: chain t residue 76 ARG Chi-restraints excluded: chain t residue 190 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 579 optimal weight: 7.9990 chunk 374 optimal weight: 5.9990 chunk 559 optimal weight: 5.9990 chunk 282 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 595 optimal weight: 4.9990 chunk 638 optimal weight: 1.9990 chunk 463 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 736 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 HIS ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN C 243 HIS C 279 HIS E 138 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 GLN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 ASN I 73 ASN J 95 ASN ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 ASN L 106 GLN ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 ASN ** R 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN S 114 HIS ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 4 GLN Y 66 GLN Z 123 GLN ** b 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 11 ASN ** d 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 GLN o 23 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 1.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.178 134814 Z= 0.341 Angle : 0.814 18.855 197712 Z= 0.407 Chirality : 0.042 0.428 25102 Planarity : 0.007 0.156 11954 Dihedral : 23.350 179.801 60018 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.63 % Favored : 90.54 % Rotamer: Outliers : 4.69 % Allowed : 26.91 % Favored : 68.41 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.89 % Twisted General : 0.05 % 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: -2.90 (0.10), residues: 5611 helix: -2.01 (0.12), residues: 1617 sheet: -1.76 (0.18), residues: 717 loop : -1.93 (0.10), residues: 3277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP P 39 HIS 0.024 0.002 HIS C 9 PHE 0.032 0.003 PHE G 222 TYR 0.035 0.003 TYR C 120 ARG 0.013 0.001 ARG Q 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1290 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1038 time to evaluate : 5.970 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: A 30 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.5732 (ptm160) REVERT: A 247 ARG cc_start: 0.6022 (mmt-90) cc_final: 0.5079 (mmm160) REVERT: B 18 PRO cc_start: 0.7441 (Cg_exo) cc_final: 0.7235 (Cg_endo) REVERT: B 37 ARG cc_start: 0.6649 (mtp85) cc_final: 0.6167 (ttm170) REVERT: B 66 LYS cc_start: 0.6914 (ttmt) cc_final: 0.6456 (tttm) REVERT: B 137 TYR cc_start: 0.5716 (OUTLIER) cc_final: 0.4748 (m-10) REVERT: B 302 LYS cc_start: 0.7334 (mtpp) cc_final: 0.6960 (tttt) REVERT: D 105 ILE cc_start: 0.4692 (tt) cc_final: 0.4484 (tp) REVERT: D 208 MET cc_start: 0.5251 (mtm) cc_final: 0.4773 (ttm) REVERT: E 51 ARG cc_start: 0.7254 (mtm-85) cc_final: 0.6927 (mtp85) REVERT: E 97 ASN cc_start: 0.5940 (t0) cc_final: 0.5306 (t0) REVERT: E 99 GLU cc_start: 0.6348 (tp30) cc_final: 0.5672 (mm-30) REVERT: F 125 GLU cc_start: 0.6279 (mm-30) cc_final: 0.6053 (mm-30) REVERT: F 219 LYS cc_start: 0.5837 (OUTLIER) cc_final: 0.5309 (ttpt) REVERT: G 86 THR cc_start: 0.6705 (OUTLIER) cc_final: 0.6498 (p) REVERT: G 98 ARG cc_start: 0.7347 (tmt170) cc_final: 0.6773 (tmt170) REVERT: G 137 ASN cc_start: 0.7749 (m-40) cc_final: 0.7232 (m110) REVERT: G 252 ASN cc_start: 0.6051 (p0) cc_final: 0.5764 (m-40) REVERT: H 51 GLN cc_start: 0.5083 (mp10) cc_final: 0.4755 (mm-40) REVERT: H 90 MET cc_start: 0.6531 (mmp) cc_final: 0.6172 (mmp) REVERT: H 115 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7132 (mtt-85) REVERT: H 138 THR cc_start: 0.6516 (t) cc_final: 0.6271 (t) REVERT: H 139 ASN cc_start: 0.6107 (OUTLIER) cc_final: 0.3631 (t0) REVERT: I 10 ARG cc_start: 0.6409 (ttt180) cc_final: 0.5985 (ttt-90) REVERT: I 34 TYR cc_start: 0.7427 (m-80) cc_final: 0.6885 (m-80) REVERT: I 55 ASN cc_start: 0.7179 (OUTLIER) cc_final: 0.6654 (m110) REVERT: I 134 ILE cc_start: 0.6514 (mp) cc_final: 0.5859 (mt) REVERT: I 181 TYR cc_start: 0.5769 (t80) cc_final: 0.4569 (t80) REVERT: I 203 LYS cc_start: 0.7333 (tptm) cc_final: 0.6879 (tttm) REVERT: J 85 LYS cc_start: 0.6613 (ttmt) cc_final: 0.6353 (mttt) REVERT: L 45 LYS cc_start: 0.7117 (tttp) cc_final: 0.6732 (ttmm) REVERT: L 68 LYS cc_start: 0.7221 (mmtm) cc_final: 0.6480 (ptpp) REVERT: L 184 GLU cc_start: 0.5752 (OUTLIER) cc_final: 0.4921 (tp30) REVERT: M 41 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: N 62 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.5822 (m-80) REVERT: N 145 ASP cc_start: 0.6703 (t0) cc_final: 0.6436 (t0) REVERT: N 202 TYR cc_start: 0.8084 (m-80) cc_final: 0.7148 (m-80) REVERT: O 14 HIS cc_start: 0.8431 (OUTLIER) cc_final: 0.6602 (t-90) REVERT: O 82 LYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6347 (tmmt) REVERT: O 155 LYS cc_start: 0.7379 (tttt) cc_final: 0.6960 (ttpt) REVERT: P 52 LEU cc_start: 0.5987 (tp) cc_final: 0.5766 (mt) REVERT: P 53 ASP cc_start: 0.7421 (t0) cc_final: 0.6984 (t0) REVERT: P 88 VAL cc_start: 0.6983 (t) cc_final: 0.6752 (p) REVERT: P 126 ARG cc_start: 0.7445 (tpt170) cc_final: 0.7226 (mmt90) REVERT: R 173 ARG cc_start: 0.4197 (OUTLIER) cc_final: 0.3004 (ptt180) REVERT: S 1 MET cc_start: 0.5720 (ptt) cc_final: 0.4559 (ttm) REVERT: S 90 MET cc_start: 0.6578 (ptp) cc_final: 0.6000 (ptp) REVERT: S 149 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6994 (mtmm) REVERT: S 172 TYR cc_start: 0.6573 (OUTLIER) cc_final: 0.4259 (m-10) REVERT: T 149 GLN cc_start: 0.6245 (pm20) cc_final: 0.5963 (pt0) REVERT: V 66 LYS cc_start: 0.7077 (mttp) cc_final: 0.6664 (ptmt) REVERT: V 71 LYS cc_start: 0.5882 (mtpm) cc_final: 0.5339 (mtmm) REVERT: W 23 ARG cc_start: 0.4756 (ttp-170) cc_final: 0.4107 (ttt90) REVERT: X 53 HIS cc_start: 0.7768 (OUTLIER) cc_final: 0.7451 (t70) REVERT: X 119 THR cc_start: 0.7051 (p) cc_final: 0.6768 (p) REVERT: X 133 LEU cc_start: 0.6646 (mt) cc_final: 0.6265 (pp) REVERT: Y 4 GLN cc_start: 0.6355 (OUTLIER) cc_final: 0.6118 (mm-40) REVERT: Y 81 GLN cc_start: 0.5758 (OUTLIER) cc_final: 0.5218 (mt0) REVERT: Z 31 GLU cc_start: 0.7353 (tp30) cc_final: 0.6751 (tt0) REVERT: Z 36 HIS cc_start: 0.4682 (OUTLIER) cc_final: 0.4351 (m-70) REVERT: Z 60 LYS cc_start: 0.6783 (mttt) cc_final: 0.6435 (tmtp) REVERT: Z 69 LYS cc_start: 0.7356 (ttmt) cc_final: 0.6981 (tttp) REVERT: a 47 LYS cc_start: 0.5655 (OUTLIER) cc_final: 0.5434 (ptmm) REVERT: b 11 ASN cc_start: 0.7838 (t0) cc_final: 0.7620 (t0) REVERT: c 24 THR cc_start: 0.7140 (t) cc_final: 0.6748 (p) REVERT: c 61 MET cc_start: 0.6944 (tmt) cc_final: 0.6733 (tmt) REVERT: c 75 ASN cc_start: 0.8425 (t0) cc_final: 0.8035 (p0) REVERT: c 76 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8448 (tm-30) REVERT: g 31 ARG cc_start: 0.6651 (mtp85) cc_final: 0.6256 (mtp85) REVERT: g 100 ILE cc_start: 0.6511 (OUTLIER) cc_final: 0.6286 (mp) REVERT: h 75 TYR cc_start: 0.6998 (m-10) cc_final: 0.6054 (m-10) REVERT: i 67 LYS cc_start: 0.7088 (tttm) cc_final: 0.6605 (pttp) REVERT: j 57 HIS cc_start: 0.5056 (OUTLIER) cc_final: 0.4338 (t-170) REVERT: k 29 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.4857 (tppt) REVERT: k 30 LYS cc_start: 0.5930 (OUTLIER) cc_final: 0.5649 (ptmt) REVERT: l 30 ARG cc_start: 0.4978 (mtm180) cc_final: 0.4737 (mtt90) REVERT: l 31 THR cc_start: 0.6969 (t) cc_final: 0.6437 (m) REVERT: m 106 ARG cc_start: 0.7281 (ttt-90) cc_final: 0.6997 (ttt-90) REVERT: n 2 ARG cc_start: 0.3452 (OUTLIER) cc_final: -0.1618 (mmt180) REVERT: o 8 ARG cc_start: 0.6429 (mtp85) cc_final: 0.5934 (ttm-80) REVERT: o 53 GLN cc_start: 0.6745 (tp40) cc_final: 0.6513 (tp40) REVERT: o 93 LEU cc_start: 0.6033 (pt) cc_final: 0.5307 (tt) REVERT: o 100 LYS cc_start: 0.2970 (OUTLIER) cc_final: 0.2424 (mttt) REVERT: p 45 LYS cc_start: 0.7159 (mtmm) cc_final: 0.6735 (mtpt) REVERT: t 1 MET cc_start: 0.2202 (mmm) cc_final: 0.1964 (mmm) REVERT: t 21 ASN cc_start: 0.2833 (t0) cc_final: 0.2511 (p0) REVERT: t 76 ARG cc_start: 0.4518 (OUTLIER) cc_final: 0.3859 (tpp-160) REVERT: t 85 MET cc_start: 0.1304 (ppp) cc_final: 0.0887 (ppp) REVERT: t 210 MET cc_start: 0.0077 (mmm) cc_final: -0.0236 (mtp) outliers start: 252 outliers final: 151 residues processed: 1207 average time/residue: 1.2258 time to fit residues: 2508.4714 Evaluate side-chains 1096 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 918 time to evaluate : 5.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 55 ASN Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 199 PHE Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 62 TYR Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 169 LYS Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 14 HIS Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 82 LYS Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain R residue 134 HIS Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 173 ARG Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 149 LYS Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 38 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 45 ASN Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 146 ASN Chi-restraints excluded: chain T residue 157 GLU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 59 MET Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain X residue 53 HIS Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain Y residue 4 GLN Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Y residue 81 GLN Chi-restraints excluded: chain Z residue 36 HIS Chi-restraints excluded: chain Z residue 51 LEU Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain b residue 3 LYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 25 LYS Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 87 MET Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 27 GLU Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain j residue 57 HIS Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 27 ILE Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 30 LYS Chi-restraints excluded: chain l residue 27 ILE Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain t residue 55 LEU Chi-restraints excluded: chain t residue 72 PHE Chi-restraints excluded: chain t residue 76 ARG Chi-restraints excluded: chain t residue 88 ASP Chi-restraints excluded: chain t residue 99 LEU Chi-restraints excluded: chain t residue 113 SER Chi-restraints excluded: chain t residue 190 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 852 optimal weight: 7.9990 chunk 897 optimal weight: 5.9990 chunk 818 optimal weight: 0.9980 chunk 873 optimal weight: 5.9990 chunk 525 optimal weight: 3.9990 chunk 380 optimal weight: 1.9990 chunk 685 optimal weight: 0.8980 chunk 267 optimal weight: 10.0000 chunk 788 optimal weight: 0.0170 chunk 825 optimal weight: 0.5980 chunk 869 optimal weight: 5.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 ASN ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 ASN ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 ASN I 73 ASN I 92 HIS J 68 HIS ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 ASN ** L 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 GLN M 62 GLN N 86 ASN ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 ASN T 49 GLN U 87 ASN Y 4 GLN Y 98 ASN b 43 HIS ** f 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 1.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 134814 Z= 0.152 Angle : 0.615 18.787 197712 Z= 0.313 Chirality : 0.034 0.486 25102 Planarity : 0.006 0.154 11954 Dihedral : 23.206 179.761 60009 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.11 % Favored : 93.16 % Rotamer: Outliers : 2.73 % Allowed : 29.56 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.89 % Twisted General : 0.03 % 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: -2.46 (0.10), residues: 5611 helix: -1.58 (0.12), residues: 1626 sheet: -1.41 (0.19), residues: 665 loop : -1.73 (0.10), residues: 3320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 358 HIS 0.022 0.001 HIS C 9 PHE 0.037 0.002 PHE G 91 TYR 0.021 0.001 TYR f 103 ARG 0.009 0.001 ARG N 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1003 time to evaluate : 6.457 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: A 38 HIS cc_start: 0.5255 (m-70) cc_final: 0.5032 (m-70) REVERT: A 247 ARG cc_start: 0.5794 (mmt-90) cc_final: 0.4856 (mmm160) REVERT: B 37 ARG cc_start: 0.6660 (mtp85) cc_final: 0.6152 (ttm170) REVERT: B 66 LYS cc_start: 0.6824 (ttmt) cc_final: 0.6434 (tttt) REVERT: B 137 TYR cc_start: 0.5734 (OUTLIER) cc_final: 0.4811 (m-10) REVERT: B 214 MET cc_start: 0.6097 (tpp) cc_final: 0.5879 (tpp) REVERT: B 277 SER cc_start: 0.7819 (m) cc_final: 0.7144 (p) REVERT: B 302 LYS cc_start: 0.7154 (mtpp) cc_final: 0.6773 (tttp) REVERT: C 260 GLN cc_start: 0.6101 (tm-30) cc_final: 0.5891 (tt0) REVERT: D 105 ILE cc_start: 0.4987 (tt) cc_final: 0.4765 (tp) REVERT: D 193 GLU cc_start: 0.7348 (tp30) cc_final: 0.7041 (mp0) REVERT: D 208 MET cc_start: 0.5225 (mtm) cc_final: 0.4737 (ttm) REVERT: E 97 ASN cc_start: 0.5512 (t0) cc_final: 0.4927 (t0) REVERT: E 99 GLU cc_start: 0.6438 (tp30) cc_final: 0.5765 (mm-30) REVERT: F 219 LYS cc_start: 0.5944 (OUTLIER) cc_final: 0.5448 (ttpt) REVERT: G 60 ARG cc_start: 0.5428 (ttp-110) cc_final: 0.5182 (ttm170) REVERT: G 98 ARG cc_start: 0.7244 (tmt170) cc_final: 0.6592 (tmt170) REVERT: G 137 ASN cc_start: 0.8234 (m-40) cc_final: 0.7524 (m110) REVERT: G 151 VAL cc_start: 0.6735 (t) cc_final: 0.6285 (m) REVERT: G 191 ASN cc_start: 0.6857 (m-40) cc_final: 0.6655 (m-40) REVERT: G 252 ASN cc_start: 0.6025 (p0) cc_final: 0.5744 (m-40) REVERT: H 9 GLN cc_start: 0.7148 (mp-120) cc_final: 0.6947 (mm110) REVERT: H 115 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6700 (mtt-85) REVERT: H 138 THR cc_start: 0.6527 (t) cc_final: 0.6311 (t) REVERT: H 139 ASN cc_start: 0.6103 (OUTLIER) cc_final: 0.3654 (t0) REVERT: I 10 ARG cc_start: 0.6186 (ttt180) cc_final: 0.5796 (ttt-90) REVERT: I 55 ASN cc_start: 0.6849 (OUTLIER) cc_final: 0.6339 (m110) REVERT: I 134 ILE cc_start: 0.6867 (mp) cc_final: 0.6143 (mt) REVERT: I 181 TYR cc_start: 0.5650 (t80) cc_final: 0.4503 (t80) REVERT: I 203 LYS cc_start: 0.7384 (tptm) cc_final: 0.7022 (tttm) REVERT: L 68 LYS cc_start: 0.7122 (mmtm) cc_final: 0.6374 (ptpp) REVERT: L 79 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6738 (pt0) REVERT: L 186 ARG cc_start: 0.3800 (mtt90) cc_final: 0.3539 (mtp180) REVERT: M 41 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6831 (mt0) REVERT: N 62 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.5693 (m-80) REVERT: N 175 ASN cc_start: 0.6922 (m110) cc_final: 0.6543 (m-40) REVERT: N 202 TYR cc_start: 0.7907 (m-80) cc_final: 0.7229 (m-80) REVERT: O 14 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.6660 (t-90) REVERT: O 64 PHE cc_start: 0.5754 (p90) cc_final: 0.5540 (p90) REVERT: O 82 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.6191 (tmmt) REVERT: P 108 ASP cc_start: 0.7509 (t0) cc_final: 0.7248 (t70) REVERT: P 126 ARG cc_start: 0.7454 (tpt170) cc_final: 0.6959 (mmt90) REVERT: S 1 MET cc_start: 0.5094 (ptt) cc_final: 0.4690 (ttm) REVERT: S 90 MET cc_start: 0.6298 (ptp) cc_final: 0.5879 (ptp) REVERT: S 149 LYS cc_start: 0.6679 (OUTLIER) cc_final: 0.6433 (mtmm) REVERT: S 172 TYR cc_start: 0.6587 (OUTLIER) cc_final: 0.4198 (m-10) REVERT: T 149 GLN cc_start: 0.5864 (pm20) cc_final: 0.5468 (pt0) REVERT: U 70 LYS cc_start: 0.5938 (tttp) cc_final: 0.4523 (mmtm) REVERT: U 99 LYS cc_start: 0.6246 (ttmm) cc_final: 0.5910 (mmtm) REVERT: V 66 LYS cc_start: 0.7007 (mttp) cc_final: 0.6605 (ptmt) REVERT: V 120 LYS cc_start: 0.5685 (ttpp) cc_final: 0.5178 (tptp) REVERT: W 23 ARG cc_start: 0.4928 (ttp-170) cc_final: 0.4209 (ttt90) REVERT: X 53 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.7348 (t70) REVERT: X 119 THR cc_start: 0.6666 (p) cc_final: 0.6336 (p) REVERT: X 133 LEU cc_start: 0.6491 (mt) cc_final: 0.6099 (pp) REVERT: Y 4 GLN cc_start: 0.6486 (OUTLIER) cc_final: 0.6064 (mm110) REVERT: Y 85 VAL cc_start: 0.3290 (m) cc_final: 0.2951 (m) REVERT: Y 121 ARG cc_start: 0.5488 (mpt-90) cc_final: 0.4793 (mtp180) REVERT: Z 31 GLU cc_start: 0.6934 (tp30) cc_final: 0.6510 (tt0) REVERT: Z 60 LYS cc_start: 0.6867 (mttt) cc_final: 0.6477 (tttp) REVERT: a 52 TYR cc_start: 0.5907 (t80) cc_final: 0.4961 (t80) REVERT: c 24 THR cc_start: 0.7198 (t) cc_final: 0.6773 (p) REVERT: c 75 ASN cc_start: 0.8353 (t0) cc_final: 0.7993 (p0) REVERT: c 76 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8436 (tm-30) REVERT: d 62 ARG cc_start: 0.6174 (ttm170) cc_final: 0.5675 (mtp180) REVERT: e 103 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7577 (tppt) REVERT: g 14 ASN cc_start: 0.7234 (t0) cc_final: 0.7024 (t0) REVERT: g 30 LEU cc_start: 0.7055 (mt) cc_final: 0.6825 (mt) REVERT: g 31 ARG cc_start: 0.6823 (mtp85) cc_final: 0.6427 (mtp85) REVERT: h 75 TYR cc_start: 0.7180 (m-10) cc_final: 0.6578 (m-10) REVERT: i 67 LYS cc_start: 0.6432 (tttm) cc_final: 0.5936 (pttp) REVERT: j 57 HIS cc_start: 0.5335 (OUTLIER) cc_final: 0.4569 (t-170) REVERT: k 29 LYS cc_start: 0.6310 (tmtt) cc_final: 0.4596 (tppt) REVERT: k 31 LEU cc_start: 0.5437 (pt) cc_final: 0.4830 (mp) REVERT: l 31 THR cc_start: 0.7138 (t) cc_final: 0.6712 (m) REVERT: m 106 ARG cc_start: 0.6854 (ttt-90) cc_final: 0.6563 (ttt-90) REVERT: n 2 ARG cc_start: 0.4843 (OUTLIER) cc_final: -0.0918 (mmt180) REVERT: o 8 ARG cc_start: 0.6578 (mtp85) cc_final: 0.6065 (ttm-80) REVERT: o 93 LEU cc_start: 0.6276 (pt) cc_final: 0.5760 (tt) REVERT: o 100 LYS cc_start: 0.3071 (OUTLIER) cc_final: 0.2403 (mttt) REVERT: p 14 TYR cc_start: 0.7133 (m-80) cc_final: 0.6787 (m-80) REVERT: p 45 LYS cc_start: 0.7119 (mtmm) cc_final: 0.6689 (mtpt) REVERT: t 1 MET cc_start: 0.2137 (mmm) cc_final: 0.1848 (mmm) REVERT: t 63 MET cc_start: 0.4987 (ppp) cc_final: 0.4686 (ppp) REVERT: t 76 ARG cc_start: 0.4784 (OUTLIER) cc_final: 0.3984 (mmt180) REVERT: t 85 MET cc_start: 0.1244 (ppp) cc_final: 0.0850 (ppp) REVERT: t 210 MET cc_start: -0.0016 (mmm) cc_final: -0.0324 (mtp) outliers start: 147 outliers final: 100 residues processed: 1091 average time/residue: 1.1601 time to fit residues: 2133.7237 Evaluate side-chains 1028 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 909 time to evaluate : 5.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 55 ASN Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain L residue 12 ASN Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 62 TYR Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 169 LYS Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 14 HIS Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 82 LYS Chi-restraints excluded: chain O residue 135 TYR Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 146 SER Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 149 LYS Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 45 ASN Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 146 ASN Chi-restraints excluded: chain T residue 157 GLU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain X residue 53 HIS Chi-restraints excluded: chain Y residue 4 GLN Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Z residue 51 LEU Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 135 ARG Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 25 LYS Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 103 LYS Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain j residue 57 HIS Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain t residue 55 LEU Chi-restraints excluded: chain t residue 72 PHE Chi-restraints excluded: chain t residue 76 ARG Chi-restraints excluded: chain t residue 190 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 573 optimal weight: 5.9990 chunk 923 optimal weight: 4.9990 chunk 563 optimal weight: 3.9990 chunk 437 optimal weight: 8.9990 chunk 641 optimal weight: 9.9990 chunk 968 optimal weight: 5.9990 chunk 891 optimal weight: 0.0170 chunk 771 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 595 optimal weight: 0.5980 chunk 472 optimal weight: 1.9990 overall best weight: 2.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN F 209 ASN F 225 GLN F 237 ASN G 191 ASN ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 ASN ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 ASN ** R 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 ASN V 132 ASN Z 123 GLN c 75 ASN ** e 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 62 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5927 moved from start: 1.6593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 134814 Z= 0.217 Angle : 0.649 34.928 197712 Z= 0.325 Chirality : 0.036 0.317 25102 Planarity : 0.006 0.222 11954 Dihedral : 23.119 179.871 60004 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.63 % Favored : 91.68 % Rotamer: Outliers : 2.62 % Allowed : 30.10 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 2.89 % Twisted General : 0.05 % 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: -2.36 (0.11), residues: 5611 helix: -1.48 (0.12), residues: 1607 sheet: -1.34 (0.19), residues: 675 loop : -1.68 (0.10), residues: 3329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP a 69 HIS 0.010 0.001 HIS d 21 PHE 0.025 0.002 PHE D 223 TYR 0.027 0.002 TYR N 6 ARG 0.009 0.001 ARG B 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11222 Ramachandran restraints generated. 5611 Oldfield, 0 Emsley, 5611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 963 time to evaluate : 5.883 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: B 37 ARG cc_start: 0.6642 (mtp85) cc_final: 0.6158 (ttm170) REVERT: B 53 MET cc_start: 0.6846 (mmm) cc_final: 0.6499 (mmm) REVERT: B 66 LYS cc_start: 0.6924 (ttmt) cc_final: 0.6445 (tttt) REVERT: B 92 TYR cc_start: 0.6895 (m-80) cc_final: 0.6483 (m-80) REVERT: B 137 TYR cc_start: 0.5850 (OUTLIER) cc_final: 0.4893 (m-10) REVERT: B 277 SER cc_start: 0.7841 (m) cc_final: 0.7114 (p) REVERT: B 302 LYS cc_start: 0.7351 (mtpp) cc_final: 0.7032 (tttm) REVERT: D 81 HIS cc_start: 0.7839 (p90) cc_final: 0.7023 (p-80) REVERT: D 105 ILE cc_start: 0.4689 (tt) cc_final: 0.4466 (tp) REVERT: D 193 GLU cc_start: 0.7334 (tp30) cc_final: 0.7042 (mp0) REVERT: D 208 MET cc_start: 0.5258 (mtm) cc_final: 0.4830 (ttm) REVERT: E 97 ASN cc_start: 0.5359 (t0) cc_final: 0.4763 (t0) REVERT: E 99 GLU cc_start: 0.6493 (tp30) cc_final: 0.5853 (mm-30) REVERT: F 164 SER cc_start: 0.8693 (p) cc_final: 0.8447 (p) REVERT: F 219 LYS cc_start: 0.5951 (OUTLIER) cc_final: 0.5426 (ttpt) REVERT: G 137 ASN cc_start: 0.8066 (m-40) cc_final: 0.7440 (m110) REVERT: G 252 ASN cc_start: 0.6005 (p0) cc_final: 0.5736 (m-40) REVERT: H 90 MET cc_start: 0.6429 (mmp) cc_final: 0.6104 (mmp) REVERT: H 97 PHE cc_start: 0.7248 (m-80) cc_final: 0.6930 (m-80) REVERT: H 115 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6884 (mtt-85) REVERT: H 139 ASN cc_start: 0.6343 (OUTLIER) cc_final: 0.3820 (t0) REVERT: H 144 ILE cc_start: 0.5214 (tt) cc_final: 0.5000 (tp) REVERT: I 10 ARG cc_start: 0.6450 (ttt180) cc_final: 0.5969 (ttt-90) REVERT: I 101 LYS cc_start: 0.7258 (tttt) cc_final: 0.6773 (mtmt) REVERT: I 134 ILE cc_start: 0.7158 (mp) cc_final: 0.6451 (mt) REVERT: I 203 LYS cc_start: 0.7301 (tptm) cc_final: 0.6984 (tttm) REVERT: L 68 LYS cc_start: 0.7593 (mmtm) cc_final: 0.6943 (ptpp) REVERT: L 79 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6907 (pt0) REVERT: M 41 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6706 (mt0) REVERT: M 102 LYS cc_start: 0.5304 (tmtt) cc_final: 0.5104 (tppt) REVERT: N 62 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.5769 (m-80) REVERT: N 145 ASP cc_start: 0.6672 (t0) cc_final: 0.6387 (t0) REVERT: N 187 ARG cc_start: 0.6232 (ttp80) cc_final: 0.5965 (ttp-110) REVERT: N 202 TYR cc_start: 0.8142 (m-80) cc_final: 0.7343 (m-80) REVERT: O 14 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.7000 (t-90) REVERT: O 82 LYS cc_start: 0.6636 (OUTLIER) cc_final: 0.6208 (tmmt) REVERT: P 53 ASP cc_start: 0.7149 (t0) cc_final: 0.6088 (m-30) REVERT: P 108 ASP cc_start: 0.7550 (t0) cc_final: 0.7284 (t70) REVERT: P 147 GLU cc_start: 0.7103 (pt0) cc_final: 0.6279 (pt0) REVERT: S 1 MET cc_start: 0.5159 (ptt) cc_final: 0.4703 (ttm) REVERT: S 90 MET cc_start: 0.6268 (ptp) cc_final: 0.6002 (ptp) REVERT: S 149 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6579 (mtmm) REVERT: S 172 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.5563 (m-10) REVERT: T 149 GLN cc_start: 0.5826 (pm20) cc_final: 0.5500 (pt0) REVERT: U 70 LYS cc_start: 0.6069 (tttp) cc_final: 0.4607 (mmtt) REVERT: U 99 LYS cc_start: 0.6115 (ttmm) cc_final: 0.5866 (mmtm) REVERT: V 66 LYS cc_start: 0.7034 (mttp) cc_final: 0.6627 (ptmt) REVERT: V 71 LYS cc_start: 0.5713 (mtpm) cc_final: 0.5190 (mtmm) REVERT: V 121 GLU cc_start: 0.6255 (mm-30) cc_final: 0.6030 (mp0) REVERT: V 132 ASN cc_start: 0.7302 (m110) cc_final: 0.7042 (p0) REVERT: W 23 ARG cc_start: 0.4920 (ttp-170) cc_final: 0.4300 (ttt90) REVERT: X 53 HIS cc_start: 0.7665 (OUTLIER) cc_final: 0.7421 (t70) REVERT: X 119 THR cc_start: 0.6708 (p) cc_final: 0.6441 (p) REVERT: X 133 LEU cc_start: 0.6675 (mt) cc_final: 0.6284 (pp) REVERT: Y 4 GLN cc_start: 0.6613 (mm-40) cc_final: 0.6376 (mm-40) REVERT: Y 121 ARG cc_start: 0.5678 (mpt-90) cc_final: 0.5036 (mtp180) REVERT: Z 31 GLU cc_start: 0.7151 (tp30) cc_final: 0.6769 (tt0) REVERT: Z 60 LYS cc_start: 0.6869 (mttt) cc_final: 0.6524 (tmtp) REVERT: a 52 TYR cc_start: 0.5937 (t80) cc_final: 0.5036 (t80) REVERT: a 58 MET cc_start: 0.4573 (mtp) cc_final: 0.4311 (mtp) REVERT: b 43 HIS cc_start: 0.4855 (t-90) cc_final: 0.4626 (t-90) REVERT: c 24 THR cc_start: 0.7275 (t) cc_final: 0.6790 (p) REVERT: c 75 ASN cc_start: 0.8520 (t160) cc_final: 0.8207 (p0) REVERT: c 76 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8425 (tm-30) REVERT: d 62 ARG cc_start: 0.6120 (ttm170) cc_final: 0.5612 (mtp180) REVERT: e 118 LYS cc_start: 0.7235 (tttp) cc_final: 0.6457 (tptt) REVERT: g 30 LEU cc_start: 0.7174 (mt) cc_final: 0.6969 (mt) REVERT: h 75 TYR cc_start: 0.7177 (m-10) cc_final: 0.6502 (m-10) REVERT: i 45 ARG cc_start: 0.6789 (tpp80) cc_final: 0.6442 (tmm-80) REVERT: i 67 LYS cc_start: 0.6890 (tttm) cc_final: 0.6323 (pttp) REVERT: j 57 HIS cc_start: 0.5314 (OUTLIER) cc_final: 0.4523 (t-170) REVERT: k 21 LYS cc_start: 0.6606 (mtmt) cc_final: 0.6232 (tptp) REVERT: k 29 LYS cc_start: 0.6784 (tmtt) cc_final: 0.5146 (tppt) REVERT: k 31 LEU cc_start: 0.5585 (pt) cc_final: 0.4975 (mp) REVERT: l 31 THR cc_start: 0.7172 (t) cc_final: 0.6727 (m) REVERT: l 47 THR cc_start: 0.7326 (m) cc_final: 0.6644 (p) REVERT: m 106 ARG cc_start: 0.7120 (ttt-90) cc_final: 0.6834 (ttt-90) REVERT: n 2 ARG cc_start: 0.4886 (OUTLIER) cc_final: -0.0782 (mmt180) REVERT: o 53 GLN cc_start: 0.6869 (tp40) cc_final: 0.6519 (tp40) REVERT: o 93 LEU cc_start: 0.6346 (pt) cc_final: 0.5737 (tt) REVERT: o 100 LYS cc_start: 0.3074 (OUTLIER) cc_final: 0.2504 (mttt) REVERT: t 1 MET cc_start: 0.2029 (mmm) cc_final: 0.1730 (mmm) REVERT: t 76 ARG cc_start: 0.4620 (OUTLIER) cc_final: 0.3871 (mmt180) REVERT: t 210 MET cc_start: 0.0186 (mmm) cc_final: -0.0085 (mtp) outliers start: 141 outliers final: 113 residues processed: 1058 average time/residue: 1.1489 time to fit residues: 2061.6050 Evaluate side-chains 1058 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 929 time to evaluate : 5.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 177 ASP Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 12 ASN Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 62 TYR Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 169 LYS Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 14 HIS Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 82 LYS Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 101 ASN Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 149 LYS Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 45 ASN Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 146 ASN Chi-restraints excluded: chain T residue 157 GLU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain X residue 53 HIS Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Z residue 51 LEU Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 25 LYS Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 38 ARG Chi-restraints excluded: chain h residue 62 GLN Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 57 HIS Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain t residue 55 LEU Chi-restraints excluded: chain t residue 72 PHE Chi-restraints excluded: chain t residue 76 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 612 optimal weight: 6.9990 chunk 821 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 711 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 214 optimal weight: 8.9990 chunk 772 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 793 optimal weight: 4.9990 chunk 97 optimal weight: 40.0000 chunk 142 optimal weight: 9.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN G 59 GLN ** H 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 GLN ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 HIS ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 ASN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 HIS Q 15 HIS ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 ASN ** Q 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 GLN Z 76 ASN Z 123 GLN b 42 ASN d 87 ASN ** e 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 GLN ** f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 62 GLN h 99 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.160538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.133398 restraints weight = 187114.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.134235 restraints weight = 121363.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.135146 restraints weight = 86989.326| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 1.7428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.205 134814 Z= 0.431 Angle : 0.888 31.306 197712 Z= 0.440 Chirality : 0.045 0.321 25102 Planarity : 0.008 0.210 11954 Dihedral : 23.420 179.455 60004 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.77 % Allowed : 9.87 % Favored : 89.36 % Rotamer: Outliers : 3.07 % Allowed : 30.10 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 2.89 % Twisted General : 0.12 % 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: -2.99 (0.10), residues: 5611 helix: -2.14 (0.12), residues: 1566 sheet: -1.69 (0.19), residues: 671 loop : -2.02 (0.10), residues: 3374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP a 79 HIS 0.014 0.002 HIS d 21 PHE 0.042 0.003 PHE G 91 TYR 0.037 0.003 TYR f 103 ARG 0.011 0.001 ARG N 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31399.05 seconds wall clock time: 550 minutes 38.32 seconds (33038.32 seconds total)