Starting phenix.real_space_refine on Fri Nov 17 13:25:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v91_2599/11_2023/4v91_2599.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v91_2599/11_2023/4v91_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_2599/11_2023/4v91_2599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v91_2599/11_2023/4v91_2599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v91_2599/11_2023/4v91_2599.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v91_2599/11_2023/4v91_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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 2 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: 47.25, per 1000 atoms: 0.38 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: 49.67 Conformation dependent library (CDL) restraints added in 7.1 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: 39.65 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: 174.15 Time building geometry restraints manager: 53.82 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: 66723 35.85 - 71.69: 5670 71.69 - 107.54: 339 107.54 - 143.39: 75 143.39 - 179.23: 66 Dihedral angle restraints: 72873 sinusoidal: 54647 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 72870 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 12.050 Check model and map are aligned: 1.420 Set scattering table: 0.890 Process input model: 399.490 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.290 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:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 420.560 ------------------------------------------------------------------------------- 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 : 20.662 179.234 60850 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 *********************** 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 : 6.047 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 outliers start: 688 outliers final: 166 residues processed: 1397 average time/residue: 1.2701 time to fit residues: 2896.6390 Evaluate side-chains 595 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 429 time to evaluate : 5.962 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 166 outliers final: 4 residues processed: 166 average time/residue: 0.9892 time to fit residues: 303.8359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 820 optimal weight: 5.9990 chunk 736 optimal weight: 5.9990 chunk 408 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 496 optimal weight: 5.9990 chunk 393 optimal weight: 8.9990 chunk 761 optimal weight: 5.9990 chunk 294 optimal weight: 5.9990 chunk 463 optimal weight: 6.9990 chunk 567 optimal weight: 5.9990 chunk 882 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN 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 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN ** G 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN I 12 GLN J 150 ASN L 13 HIS ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 ASN L 137 GLN M 119 GLN ** N 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 HIS N 175 ASN N 194 GLN ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN P 45 GLN ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN P 96 GLN P 121 GLN ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 GLN R 58 HIS ** R 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 141 HIS ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 26 HIS T 95 HIS T 98 HIS ** T 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 98 ASN V 132 ASN ** X 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 111 ASN Z 78 ASN Z 106 GLN a 25 HIS ** a 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 67 HIS b 6 ASN b 10 HIS ** b 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 11 ASN ** d 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 104 ASN f 17 GLN ** f 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 3 GLN g 33 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 19 GLN 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 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 44 GLN t 94 ASN t 158 GLN t 188 ASN t 199 GLN t 200 ASN Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5148 moved from start: 0.9054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.352 134814 Z= 0.668 Angle : 1.646 35.440 197712 Z= 0.794 Chirality : 0.077 1.409 25102 Planarity : 0.014 0.204 11954 Dihedral : 18.271 179.752 47889 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 33.98 Ramachandran Plot: Outliers : 4.28 % Allowed : 14.20 % Favored : 81.52 % Rotamer: Outliers : 9.52 % Allowed : 19.52 % Favored : 70.96 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 4.96 % Twisted General : 0.43 % 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: -5.27 (0.09), residues: 5611 helix: -4.02 (0.08), residues: 1588 sheet: -3.13 (0.18), residues: 618 loop : -3.46 (0.09), residues: 3405 *********************** 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 1536 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 512 poor density : 1024 time to evaluate : 6.180 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 outliers start: 512 outliers final: 142 residues processed: 1412 average time/residue: 1.2843 time to fit residues: 3037.5393 Evaluate side-chains 890 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 748 time to evaluate : 6.084 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 142 outliers final: 2 residues processed: 142 average time/residue: 0.9672 time to fit residues: 265.8093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 490 optimal weight: 3.9990 chunk 273 optimal weight: 7.9990 chunk 734 optimal weight: 5.9990 chunk 601 optimal weight: 2.9990 chunk 243 optimal weight: 7.9990 chunk 884 optimal weight: 0.8980 chunk 955 optimal weight: 10.0000 chunk 787 optimal weight: 4.9990 chunk 876 optimal weight: 2.9990 chunk 301 optimal weight: 9.9990 chunk 709 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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** C 45 ASN C 114 ASN C 307 GLN ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 ASN F 194 HIS ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 GLN G 232 HIS ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 GLN H 9 GLN ** H 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN L 103 ASN N 37 HIS ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 156 HIS ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 GLN ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 ASN O 55 HIS O 65 ASN O 122 GLN P 45 GLN P 50 GLN P 92 GLN P 101 ASN P 116 HIS ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 HIS ** Q 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 141 HIS T 95 HIS U 49 ASN X 111 ASN a 14 HIS b 42 ASN c 71 GLN d 105 GLN ** e 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 49 ASN f 26 ASN f 87 ASN f 88 ASN g 52 GLN h 61 GLN j 30 GLN k 40 GLN l 11 GLN l 20 ASN ** o 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 99 GLN p 32 GLN ** t 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 127 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5436 moved from start: 1.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.163 134814 Z= 0.333 Angle : 0.871 17.633 197712 Z= 0.441 Chirality : 0.046 0.583 25102 Planarity : 0.008 0.155 11954 Dihedral : 16.727 179.961 47889 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 1.09 % Allowed : 9.94 % Favored : 88.97 % Rotamer: Outliers : 4.54 % Allowed : 23.13 % Favored : 72.33 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 3.31 % 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: -4.19 (0.09), residues: 5611 helix: -3.01 (0.10), residues: 1628 sheet: -2.52 (0.18), residues: 674 loop : -2.81 (0.09), residues: 3309 *********************** 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 1211 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 967 time to evaluate : 6.188 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 outliers start: 244 outliers final: 110 residues processed: 1146 average time/residue: 1.2611 time to fit residues: 2425.9597 Evaluate side-chains 881 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 771 time to evaluate : 6.131 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 1 residues processed: 110 average time/residue: 1.0024 time to fit residues: 210.3024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 458 optimal weight: 20.0000 chunk 97 optimal weight: 40.0000 chunk 422 optimal weight: 0.6980 chunk 593 optimal weight: 0.7980 chunk 887 optimal weight: 7.9990 chunk 939 optimal weight: 8.9990 chunk 463 optimal weight: 5.9990 chunk 841 optimal weight: 0.0980 chunk 253 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS B 269 GLN C 48 GLN C 115 HIS C 307 GLN F 166 ASN ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 HIS H 100 ASN I 23 ASN I 55 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN L 66 ASN ** L 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN P 50 GLN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 ASN Q 126 GLN T 16 GLN ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 HIS X 53 HIS X 65 GLN Z 122 HIS ** a 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN d 57 GLN i 100 HIS j 48 ASN l 20 ASN l 33 ASN o 3 ASN ** t 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5397 moved from start: 1.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 134814 Z= 0.154 Angle : 0.640 19.150 197712 Z= 0.329 Chirality : 0.036 0.361 25102 Planarity : 0.006 0.157 11954 Dihedral : 16.113 178.819 47889 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.94 % Allowed : 6.51 % Favored : 92.55 % Rotamer: Outliers : 2.36 % Allowed : 25.23 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 3.31 % 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: -3.17 (0.10), residues: 5611 helix: -1.98 (0.11), residues: 1634 sheet: -1.99 (0.18), residues: 700 loop : -2.24 (0.10), residues: 3277 *********************** 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 990 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 863 time to evaluate : 6.217 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 outliers start: 127 outliers final: 59 residues processed: 964 average time/residue: 1.2712 time to fit residues: 2097.9407 Evaluate side-chains 819 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 760 time to evaluate : 5.797 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 1.0146 time to fit residues: 119.4926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 782 optimal weight: 10.0000 chunk 533 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 699 optimal weight: 0.5980 chunk 387 optimal weight: 10.0000 chunk 801 optimal weight: 9.9990 chunk 649 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 479 optimal weight: 10.0000 chunk 843 optimal weight: 1.9990 chunk 237 optimal weight: 9.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 97 ASN B 121 ASN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 HIS C 307 GLN C 311 HIS ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN F 166 ASN H 50 ASN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN I 12 GLN I 23 ASN I 55 ASN I 92 HIS J 95 ASN ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 HIS ** L 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 GLN N 95 GLN ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 156 HIS P 50 GLN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 45 ASN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 114 HIS T 5 HIS T 49 GLN W 59 HIS X 65 GLN ** Y 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 57 HIS ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 57 GLN d 87 ASN ** e 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 71 HIS ** f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 100 HIS j 48 ASN j 79 GLN l 20 ASN m 90 ASN o 3 ASN ** o 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 57 ASN t 140 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5842 moved from start: 1.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 134814 Z= 0.425 Angle : 0.983 21.073 197712 Z= 0.486 Chirality : 0.050 0.663 25102 Planarity : 0.008 0.155 11954 Dihedral : 16.744 179.878 47889 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.93 % Allowed : 11.03 % Favored : 88.04 % Rotamer: Outliers : 4.89 % Allowed : 25.51 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 3.31 % 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: -3.60 (0.10), residues: 5611 helix: -2.61 (0.11), residues: 1596 sheet: -1.95 (0.19), residues: 662 loop : -2.45 (0.10), residues: 3353 *********************** 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 1319 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1056 time to evaluate : 6.306 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 outliers start: 263 outliers final: 112 residues processed: 1231 average time/residue: 1.2624 time to fit residues: 2636.2875 Evaluate side-chains 983 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 871 time to evaluate : 5.561 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 0 residues processed: 112 average time/residue: 0.9286 time to fit residues: 202.7139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 185 optimal weight: 8.9990 chunk 551 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 940 optimal weight: 0.0570 chunk 780 optimal weight: 3.9990 chunk 435 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 chunk 493 optimal weight: 0.0970 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN B 231 HIS C 175 HIS C 213 ASN C 279 HIS D 40 HIS E 97 ASN F 112 ASN F 166 ASN ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 ASN G 191 ASN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 HIS ** J 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 ASN Q 45 ASN S 88 HIS ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 53 HIS Z 122 HIS b 42 ASN ** e 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 GLN j 48 ASN ** o 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 27 ASN ** t 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 57 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5803 moved from start: 1.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 134814 Z= 0.181 Angle : 0.656 19.221 197712 Z= 0.336 Chirality : 0.037 0.406 25102 Planarity : 0.006 0.171 11954 Dihedral : 16.004 177.651 47889 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.29 % Favored : 92.85 % Rotamer: Outliers : 2.51 % Allowed : 26.63 % Favored : 70.86 % 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: -2.96 (0.10), residues: 5611 helix: -1.95 (0.12), residues: 1604 sheet: -1.68 (0.19), residues: 691 loop : -2.07 (0.10), residues: 3316 *********************** 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 1097 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 962 time to evaluate : 6.233 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 outliers start: 135 outliers final: 68 residues processed: 1040 average time/residue: 1.2825 time to fit residues: 2284.4710 Evaluate side-chains 936 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 868 time to evaluate : 6.201 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 1.0945 time to fit residues: 142.5389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 906 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 535 optimal weight: 8.9990 chunk 686 optimal weight: 0.8980 chunk 532 optimal weight: 1.9990 chunk 791 optimal weight: 5.9990 chunk 525 optimal weight: 6.9990 chunk 936 optimal weight: 3.9990 chunk 586 optimal weight: 20.0000 chunk 571 optimal weight: 2.9990 chunk 432 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS C 307 GLN D 111 GLN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN F 166 ASN G 137 ASN ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 GLN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 ASN N 15 GLN ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 GLN P 101 ASN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 GLN ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 36 HIS b 42 ASN ** f 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 23 HIS o 47 GLN t 40 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 moved from start: 1.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 134814 Z= 0.221 Angle : 0.662 19.078 197712 Z= 0.336 Chirality : 0.037 0.328 25102 Planarity : 0.006 0.159 11954 Dihedral : 15.810 179.957 47889 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.75 % Allowed : 8.25 % Favored : 91.00 % Rotamer: Outliers : 2.38 % Allowed : 27.24 % Favored : 70.38 % 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: -2.76 (0.10), residues: 5611 helix: -1.77 (0.12), residues: 1625 sheet: -1.52 (0.19), residues: 670 loop : -1.96 (0.10), residues: 3316 *********************** 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 1073 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 945 time to evaluate : 6.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 128 outliers final: 73 residues processed: 1016 average time/residue: 1.2376 time to fit residues: 2145.7467 Evaluate side-chains 938 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 865 time to evaluate : 6.425 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.9668 time to fit residues: 141.0168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 579 optimal weight: 5.9990 chunk 374 optimal weight: 10.0000 chunk 559 optimal weight: 4.9990 chunk 282 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 595 optimal weight: 4.9990 chunk 638 optimal weight: 3.9990 chunk 463 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 736 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN B 256 HIS ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 ASN G 59 GLN G 191 ASN ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 HIS ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 HIS Q 45 ASN ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 HIS ** Z 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 122 HIS Z 123 GLN b 42 ASN ** e 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 GLN g 52 GLN ** h 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 57 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 1.6835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 134814 Z= 0.374 Angle : 0.838 19.769 197712 Z= 0.420 Chirality : 0.044 0.371 25102 Planarity : 0.007 0.181 11954 Dihedral : 16.303 179.228 47889 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.82 % Allowed : 9.23 % Favored : 89.95 % Rotamer: Outliers : 1.88 % Allowed : 28.21 % Favored : 69.91 % 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: -3.16 (0.10), residues: 5611 helix: -2.25 (0.11), residues: 1595 sheet: -1.65 (0.19), residues: 692 loop : -2.17 (0.10), residues: 3324 *********************** 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 1182 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1081 time to evaluate : 6.353 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 outliers start: 101 outliers final: 57 residues processed: 1144 average time/residue: 1.2536 time to fit residues: 2410.2505 Evaluate side-chains 987 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 930 time to evaluate : 6.300 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 1 residues processed: 57 average time/residue: 0.9643 time to fit residues: 109.2384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 852 optimal weight: 0.8980 chunk 897 optimal weight: 0.0030 chunk 818 optimal weight: 0.8980 chunk 873 optimal weight: 5.9990 chunk 525 optimal weight: 0.0470 chunk 380 optimal weight: 0.7980 chunk 685 optimal weight: 0.7980 chunk 267 optimal weight: 10.0000 chunk 788 optimal weight: 0.7980 chunk 825 optimal weight: 0.9990 chunk 869 optimal weight: 5.9990 overall best weight: 0.4888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS B 3 HIS B 319 ASN ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN G 77 GLN G 137 ASN G 191 ASN ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 GLN I 73 ASN J 68 HIS ** J 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 HIS N 70 ASN N 86 ASN P 50 GLN P 101 ASN ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 132 ASN Z 36 HIS Z 40 HIS d 43 HIS g 52 GLN g 61 GLN h 76 GLN o 20 HIS ** o 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 105 GLN t 57 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 1.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 134814 Z= 0.153 Angle : 0.621 20.141 197712 Z= 0.317 Chirality : 0.034 0.379 25102 Planarity : 0.006 0.175 11954 Dihedral : 15.757 179.674 47889 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.45 % Favored : 92.87 % Rotamer: Outliers : 1.04 % Allowed : 29.36 % Favored : 69.60 % 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: -2.67 (0.10), residues: 5611 helix: -1.74 (0.12), residues: 1603 sheet: -1.34 (0.19), residues: 697 loop : -1.92 (0.10), residues: 3311 *********************** 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 1094 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1038 time to evaluate : 6.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 29 residues processed: 1062 average time/residue: 1.2477 time to fit residues: 2241.0970 Evaluate side-chains 925 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 896 time to evaluate : 6.207 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 1 residues processed: 29 average time/residue: 1.0289 time to fit residues: 62.6118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 573 optimal weight: 9.9990 chunk 923 optimal weight: 9.9990 chunk 563 optimal weight: 2.9990 chunk 437 optimal weight: 1.9990 chunk 641 optimal weight: 0.6980 chunk 968 optimal weight: 5.9990 chunk 891 optimal weight: 9.9990 chunk 771 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 595 optimal weight: 5.9990 chunk 472 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN ** J 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN P 101 ASN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 ASN T 127 GLN U 40 HIS Y 81 GLN Z 122 HIS b 42 ASN h 62 GLN ** h 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 1.7248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 134814 Z= 0.294 Angle : 0.712 20.301 197712 Z= 0.357 Chirality : 0.039 0.388 25102 Planarity : 0.006 0.165 11954 Dihedral : 15.812 179.776 47889 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.91 % Favored : 90.43 % Rotamer: Outliers : 0.76 % Allowed : 30.18 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 3.31 % 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: -2.71 (0.10), residues: 5611 helix: -1.81 (0.12), residues: 1615 sheet: -1.35 (0.19), residues: 708 loop : -1.93 (0.10), residues: 3288 ********************** 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 1016 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 975 time to evaluate : 6.362 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 outliers start: 41 outliers final: 30 residues processed: 990 average time/residue: 1.2061 time to fit residues: 2029.2212 Evaluate side-chains 951 residues out of total 5398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 921 time to evaluate : 6.258 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 1 residues processed: 30 average time/residue: 0.9911 time to fit residues: 61.9292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 113 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 772 optimal weight: 0.9990 chunk 323 optimal weight: 10.0000 chunk 793 optimal weight: 0.7980 chunk 97 optimal weight: 40.0000 chunk 142 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN F 159 GLN F 166 ASN G 137 ASN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 ASN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN Z 76 ASN b 42 ASN f 24 ASN g 3 GLN h 99 GLN ** h 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN o 105 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.164334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.137435 restraints weight = 186033.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.138710 restraints weight = 113098.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.139544 restraints weight = 84710.625| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 1.7758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 134814 Z= 0.297 Angle : 0.720 20.521 197712 Z= 0.363 Chirality : 0.039 0.398 25102 Planarity : 0.007 0.156 11954 Dihedral : 15.906 179.670 47889 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.52 % Favored : 90.79 % Rotamer: Outliers : 1.00 % Allowed : 29.92 % Favored : 69.08 % 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: -2.81 (0.10), residues: 5611 helix: -1.92 (0.12), residues: 1609 sheet: -1.38 (0.20), residues: 691 loop : -1.98 (0.10), residues: 3311 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33459.51 seconds wall clock time: 585 minutes 38.55 seconds (35138.55 seconds total)