Starting phenix.real_space_refine on Fri Jan 19 22:27:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/01_2024/6neq_9358.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/01_2024/6neq_9358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/01_2024/6neq_9358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/01_2024/6neq_9358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/01_2024/6neq_9358.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/01_2024/6neq_9358.pdb" } resolution = 3.32 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= -0.001 sd= 0.077 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 952 5.49 5 S 212 5.16 5 C 37974 2.51 5 N 11974 2.21 5 O 14664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ARG 315": "NH1" <-> "NH2" Residue "e ARG 38": "NH1" <-> "NH2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e ARG 82": "NH1" <-> "NH2" Residue "e ARG 202": "NH1" <-> "NH2" Residue "e TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 252": "NH1" <-> "NH2" Residue "e ARG 277": "NH1" <-> "NH2" Residue "e ARG 330": "NH1" <-> "NH2" Residue "e GLU 399": "OE1" <-> "OE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G ARG 216": "NH1" <-> "NH2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I GLU 102": "OE1" <-> "OE2" Residue "I PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "I TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 173": "OE1" <-> "OE2" Residue "I ARG 175": "NH1" <-> "NH2" Residue "I GLU 206": "OE1" <-> "OE2" Residue "I GLU 207": "OE1" <-> "OE2" Residue "I GLU 239": "OE1" <-> "OE2" Residue "I GLU 282": "OE1" <-> "OE2" Residue "I GLU 294": "OE1" <-> "OE2" Residue "I GLU 358": "OE1" <-> "OE2" Residue "I GLU 385": "OE1" <-> "OE2" Residue "g TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 196": "NH1" <-> "NH2" Residue "g ARG 256": "NH1" <-> "NH2" Residue "g GLU 326": "OE1" <-> "OE2" Residue "g PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 374": "OE1" <-> "OE2" Residue "i TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 80": "NH1" <-> "NH2" Residue "o TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 65776 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 20256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 20256 Classifications: {'RNA': 952} Modifications used: {'rna2p_pur': 90, 'rna2p_pyr': 68, 'rna3p_pur': 432, 'rna3p_pyr': 362} Link IDs: {'rna2p': 158, 'rna3p': 793} Chain: "C" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 998 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "E" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2464 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 13, 'TRANS': 295} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 853 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 11, 'TRANS': 97} Chain: "P" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 916 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 857 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "a" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2356 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 13, 'TRANS': 275} Chain: "c" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1374 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 11, 'TRANS': 156} Chain: "d" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1463 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "e" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2950 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 10, 'TRANS': 347} Chain breaks: 1 Chain: "j" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1792 Classifications: {'peptide': 213} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 192} Chain: "p" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1531 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 20, 'TRANS': 166} Chain: "G" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1721 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 194} Chain: "I" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2541 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 12, 'TRANS': 298} Chain breaks: 1 Chain: "J" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1049 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "N" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 861 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "g" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2855 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 17, 'TRANS': 333} Chain: "h" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 871 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 98} Chain: "i" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 818 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "k" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2227 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 17, 'TRANS': 257} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 9, 'TRANS': 108} Chain: "o" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3273 Classifications: {'peptide': 461} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 145} Link IDs: {'PTRANS': 18, 'TRANS': 442} Chain breaks: 14 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 147} Unresolved non-hydrogen planarities: 147 Chain: "B" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1726 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain: "F" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 991 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain: "K" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1001 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "O" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1421 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain: "R" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 8, 'TRANS': 88} Chain: "U" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 737 Classifications: {'peptide': 86} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 82} Chain: "b" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1108 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "f" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 775 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "n" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 642 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "z" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1616 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 201} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 25.18, per 1000 atoms: 0.38 Number of scatterers: 65776 At special positions: 0 Unit cell: (206.064, 192.112, 266.166, 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 212 16.00 P 952 15.00 O 14664 8.00 N 11974 7.00 C 37974 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 76 " distance=2.03 Simple disulfide: pdb=" SG CYS m 55 " - pdb=" SG CYS m 66 " distance=2.03 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: 22.94 Conformation dependent library (CDL) restraints added in 6.0 seconds 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10730 Finding SS restraints... Secondary structure from input PDB file: 225 helices and 37 sheets defined 50.3% alpha, 8.6% beta 232 base pairs and 391 stacking pairs defined. Time for finding SS restraints: 19.80 Creating SS restraints... Processing helix chain 'C' and resid 58 through 62 removed outlier: 3.664A pdb=" N ILE C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 100 removed outlier: 3.700A pdb=" N ASP C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.570A pdb=" N SER C 144 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR C 147 " --> pdb=" O LEU C 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 185 Processing helix chain 'E' and resid 263 through 276 removed outlier: 3.535A pdb=" N ALA E 267 " --> pdb=" O GLU E 263 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL E 276 " --> pdb=" O LYS E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 328 Processing helix chain 'E' and resid 341 through 355 removed outlier: 3.568A pdb=" N ARG E 355 " --> pdb=" O GLN E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 367 Processing helix chain 'E' and resid 408 through 414 Processing helix chain 'L' and resid 32 through 40 Processing helix chain 'L' and resid 71 through 75 removed outlier: 3.505A pdb=" N SER L 75 " --> pdb=" O LYS L 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 78 removed outlier: 3.858A pdb=" N HIS P 75 " --> pdb=" O ASP P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 95 Processing helix chain 'P' and resid 100 through 124 Processing helix chain 'a' and resid 71 through 83 removed outlier: 4.128A pdb=" N ILE a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS a 80 " --> pdb=" O SER a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 90 Processing helix chain 'a' and resid 106 through 125 removed outlier: 3.651A pdb=" N VAL a 123 " --> pdb=" O GLU a 119 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG a 124 " --> pdb=" O ALA a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 148 Processing helix chain 'a' and resid 165 through 169 removed outlier: 3.649A pdb=" N GLU a 168 " --> pdb=" O PRO a 165 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG a 169 " --> pdb=" O HIS a 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 165 through 169' Processing helix chain 'a' and resid 184 through 196 removed outlier: 3.598A pdb=" N ARG a 190 " --> pdb=" O GLU a 186 " (cutoff:3.500A) Processing helix chain 'a' and resid 210 through 220 removed outlier: 4.641A pdb=" N THR a 216 " --> pdb=" O GLU a 212 " (cutoff:3.500A) Processing helix chain 'a' and resid 222 through 234 removed outlier: 3.848A pdb=" N LEU a 227 " --> pdb=" O HIS a 223 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN a 228 " --> pdb=" O VAL a 224 " (cutoff:3.500A) Processing helix chain 'a' and resid 238 through 256 removed outlier: 3.791A pdb=" N ILE a 242 " --> pdb=" O SER a 238 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS a 254 " --> pdb=" O GLU a 250 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR a 255 " --> pdb=" O ASP a 251 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 278 Processing helix chain 'a' and resid 280 through 290 Processing helix chain 'a' and resid 292 through 306 removed outlier: 3.513A pdb=" N ALA a 296 " --> pdb=" O LEU a 292 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL a 300 " --> pdb=" O ALA a 296 " (cutoff:3.500A) Processing helix chain 'a' and resid 310 through 319 removed outlier: 3.772A pdb=" N GLN a 314 " --> pdb=" O GLY a 310 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU a 315 " --> pdb=" O GLN a 311 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS a 317 " --> pdb=" O ALA a 313 " (cutoff:3.500A) Processing helix chain 'a' and resid 324 through 333 removed outlier: 3.869A pdb=" N PHE a 330 " --> pdb=" O LEU a 326 " (cutoff:3.500A) Processing helix chain 'a' and resid 337 through 353 removed outlier: 4.085A pdb=" N ILE a 341 " --> pdb=" O LYS a 337 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU a 343 " --> pdb=" O ALA a 339 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN a 346 " --> pdb=" O GLU a 342 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE a 353 " --> pdb=" O GLN a 349 " (cutoff:3.500A) Processing helix chain 'c' and resid 12 through 17 Processing helix chain 'c' and resid 41 through 58 removed outlier: 4.318A pdb=" N ILE c 52 " --> pdb=" O VAL c 48 " (cutoff:3.500A) Proline residue: c 53 - end of helix removed outlier: 3.616A pdb=" N LYS c 58 " --> pdb=" O GLN c 54 " (cutoff:3.500A) Processing helix chain 'c' and resid 94 through 106 Processing helix chain 'c' and resid 109 through 124 removed outlier: 3.559A pdb=" N LEU c 123 " --> pdb=" O GLU c 119 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER c 124 " --> pdb=" O ARG c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 139 through 143 Processing helix chain 'c' and resid 160 through 168 Processing helix chain 'd' and resid 35 through 39 removed outlier: 3.685A pdb=" N ILE d 39 " --> pdb=" O LYS d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 87 removed outlier: 3.683A pdb=" N PHE d 54 " --> pdb=" O PRO d 50 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU d 56 " --> pdb=" O GLU d 52 " (cutoff:3.500A) Processing helix chain 'd' and resid 88 through 164 removed outlier: 3.761A pdb=" N GLN d 126 " --> pdb=" O ALA d 122 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU d 137 " --> pdb=" O GLN d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 167 No H-bonds generated for 'chain 'd' and resid 165 through 167' Processing helix chain 'd' and resid 169 through 173 removed outlier: 3.545A pdb=" N LEU d 173 " --> pdb=" O ARG d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 182 removed outlier: 3.827A pdb=" N GLU d 178 " --> pdb=" O GLU d 174 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 33 Processing helix chain 'e' and resid 35 through 41 Processing helix chain 'e' and resid 42 through 44 No H-bonds generated for 'chain 'e' and resid 42 through 44' Processing helix chain 'e' and resid 49 through 63 Processing helix chain 'e' and resid 68 through 77 removed outlier: 3.941A pdb=" N ILE e 72 " --> pdb=" O SER e 68 " (cutoff:3.500A) Processing helix chain 'e' and resid 81 through 96 Processing helix chain 'e' and resid 100 through 104 removed outlier: 3.637A pdb=" N LEU e 104 " --> pdb=" O CYS e 101 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 119 removed outlier: 3.803A pdb=" N TYR e 119 " --> pdb=" O GLN e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 123 through 132 removed outlier: 3.585A pdb=" N LYS e 132 " --> pdb=" O THR e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 154 Processing helix chain 'e' and resid 157 through 169 Processing helix chain 'e' and resid 177 through 192 Processing helix chain 'e' and resid 197 through 210 removed outlier: 3.565A pdb=" N GLU e 201 " --> pdb=" O SER e 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 217 through 238 removed outlier: 4.303A pdb=" N LEU e 221 " --> pdb=" O ASN e 217 " (cutoff:3.500A) Processing helix chain 'e' and resid 239 through 245 removed outlier: 3.843A pdb=" N VAL e 243 " --> pdb=" O GLY e 239 " (cutoff:3.500A) Processing helix chain 'e' and resid 255 through 265 Processing helix chain 'e' and resid 266 through 268 No H-bonds generated for 'chain 'e' and resid 266 through 268' Processing helix chain 'e' and resid 275 through 291 Processing helix chain 'e' and resid 327 through 345 removed outlier: 3.522A pdb=" N GLU e 333 " --> pdb=" O PRO e 329 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS e 341 " --> pdb=" O ALA e 337 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN e 343 " --> pdb=" O HIS e 339 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA e 344 " --> pdb=" O SER e 340 " (cutoff:3.500A) Processing helix chain 'e' and resid 352 through 364 Processing helix chain 'e' and resid 364 through 406 removed outlier: 3.909A pdb=" N CYS e 368 " --> pdb=" O GLN e 364 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU e 369 " --> pdb=" O LEU e 365 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA e 370 " --> pdb=" O PRO e 366 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU e 371 " --> pdb=" O THR e 367 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA e 374 " --> pdb=" O ALA e 370 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG e 393 " --> pdb=" O ASN e 389 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU e 394 " --> pdb=" O LEU e 390 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG e 398 " --> pdb=" O GLU e 394 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA e 401 " --> pdb=" O MET e 397 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS e 404 " --> pdb=" O LYS e 400 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 27 removed outlier: 4.069A pdb=" N GLU j 13 " --> pdb=" O ARG j 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU j 14 " --> pdb=" O LEU j 10 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG j 16 " --> pdb=" O ALA j 12 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG j 17 " --> pdb=" O GLU j 13 " (cutoff:3.500A) Processing helix chain 'j' and resid 29 through 34 Processing helix chain 'j' and resid 51 through 53 No H-bonds generated for 'chain 'j' and resid 51 through 53' Processing helix chain 'j' and resid 54 through 61 removed outlier: 3.699A pdb=" N VAL j 58 " --> pdb=" O ALA j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 63 through 69 removed outlier: 3.575A pdb=" N LEU j 67 " --> pdb=" O ARG j 63 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 89 removed outlier: 3.504A pdb=" N GLN j 88 " --> pdb=" O SER j 84 " (cutoff:3.500A) Processing helix chain 'j' and resid 167 through 182 Processing helix chain 'p' and resid 55 through 61 removed outlier: 4.234A pdb=" N LEU p 59 " --> pdb=" O PRO p 55 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP p 60 " --> pdb=" O TRP p 56 " (cutoff:3.500A) Processing helix chain 'p' and resid 61 through 68 removed outlier: 3.695A pdb=" N HIS p 65 " --> pdb=" O SER p 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN p 68 " --> pdb=" O TYR p 64 " (cutoff:3.500A) Processing helix chain 'p' and resid 119 through 124 Processing helix chain 'p' and resid 125 through 127 No H-bonds generated for 'chain 'p' and resid 125 through 127' Processing helix chain 'p' and resid 136 through 141 Processing helix chain 'p' and resid 143 through 161 Processing helix chain 'p' and resid 190 through 196 Processing helix chain 'p' and resid 200 through 204 removed outlier: 3.606A pdb=" N TYR p 203 " --> pdb=" O TYR p 200 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER p 204 " --> pdb=" O PRO p 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 200 through 204' Processing helix chain 'p' and resid 210 through 220 Processing helix chain 'G' and resid 58 through 69 Processing helix chain 'G' and resid 88 through 99 Processing helix chain 'G' and resid 103 through 128 removed outlier: 3.619A pdb=" N ALA G 107 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 137 Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 175 through 194 Processing helix chain 'G' and resid 200 through 214 removed outlier: 3.715A pdb=" N LYS G 204 " --> pdb=" O LEU G 200 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS G 214 " --> pdb=" O LEU G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 232 Processing helix chain 'G' and resid 233 through 240 removed outlier: 4.458A pdb=" N HIS G 238 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR G 239 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG G 240 " --> pdb=" O ALA G 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 93 Processing helix chain 'I' and resid 100 through 112 Processing helix chain 'I' and resid 127 through 132 Processing helix chain 'I' and resid 150 through 154 removed outlier: 3.599A pdb=" N THR I 153 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY I 154 " --> pdb=" O PHE I 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 150 through 154' Processing helix chain 'I' and resid 155 through 178 Processing helix chain 'I' and resid 201 through 209 Processing helix chain 'I' and resid 214 through 230 Processing helix chain 'I' and resid 235 through 243 Processing helix chain 'I' and resid 300 through 304 Processing helix chain 'I' and resid 306 through 321 removed outlier: 3.509A pdb=" N GLN I 312 " --> pdb=" O GLN I 308 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU I 313 " --> pdb=" O ASP I 309 " (cutoff:3.500A) Proline residue: I 316 - end of helix removed outlier: 3.639A pdb=" N LEU I 320 " --> pdb=" O PRO I 316 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 353 removed outlier: 3.529A pdb=" N ALA I 341 " --> pdb=" O ARG I 337 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA I 351 " --> pdb=" O ALA I 347 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS I 353 " --> pdb=" O SER I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 357 through 366 removed outlier: 3.680A pdb=" N GLU I 362 " --> pdb=" O GLU I 358 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP I 363 " --> pdb=" O ASP I 359 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN I 366 " --> pdb=" O GLU I 362 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 103 Processing helix chain 'J' and resid 150 through 162 Processing helix chain 'N' and resid 31 through 59 removed outlier: 3.868A pdb=" N LEU N 35 " --> pdb=" O ASP N 31 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASP N 49 " --> pdb=" O TYR N 45 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLU N 50 " --> pdb=" O GLU N 46 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN N 55 " --> pdb=" O ARG N 51 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER N 56 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU N 57 " --> pdb=" O ARG N 53 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG N 58 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS N 59 " --> pdb=" O ASN N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 78 removed outlier: 4.074A pdb=" N GLN N 68 " --> pdb=" O PRO N 64 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU N 69 " --> pdb=" O LYS N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 107 through 116 Processing helix chain 'g' and resid 54 through 58 removed outlier: 3.816A pdb=" N HIS g 58 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 63 Processing helix chain 'g' and resid 70 through 78 Processing helix chain 'g' and resid 83 through 94 Processing helix chain 'g' and resid 101 through 113 removed outlier: 3.603A pdb=" N ASN g 113 " --> pdb=" O HIS g 109 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 147 removed outlier: 3.814A pdb=" N SER g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) Processing helix chain 'g' and resid 157 through 161 Processing helix chain 'g' and resid 171 through 174 removed outlier: 3.754A pdb=" N LYS g 174 " --> pdb=" O THR g 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 171 through 174' Processing helix chain 'g' and resid 179 through 194 removed outlier: 3.719A pdb=" N THR g 192 " --> pdb=" O LYS g 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN g 194 " --> pdb=" O PHE g 190 " (cutoff:3.500A) Processing helix chain 'g' and resid 220 through 231 removed outlier: 3.514A pdb=" N VAL g 224 " --> pdb=" O PRO g 220 " (cutoff:3.500A) Processing helix chain 'g' and resid 234 through 250 Processing helix chain 'g' and resid 264 through 269 removed outlier: 3.505A pdb=" N GLY g 269 " --> pdb=" O ALA g 266 " (cutoff:3.500A) Processing helix chain 'g' and resid 282 through 285 Processing helix chain 'g' and resid 286 through 293 Processing helix chain 'g' and resid 294 through 296 No H-bonds generated for 'chain 'g' and resid 294 through 296' Processing helix chain 'g' and resid 323 through 336 removed outlier: 3.521A pdb=" N LEU g 327 " --> pdb=" O LEU g 323 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LYS g 330 " --> pdb=" O GLU g 326 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLU g 331 " --> pdb=" O LEU g 327 " (cutoff:3.500A) Processing helix chain 'g' and resid 348 through 362 Processing helix chain 'g' and resid 367 through 371 removed outlier: 3.554A pdb=" N HIS g 371 " --> pdb=" O GLU g 368 " (cutoff:3.500A) Processing helix chain 'g' and resid 372 through 384 removed outlier: 3.631A pdb=" N LYS g 376 " --> pdb=" O THR g 372 " (cutoff:3.500A) Processing helix chain 'g' and resid 386 through 397 removed outlier: 3.916A pdb=" N TYR g 396 " --> pdb=" O ARG g 392 " (cutoff:3.500A) Processing helix chain 'h' and resid 287 through 299 removed outlier: 3.687A pdb=" N GLU h 291 " --> pdb=" O ASN h 287 " (cutoff:3.500A) Processing helix chain 'h' and resid 313 through 317 Processing helix chain 'h' and resid 326 through 330 removed outlier: 3.602A pdb=" N GLU h 330 " --> pdb=" O LYS h 327 " (cutoff:3.500A) Processing helix chain 'h' and resid 336 through 351 removed outlier: 3.569A pdb=" N LYS h 351 " --> pdb=" O CYS h 347 " (cutoff:3.500A) Processing helix chain 'h' and resid 356 through 374 removed outlier: 3.903A pdb=" N PHE h 367 " --> pdb=" O HIS h 363 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG h 368 " --> pdb=" O ILE h 364 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU h 373 " --> pdb=" O ASN h 369 " (cutoff:3.500A) Processing helix chain 'h' and resid 375 through 382 Processing helix chain 'i' and resid 5 through 20 removed outlier: 3.660A pdb=" N LEU i 9 " --> pdb=" O SER i 5 " (cutoff:3.500A) Processing helix chain 'i' and resid 30 through 39 removed outlier: 4.059A pdb=" N VAL i 34 " --> pdb=" O SER i 30 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU i 39 " --> pdb=" O LYS i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 69 removed outlier: 3.753A pdb=" N PHE i 59 " --> pdb=" O HIS i 55 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA i 60 " --> pdb=" O ASN i 56 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU i 61 " --> pdb=" O THR i 57 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET i 62 " --> pdb=" O TYR i 58 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER i 67 " --> pdb=" O GLY i 63 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 87 removed outlier: 3.671A pdb=" N LYS i 87 " --> pdb=" O LEU i 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 62 removed outlier: 4.117A pdb=" N LYS k 61 " --> pdb=" O PRO k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 72 removed outlier: 4.063A pdb=" N VAL k 71 " --> pdb=" O ASP k 67 " (cutoff:3.500A) Processing helix chain 'k' and resid 105 through 110 removed outlier: 3.500A pdb=" N LYS k 109 " --> pdb=" O LEU k 105 " (cutoff:3.500A) Processing helix chain 'k' and resid 113 through 116 Processing helix chain 'k' and resid 117 through 125 Processing helix chain 'k' and resid 126 through 130 removed outlier: 3.639A pdb=" N LYS k 129 " --> pdb=" O GLU k 126 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP k 130 " --> pdb=" O ALA k 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 126 through 130' Processing helix chain 'k' and resid 141 through 149 removed outlier: 3.557A pdb=" N CYS k 145 " --> pdb=" O SER k 141 " (cutoff:3.500A) Processing helix chain 'k' and resid 185 through 197 removed outlier: 3.965A pdb=" N LYS k 190 " --> pdb=" O ASP k 186 " (cutoff:3.500A) Processing helix chain 'k' and resid 216 through 233 removed outlier: 3.641A pdb=" N THR k 229 " --> pdb=" O MET k 225 " (cutoff:3.500A) Processing helix chain 'k' and resid 258 through 275 removed outlier: 4.205A pdb=" N LYS k 262 " --> pdb=" O SER k 258 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN k 263 " --> pdb=" O ALA k 259 " (cutoff:3.500A) Processing helix chain 'k' and resid 282 through 288 removed outlier: 3.526A pdb=" N THR k 288 " --> pdb=" O GLU k 284 " (cutoff:3.500A) Processing helix chain 'k' and resid 289 through 303 removed outlier: 3.686A pdb=" N ASP k 293 " --> pdb=" O LYS k 289 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR k 294 " --> pdb=" O GLU k 290 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL k 299 " --> pdb=" O LYS k 295 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER k 300 " --> pdb=" O ASN k 296 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU k 301 " --> pdb=" O SER k 297 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN k 303 " --> pdb=" O VAL k 299 " (cutoff:3.500A) Processing helix chain 'k' and resid 307 through 322 removed outlier: 3.970A pdb=" N ILE k 311 " --> pdb=" O ASN k 307 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER k 312 " --> pdb=" O GLU k 308 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG k 320 " --> pdb=" O GLU k 316 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU k 322 " --> pdb=" O VAL k 318 " (cutoff:3.500A) Processing helix chain 'm' and resid 45 through 53 Processing helix chain 'm' and resid 67 through 88 Processing helix chain 'm' and resid 100 through 111 removed outlier: 3.681A pdb=" N LYS m 106 " --> pdb=" O ARG m 102 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG m 110 " --> pdb=" O LYS m 106 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE m 111 " --> pdb=" O LEU m 107 " (cutoff:3.500A) Processing helix chain 'o' and resid 69 through 78 removed outlier: 3.603A pdb=" N ALA o 73 " --> pdb=" O ALA o 69 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL o 78 " --> pdb=" O LEU o 74 " (cutoff:3.500A) Processing helix chain 'o' and resid 99 through 123 Processing helix chain 'o' and resid 124 through 129 removed outlier: 4.037A pdb=" N GLN o 129 " --> pdb=" O LYS o 126 " (cutoff:3.500A) Processing helix chain 'o' and resid 146 through 156 removed outlier: 3.535A pdb=" N UNK o 150 " --> pdb=" O UNK o 146 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N UNK o 151 " --> pdb=" O UNK o 147 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N UNK o 152 " --> pdb=" O UNK o 148 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N UNK o 153 " --> pdb=" O UNK o 149 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N UNK o 154 " --> pdb=" O UNK o 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 162 through 173 removed outlier: 3.562A pdb=" N UNK o 166 " --> pdb=" O UNK o 162 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N UNK o 167 " --> pdb=" O UNK o 163 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N UNK o 168 " --> pdb=" O UNK o 164 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N UNK o 169 " --> pdb=" O UNK o 165 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N UNK o 170 " --> pdb=" O UNK o 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N UNK o 171 " --> pdb=" O UNK o 167 " (cutoff:3.500A) Processing helix chain 'o' and resid 221 through 232 removed outlier: 3.816A pdb=" N UNK o 225 " --> pdb=" O UNK o 221 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N UNK o 226 " --> pdb=" O UNK o 222 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N UNK o 227 " --> pdb=" O UNK o 223 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N UNK o 228 " --> pdb=" O UNK o 224 " (cutoff:3.500A) Processing helix chain 'o' and resid 238 through 250 removed outlier: 3.586A pdb=" N UNK o 242 " --> pdb=" O UNK o 238 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N UNK o 243 " --> pdb=" O UNK o 239 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N UNK o 244 " --> pdb=" O UNK o 240 " (cutoff:3.500A) Processing helix chain 'o' and resid 256 through 269 removed outlier: 3.788A pdb=" N UNK o 260 " --> pdb=" O UNK o 256 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N UNK o 261 " --> pdb=" O UNK o 257 " (cutoff:3.500A) Processing helix chain 'o' and resid 273 through 285 removed outlier: 3.604A pdb=" N UNK o 277 " --> pdb=" O UNK o 273 " (cutoff:3.500A) Processing helix chain 'o' and resid 291 through 299 removed outlier: 3.534A pdb=" N UNK o 295 " --> pdb=" O UNK o 291 " (cutoff:3.500A) Processing helix chain 'o' and resid 316 through 326 removed outlier: 3.653A pdb=" N UNK o 320 " --> pdb=" O UNK o 316 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N UNK o 321 " --> pdb=" O UNK o 317 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNK o 322 " --> pdb=" O UNK o 318 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N UNK o 323 " --> pdb=" O UNK o 319 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N UNK o 324 " --> pdb=" O UNK o 320 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N UNK o 325 " --> pdb=" O UNK o 321 " (cutoff:3.500A) Processing helix chain 'o' and resid 332 through 341 removed outlier: 3.832A pdb=" N UNK o 336 " --> pdb=" O UNK o 332 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N UNK o 337 " --> pdb=" O UNK o 333 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N UNK o 338 " --> pdb=" O UNK o 334 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N UNK o 339 " --> pdb=" O UNK o 335 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK o 341 " --> pdb=" O UNK o 337 " (cutoff:3.500A) Processing helix chain 'o' and resid 354 through 362 removed outlier: 3.626A pdb=" N UNK o 358 " --> pdb=" O UNK o 354 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N UNK o 359 " --> pdb=" O UNK o 355 " (cutoff:3.500A) Processing helix chain 'o' and resid 375 through 383 removed outlier: 3.801A pdb=" N ILE o 379 " --> pdb=" O TYR o 375 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN o 380 " --> pdb=" O HIS o 376 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU o 381 " --> pdb=" O HIS o 377 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE o 382 " --> pdb=" O ILE o 378 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR o 383 " --> pdb=" O ILE o 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 375 through 383' Processing helix chain 'o' and resid 387 through 399 Processing helix chain 'o' and resid 418 through 430 removed outlier: 3.546A pdb=" N ALA o 422 " --> pdb=" O PHE o 418 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET o 423 " --> pdb=" O PHE o 419 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG o 424 " --> pdb=" O GLN o 420 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL o 425 " --> pdb=" O SER o 421 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS o 426 " --> pdb=" O ALA o 422 " (cutoff:3.500A) Processing helix chain 'o' and resid 432 through 440 removed outlier: 3.774A pdb=" N TYR o 436 " --> pdb=" O LEU o 432 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN o 437 " --> pdb=" O GLU o 433 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL o 438 " --> pdb=" O LEU o 434 " (cutoff:3.500A) Processing helix chain 'o' and resid 460 through 467 removed outlier: 3.857A pdb=" N PHE o 464 " --> pdb=" O TYR o 460 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE o 465 " --> pdb=" O TYR o 461 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU o 467 " --> pdb=" O LYS o 463 " (cutoff:3.500A) Processing helix chain 'o' and resid 468 through 471 removed outlier: 3.909A pdb=" N MET o 471 " --> pdb=" O LEU o 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 468 through 471' Processing helix chain 'o' and resid 473 through 485 removed outlier: 3.654A pdb=" N ASP o 483 " --> pdb=" O LYS o 479 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE o 485 " --> pdb=" O TYR o 481 " (cutoff:3.500A) Processing helix chain 'o' and resid 492 through 507 removed outlier: 4.405A pdb=" N LEU o 496 " --> pdb=" O HIS o 492 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE o 497 " --> pdb=" O SER o 493 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP o 498 " --> pdb=" O GLN o 494 " (cutoff:3.500A) Processing helix chain 'o' and resid 511 through 522 Processing helix chain 'o' and resid 530 through 537 Processing helix chain 'o' and resid 544 through 548 removed outlier: 3.760A pdb=" N GLN o 548 " --> pdb=" O PRO o 545 " (cutoff:3.500A) Processing helix chain 'o' and resid 549 through 560 removed outlier: 3.745A pdb=" N ASP o 553 " --> pdb=" O ALA o 549 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP o 557 " --> pdb=" O ASP o 553 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE o 558 " --> pdb=" O CYS o 554 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS o 559 " --> pdb=" O ALA o 555 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER o 560 " --> pdb=" O ALA o 556 " (cutoff:3.500A) Processing helix chain 'o' and resid 581 through 588 removed outlier: 4.249A pdb=" N LEU o 585 " --> pdb=" O TYR o 581 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE o 586 " --> pdb=" O ILE o 582 " (cutoff:3.500A) Processing helix chain 'o' and resid 592 through 602 removed outlier: 3.998A pdb=" N LYS o 597 " --> pdb=" O GLN o 593 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N MET o 598 " --> pdb=" O GLU o 594 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU o 599 " --> pdb=" O ALA o 595 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY o 600 " --> pdb=" O TRP o 596 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU o 601 " --> pdb=" O LYS o 597 " (cutoff:3.500A) Processing helix chain 'o' and resid 627 through 641 removed outlier: 3.825A pdb=" N VAL o 631 " --> pdb=" O PRO o 627 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU o 632 " --> pdb=" O ALA o 628 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL o 633 " --> pdb=" O GLN o 629 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL o 634 " --> pdb=" O ALA o 630 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER o 639 " --> pdb=" O LYS o 635 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE o 640 " --> pdb=" O LEU o 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 106 through 127 removed outlier: 3.681A pdb=" N THR B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 127 " --> pdb=" O HIS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 152 removed outlier: 3.689A pdb=" N CYS B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 195 through 204 removed outlier: 3.528A pdb=" N ARG B 199 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA B 202 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS B 203 " --> pdb=" O ARG B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 261 removed outlier: 3.705A pdb=" N ARG B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 31 Processing helix chain 'F' and resid 73 through 84 removed outlier: 3.506A pdb=" N SER F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG F 84 " --> pdb=" O GLU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 100 Processing helix chain 'K' and resid 114 through 119 Processing helix chain 'K' and resid 123 through 126 removed outlier: 3.829A pdb=" N GLY K 126 " --> pdb=" O ALA K 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 123 through 126' Processing helix chain 'K' and resid 127 through 144 removed outlier: 3.550A pdb=" N ALA K 131 " --> pdb=" O THR K 127 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY K 144 " --> pdb=" O ALA K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 171 removed outlier: 3.573A pdb=" N ILE K 165 " --> pdb=" O ARG K 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 76 removed outlier: 4.172A pdb=" N GLN O 76 " --> pdb=" O LYS O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 92 Processing helix chain 'O' and resid 93 through 97 Processing helix chain 'O' and resid 98 through 112 removed outlier: 3.911A pdb=" N MET O 102 " --> pdb=" O ASN O 98 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER O 112 " --> pdb=" O GLU O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 145 removed outlier: 3.923A pdb=" N GLN O 127 " --> pdb=" O SER O 123 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE O 128 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL O 129 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 171 removed outlier: 3.590A pdb=" N LYS O 152 " --> pdb=" O ASP O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 184 Processing helix chain 'O' and resid 199 through 235 removed outlier: 3.518A pdb=" N ALA O 229 " --> pdb=" O ALA O 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 82 Processing helix chain 'R' and resid 83 through 85 No H-bonds generated for 'chain 'R' and resid 83 through 85' Processing helix chain 'R' and resid 94 through 99 Processing helix chain 'R' and resid 101 through 118 removed outlier: 4.465A pdb=" N ARG R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 131 Processing helix chain 'U' and resid 19 through 34 Processing helix chain 'U' and resid 35 through 44 removed outlier: 4.172A pdb=" N TYR U 44 " --> pdb=" O LYS U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 75 removed outlier: 3.549A pdb=" N GLN U 53 " --> pdb=" O CYS U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 4.116A pdb=" N ARG U 80 " --> pdb=" O ARG U 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 22 removed outlier: 3.536A pdb=" N ALA b 22 " --> pdb=" O ASP b 18 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 38 removed outlier: 3.776A pdb=" N VAL b 34 " --> pdb=" O LEU b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 66 through 79 removed outlier: 3.972A pdb=" N ILE b 70 " --> pdb=" O HIS b 66 " (cutoff:3.500A) Processing helix chain 'b' and resid 94 through 110 removed outlier: 3.933A pdb=" N GLY b 110 " --> pdb=" O LEU b 106 " (cutoff:3.500A) Processing helix chain 'b' and resid 113 through 127 Processing helix chain 'f' and resid 80 through 87 removed outlier: 3.808A pdb=" N ARG f 86 " --> pdb=" O ALA f 82 " (cutoff:3.500A) Processing helix chain 'f' and resid 88 through 94 Processing helix chain 'n' and resid 129 through 150 removed outlier: 4.429A pdb=" N ARG n 134 " --> pdb=" O VAL n 130 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG n 135 " --> pdb=" O LEU n 131 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 181 Processing helix chain 'z' and resid 101 through 113 removed outlier: 3.833A pdb=" N VAL z 105 " --> pdb=" O HIS z 101 " (cutoff:3.500A) Processing helix chain 'z' and resid 132 through 150 Processing helix chain 'z' and resid 169 through 184 Processing helix chain 'z' and resid 202 through 216 Processing helix chain 'z' and resid 246 through 263 removed outlier: 4.054A pdb=" N ALA z 250 " --> pdb=" O ASN z 246 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 110 through 112 removed outlier: 6.936A pdb=" N VAL C 117 " --> pdb=" O ARG C 152 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N HIS C 154 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE C 119 " --> pdb=" O HIS C 154 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N GLN C 156 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA C 121 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N VAL C 158 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 123 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 221 through 228 removed outlier: 5.413A pdb=" N ILE E 222 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA E 246 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA E 261 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 253 through 254 Processing sheet with id=AA4, first strand: chain 'E' and resid 294 through 295 Processing sheet with id=AA5, first strand: chain 'E' and resid 301 through 302 removed outlier: 3.619A pdb=" N SER E 337 " --> pdb=" O HIS E 302 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 382 through 385 removed outlier: 3.695A pdb=" N VAL E 384 " --> pdb=" O VAL E 370 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL E 370 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL E 371 " --> pdb=" O LYS a 103 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS a 103 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR a 101 " --> pdb=" O PHE E 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 57 through 68 removed outlier: 4.045A pdb=" N ARG L 64 " --> pdb=" O ARG L 82 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS L 81 " --> pdb=" O CYS L 93 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE L 94 " --> pdb=" O VAL L 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 18 through 19 Processing sheet with id=AA9, first strand: chain 'P' and resid 52 through 54 removed outlier: 3.532A pdb=" N SER P 53 " --> pdb=" O ALA P 67 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR a 179 " --> pdb=" O GLU a 175 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA a 142 " --> pdb=" O LEU a 180 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS a 182 " --> pdb=" O VAL a 140 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL a 140 " --> pdb=" O LYS a 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 12 through 14 removed outlier: 7.390A pdb=" N ILE Q 63 " --> pdb=" O ILE Q 84 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE Q 84 " --> pdb=" O ILE Q 63 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU Q 65 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 16 through 19 removed outlier: 6.648A pdb=" N LYS Q 27 " --> pdb=" O ILE Q 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 92 through 93 Processing sheet with id=AB4, first strand: chain 'c' and resid 63 through 68 removed outlier: 3.744A pdb=" N VAL c 29 " --> pdb=" O TYR c 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN c 33 " --> pdb=" O PHE c 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 190 through 191 removed outlier: 3.538A pdb=" N ALA d 190 " --> pdb=" O VAL d 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 42 through 43 Processing sheet with id=AB7, first strand: chain 'j' and resid 123 through 130 removed outlier: 3.641A pdb=" N LEU j 118 " --> pdb=" O GLU j 125 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU j 127 " --> pdb=" O GLY j 116 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLY j 116 " --> pdb=" O GLU j 127 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ARG j 129 " --> pdb=" O ALA j 114 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA j 114 " --> pdb=" O ARG j 129 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG j 99 " --> pdb=" O TRP j 115 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE j 117 " --> pdb=" O LEU j 97 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU j 97 " --> pdb=" O ILE j 117 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR j 119 " --> pdb=" O TRP j 95 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N TRP j 95 " --> pdb=" O THR j 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 156 through 162 removed outlier: 3.535A pdb=" N TYR G 168 " --> pdb=" O ILE G 161 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 260 through 261 removed outlier: 3.664A pdb=" N ASP I 327 " --> pdb=" O TYR I 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 260 through 261 removed outlier: 3.709A pdb=" N ASN I 280 " --> pdb=" O SER I 333 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 333 " --> pdb=" O ASN I 280 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 294 through 295 Processing sheet with id=AC3, first strand: chain 'J' and resid 143 through 149 removed outlier: 6.599A pdb=" N GLU J 144 " --> pdb=" O SER J 77 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER J 77 " --> pdb=" O GLU J 144 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU J 146 " --> pdb=" O ARG J 75 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG J 75 " --> pdb=" O GLU J 146 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR J 73 " --> pdb=" O LEU J 177 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU J 177 " --> pdb=" O TYR J 73 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG J 75 " --> pdb=" O THR J 175 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR J 175 " --> pdb=" O ARG J 75 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET J 170 " --> pdb=" O ILE k 159 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU J 178 " --> pdb=" O ILE k 151 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU k 152 " --> pdb=" O ARG k 176 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG k 176 " --> pdb=" O GLU k 152 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR k 174 " --> pdb=" O ASP k 154 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 81 through 82 Processing sheet with id=AC5, first strand: chain 'J' and resid 118 through 121 removed outlier: 3.840A pdb=" N PHE J 118 " --> pdb=" O TYR J 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR J 134 " --> pdb=" O PHE J 118 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN N 124 " --> pdb=" O GLU J 135 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 66 through 68 removed outlier: 3.817A pdb=" N LEU g 98 " --> pdb=" O TYR g 67 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 150 through 154 removed outlier: 7.053A pdb=" N LEU g 257 " --> pdb=" O ALA g 304 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL g 306 " --> pdb=" O LEU g 257 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL g 259 " --> pdb=" O VAL g 306 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR g 308 " --> pdb=" O VAL g 259 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL g 261 " --> pdb=" O THR g 308 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL g 121 " --> pdb=" O ILE g 305 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU g 307 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR g 123 " --> pdb=" O LEU g 307 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARG g 122 " --> pdb=" O ILE g 340 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE g 342 " --> pdb=" O ARG g 122 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL g 124 " --> pdb=" O ILE g 342 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'g' and resid 168 through 170 Processing sheet with id=AC9, first strand: chain 'g' and resid 207 through 208 removed outlier: 3.942A pdb=" N TYR g 207 " --> pdb=" O THR g 215 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR g 215 " --> pdb=" O TYR g 207 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.871A pdb=" N ILE B 104 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER B 98 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLN B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 154 through 156 removed outlier: 6.312A pdb=" N ILE B 131 " --> pdb=" O TYR B 154 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N HIS B 156 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE B 133 " --> pdb=" O HIS B 156 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU B 132 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 182 " --> pdb=" O VAL B 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 35 through 52 removed outlier: 6.774A pdb=" N ASP F 67 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU F 39 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU F 65 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASN F 41 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N TYR F 63 " --> pdb=" O ASN F 41 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLY F 43 " --> pdb=" O GLY F 61 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY F 61 " --> pdb=" O GLY F 43 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ARG F 45 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR F 59 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 10.698A pdb=" N LEU F 47 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 13.025A pdb=" N ARG F 57 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE F 68 " --> pdb=" O TYR F 4 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR F 4 " --> pdb=" O PHE F 68 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 98 through 103 removed outlier: 6.813A pdb=" N ALA K 89 " --> pdb=" O VAL K 153 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 177 through 179 Processing sheet with id=AD6, first strand: chain 'f' and resid 123 through 126 removed outlier: 7.465A pdb=" N ASP f 112 " --> pdb=" O ILE f 108 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE f 108 " --> pdb=" O ASP f 112 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR f 114 " --> pdb=" O PHE f 106 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLU f 167 " --> pdb=" O LEU f 146 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'f' and resid 123 through 126 removed outlier: 7.465A pdb=" N ASP f 112 " --> pdb=" O ILE f 108 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE f 108 " --> pdb=" O ASP f 112 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR f 114 " --> pdb=" O PHE f 106 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY f 172 " --> pdb=" O ARG f 142 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'f' and resid 151 through 152 removed outlier: 4.173A pdb=" N SER f 152 " --> pdb=" O THR f 161 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR f 161 " --> pdb=" O SER f 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'z' and resid 88 through 90 removed outlier: 6.313A pdb=" N HIS z 88 " --> pdb=" O TYR z 128 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N LEU z 130 " --> pdb=" O HIS z 88 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N PHE z 90 " --> pdb=" O LEU z 130 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU z 127 " --> pdb=" O ARG z 119 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'z' and resid 159 through 164 removed outlier: 3.686A pdb=" N VAL z 189 " --> pdb=" O LEU z 240 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL z 239 " --> pdb=" O SER z 224 " (cutoff:3.500A) 1847 hydrogen bonds defined for protein. 5331 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 571 hydrogen bonds 1006 hydrogen bond angles 0 basepair planarities 232 basepair parallelities 391 stacking parallelities Total time for adding SS restraints: 28.21 Time building geometry restraints manager: 25.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 17445 1.34 - 1.45: 16738 1.45 - 1.57: 32733 1.57 - 1.69: 1903 1.69 - 1.81: 342 Bond restraints: 69161 Sorted by residual: bond pdb=" N MET F 1 " pdb=" CA MET F 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" N MET U 1 " pdb=" CA MET U 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 bond pdb=" N MET Q 1 " pdb=" CA MET Q 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N MET m 1 " pdb=" CA MET m 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N MET j 1 " pdb=" CA MET j 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 ... (remaining 69156 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.14: 7110 107.14 - 113.85: 40330 113.85 - 120.56: 26319 120.56 - 127.27: 21664 127.27 - 133.98: 2540 Bond angle restraints: 97963 Sorted by residual: angle pdb=" N ILE p 107 " pdb=" CA ILE p 107 " pdb=" C ILE p 107 " ideal model delta sigma weight residual 111.81 108.96 2.85 8.60e-01 1.35e+00 1.10e+01 angle pdb=" N LYS R 104 " pdb=" CA LYS R 104 " pdb=" C LYS R 104 " ideal model delta sigma weight residual 114.62 111.06 3.56 1.14e+00 7.69e-01 9.74e+00 angle pdb=" C LYS j 5 " pdb=" N VAL j 6 " pdb=" CA VAL j 6 " ideal model delta sigma weight residual 121.70 127.22 -5.52 1.80e+00 3.09e-01 9.41e+00 angle pdb=" N VAL k 64 " pdb=" CA VAL k 64 " pdb=" C VAL k 64 " ideal model delta sigma weight residual 111.81 109.31 2.50 8.60e-01 1.35e+00 8.43e+00 angle pdb=" N VAL B 191 " pdb=" CA VAL B 191 " pdb=" C VAL B 191 " ideal model delta sigma weight residual 111.91 109.41 2.50 8.90e-01 1.26e+00 7.91e+00 ... (remaining 97958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 40001 35.40 - 70.79: 1627 70.79 - 106.19: 273 106.19 - 141.58: 10 141.58 - 176.98: 4 Dihedral angle restraints: 41915 sinusoidal: 25382 harmonic: 16533 Sorted by residual: dihedral pdb=" O4' C A 499 " pdb=" C1' C A 499 " pdb=" N1 C A 499 " pdb=" C2 C A 499 " ideal model delta sinusoidal sigma weight residual -128.00 48.98 -176.98 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A 620 " pdb=" C1' U A 620 " pdb=" N1 U A 620 " pdb=" C2 U A 620 " ideal model delta sinusoidal sigma weight residual -128.00 32.51 -160.51 1 1.70e+01 3.46e-03 6.45e+01 dihedral pdb=" O4' U A 881 " pdb=" C1' U A 881 " pdb=" N1 U A 881 " pdb=" C2 U A 881 " ideal model delta sinusoidal sigma weight residual -128.00 -21.32 -106.68 1 1.70e+01 3.46e-03 4.28e+01 ... (remaining 41912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 8597 0.028 - 0.057: 2209 0.057 - 0.085: 394 0.085 - 0.114: 296 0.114 - 0.142: 48 Chirality restraints: 11544 Sorted by residual: chirality pdb=" CA ILE g 340 " pdb=" N ILE g 340 " pdb=" C ILE g 340 " pdb=" CB ILE g 340 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE K 69 " pdb=" N ILE K 69 " pdb=" C ILE K 69 " pdb=" CB ILE K 69 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE g 208 " pdb=" N ILE g 208 " pdb=" C ILE g 208 " pdb=" CB ILE g 208 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 11541 not shown) Planarity restraints: 9033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER e 269 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO e 270 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO e 270 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO e 270 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G A 683 " -0.009 2.00e-02 2.50e+03 7.69e-03 1.78e+00 pdb=" N9 G A 683 " 0.008 2.00e-02 2.50e+03 pdb=" C8 G A 683 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G A 683 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 683 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 683 " -0.017 2.00e-02 2.50e+03 pdb=" O6 G A 683 " 0.005 2.00e-02 2.50e+03 pdb=" N1 G A 683 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 683 " -0.011 2.00e-02 2.50e+03 pdb=" N2 G A 683 " 0.010 2.00e-02 2.50e+03 pdb=" N3 G A 683 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G A 683 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 946 " 0.017 2.00e-02 2.50e+03 8.55e-03 1.64e+00 pdb=" N1 U A 946 " -0.016 2.00e-02 2.50e+03 pdb=" C2 U A 946 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U A 946 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U A 946 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U A 946 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U A 946 " 0.008 2.00e-02 2.50e+03 pdb=" C5 U A 946 " -0.004 2.00e-02 2.50e+03 pdb=" C6 U A 946 " -0.002 2.00e-02 2.50e+03 ... (remaining 9030 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 434 2.54 - 3.13: 48818 3.13 - 3.72: 105272 3.72 - 4.31: 145505 4.31 - 4.90: 225793 Nonbonded interactions: 525822 Sorted by model distance: nonbonded pdb=" O2' C A 580 " pdb=" OP1 U A 581 " model vdw 1.949 2.440 nonbonded pdb=" O TYR e 157 " pdb=" OH TYR e 184 " model vdw 1.983 2.440 nonbonded pdb=" O2' G A 242 " pdb=" O2' C A 257 " model vdw 2.024 2.440 nonbonded pdb=" OH TYR G 37 " pdb=" OD1 ASP I 373 " model vdw 2.031 2.440 nonbonded pdb=" O2' A A 865 " pdb=" O4' G A 866 " model vdw 2.032 2.440 ... (remaining 525817 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 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: 0.060 Extract box with map and model: 15.370 Check model and map are aligned: 0.740 Set scattering table: 0.510 Process input model: 150.090 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.220 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5134 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 : 0.001 0.037 69161 Z= 0.096 Angle : 0.371 5.523 97963 Z= 0.209 Chirality : 0.029 0.142 11544 Planarity : 0.002 0.043 9033 Dihedral : 16.684 176.977 31179 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 1.60 % Allowed : 10.28 % Favored : 88.12 % Rotamer: Outliers : 0.35 % Allowed : 3.03 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.11), residues: 5437 helix: -0.07 (0.10), residues: 2279 sheet: -3.11 (0.22), residues: 413 loop : -2.81 (0.11), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP e 107 HIS 0.003 0.000 HIS e 97 PHE 0.019 0.000 PHE G 123 TYR 0.005 0.000 TYR G 64 ARG 0.002 0.000 ARG I 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1912 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1895 time to evaluate : 4.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: C 95 PHE cc_start: 0.6212 (t80) cc_final: 0.5980 (t80) REVERT: E 294 ILE cc_start: 0.7996 (mt) cc_final: 0.7627 (mt) REVERT: E 377 CYS cc_start: 0.6994 (m) cc_final: 0.6786 (m) REVERT: Q 1 MET cc_start: 0.1185 (mmm) cc_final: -0.1110 (pmm) REVERT: Q 96 THR cc_start: 0.7398 (p) cc_final: 0.6703 (m) REVERT: a 231 VAL cc_start: 0.6685 (t) cc_final: 0.6391 (p) REVERT: a 272 TRP cc_start: 0.6426 (t60) cc_final: 0.5861 (t60) REVERT: a 274 PHE cc_start: 0.6817 (m-10) cc_final: 0.6496 (m-80) REVERT: d 66 THR cc_start: 0.6844 (m) cc_final: 0.6245 (p) REVERT: e 75 PHE cc_start: 0.7445 (t80) cc_final: 0.6837 (t80) REVERT: e 203 ASN cc_start: 0.6733 (m-40) cc_final: 0.5987 (m-40) REVERT: j 95 TRP cc_start: 0.6151 (t-100) cc_final: 0.5918 (t-100) REVERT: j 134 VAL cc_start: 0.4006 (t) cc_final: 0.3628 (p) REVERT: p 146 GLN cc_start: 0.6697 (mm-40) cc_final: 0.6328 (mt0) REVERT: p 167 ILE cc_start: 0.6839 (mt) cc_final: 0.6093 (mt) REVERT: G 58 LEU cc_start: 0.7576 (tt) cc_final: 0.7245 (pp) REVERT: G 61 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7189 (mt-10) REVERT: G 66 ARG cc_start: 0.6313 (ttm110) cc_final: 0.6023 (ttm170) REVERT: G 94 PHE cc_start: 0.7066 (t80) cc_final: 0.6839 (t80) REVERT: G 220 ILE cc_start: 0.8422 (mm) cc_final: 0.8006 (pt) REVERT: G 226 MET cc_start: 0.7668 (tpp) cc_final: 0.7374 (tmm) REVERT: I 201 ILE cc_start: 0.8163 (tt) cc_final: 0.7915 (tp) REVERT: J 62 THR cc_start: 0.5791 (p) cc_final: 0.5534 (p) REVERT: J 69 PRO cc_start: 0.7572 (Cg_endo) cc_final: 0.7047 (Cg_exo) REVERT: J 77 SER cc_start: 0.8476 (m) cc_final: 0.8242 (t) REVERT: J 127 PHE cc_start: 0.5198 (m-10) cc_final: 0.4437 (m-10) REVERT: J 138 THR cc_start: 0.7797 (m) cc_final: 0.7507 (p) REVERT: N 42 LYS cc_start: 0.8731 (mttt) cc_final: 0.8241 (mtpt) REVERT: N 60 ASN cc_start: 0.5767 (m-40) cc_final: 0.4796 (t0) REVERT: N 66 HIS cc_start: 0.8224 (t-90) cc_final: 0.7805 (t-170) REVERT: N 72 ASP cc_start: 0.7172 (t70) cc_final: 0.6808 (t70) REVERT: N 73 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8385 (pp20) REVERT: g 179 GLN cc_start: 0.6648 (tp-100) cc_final: 0.6418 (tp-100) REVERT: g 367 HIS cc_start: 0.4927 (OUTLIER) cc_final: 0.4293 (t70) REVERT: h 287 ASN cc_start: 0.5425 (m-40) cc_final: 0.4843 (m-40) REVERT: h 294 GLN cc_start: 0.8712 (mm110) cc_final: 0.8217 (tt0) REVERT: h 323 ILE cc_start: 0.6571 (mt) cc_final: 0.5839 (mm) REVERT: h 342 MET cc_start: 0.6668 (mmm) cc_final: 0.6289 (mmp) REVERT: h 364 ILE cc_start: 0.7736 (mt) cc_final: 0.7476 (pt) REVERT: h 377 ILE cc_start: 0.7844 (mt) cc_final: 0.6675 (mt) REVERT: m 53 MET cc_start: 0.7938 (mmp) cc_final: 0.6779 (mtp) REVERT: m 100 PRO cc_start: 0.7088 (Cg_exo) cc_final: 0.6849 (Cg_endo) REVERT: B 51 ILE cc_start: 0.8670 (tt) cc_final: 0.8379 (mp) REVERT: B 130 ILE cc_start: 0.7396 (mt) cc_final: 0.7045 (mp) REVERT: K 136 ILE cc_start: 0.8884 (mt) cc_final: 0.7973 (mt) REVERT: O 161 LYS cc_start: 0.7698 (mttt) cc_final: 0.6991 (mmtm) REVERT: R 116 GLN cc_start: 0.7496 (mt0) cc_final: 0.7265 (mt0) REVERT: b 58 SER cc_start: 0.6486 (p) cc_final: 0.6115 (p) outliers start: 17 outliers final: 2 residues processed: 1910 average time/residue: 0.7114 time to fit residues: 2172.8292 Evaluate side-chains 971 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 968 time to evaluate : 4.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 97 HIS Chi-restraints excluded: chain e residue 123 ASP Chi-restraints excluded: chain g residue 367 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 504 optimal weight: 5.9990 chunk 452 optimal weight: 8.9990 chunk 251 optimal weight: 0.0870 chunk 154 optimal weight: 0.5980 chunk 305 optimal weight: 4.9990 chunk 241 optimal weight: 9.9990 chunk 467 optimal weight: 0.4980 chunk 181 optimal weight: 5.9990 chunk 284 optimal weight: 0.9980 chunk 348 optimal weight: 10.0000 chunk 542 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 HIS L 106 HIS P 16 HIS ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 133 GLN ** d 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 100 ASN j 66 GLN p 68 ASN G 103 ASN G 146 HIS G 147 GLN G 151 ASN G 224 HIS I 127 HIS I 366 GLN ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 55 ASN g 163 ASN h 294 GLN h 322 HIS h 359 GLN ** i 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN B 123 HIS B 139 GLN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 HIS ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 163 GLN O 222 GLN U 79 ASN f 92 GLN f 107 HIS z 211 HIS z 212 GLN z 215 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5519 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 69161 Z= 0.183 Angle : 0.585 12.098 97963 Z= 0.288 Chirality : 0.034 0.279 11544 Planarity : 0.005 0.073 9033 Dihedral : 18.203 179.296 19570 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.92 % Favored : 93.88 % Rotamer: Outliers : 3.26 % Allowed : 14.86 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.11), residues: 5437 helix: 0.68 (0.11), residues: 2334 sheet: -2.50 (0.22), residues: 430 loop : -2.34 (0.11), residues: 2673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP e 198 HIS 0.013 0.001 HIS z 211 PHE 0.021 0.002 PHE f 117 TYR 0.047 0.002 TYR e 228 ARG 0.012 0.001 ARG R 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1071 time to evaluate : 4.506 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: E 245 VAL cc_start: 0.8003 (t) cc_final: 0.7744 (p) REVERT: E 298 PHE cc_start: 0.6026 (t80) cc_final: 0.5738 (t80) REVERT: P 29 ARG cc_start: 0.4647 (tpt90) cc_final: 0.3934 (tmm160) REVERT: Q 1 MET cc_start: 0.1495 (mmm) cc_final: -0.0882 (pmm) REVERT: a 274 PHE cc_start: 0.6887 (m-10) cc_final: 0.6646 (m-80) REVERT: c 99 MET cc_start: 0.7339 (tpp) cc_final: 0.6995 (tpt) REVERT: c 114 ARG cc_start: 0.7009 (ptp-110) cc_final: 0.6780 (ptp-170) REVERT: d 81 LYS cc_start: 0.8288 (mmtm) cc_final: 0.7991 (mmtm) REVERT: d 188 ASN cc_start: 0.6796 (t0) cc_final: 0.6160 (t0) REVERT: e 75 PHE cc_start: 0.7318 (t80) cc_final: 0.6770 (t80) REVERT: e 209 LEU cc_start: 0.4373 (OUTLIER) cc_final: 0.4130 (mm) REVERT: e 235 GLU cc_start: 0.6278 (tt0) cc_final: 0.5725 (tp30) REVERT: e 397 MET cc_start: 0.4081 (mtt) cc_final: 0.3331 (ttt) REVERT: j 190 MET cc_start: 0.8228 (mmt) cc_final: 0.7846 (mmt) REVERT: p 146 GLN cc_start: 0.6761 (mm-40) cc_final: 0.6291 (mt0) REVERT: p 167 ILE cc_start: 0.7018 (mt) cc_final: 0.6807 (mt) REVERT: G 58 LEU cc_start: 0.7497 (tt) cc_final: 0.7252 (pp) REVERT: G 81 LYS cc_start: 0.6822 (mmmt) cc_final: 0.6022 (tttp) REVERT: G 98 MET cc_start: 0.8187 (mtm) cc_final: 0.7616 (mtp) REVERT: G 113 GLN cc_start: 0.9009 (mt0) cc_final: 0.8738 (mt0) REVERT: G 184 MET cc_start: 0.7150 (mtt) cc_final: 0.6856 (mtt) REVERT: G 201 MET cc_start: 0.8558 (tpp) cc_final: 0.8014 (tpp) REVERT: G 226 MET cc_start: 0.7682 (tpp) cc_final: 0.7289 (tmm) REVERT: I 79 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7709 (pp20) REVERT: I 344 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8286 (mm) REVERT: J 91 TYR cc_start: 0.7255 (t80) cc_final: 0.6970 (t80) REVERT: N 42 LYS cc_start: 0.8787 (mttt) cc_final: 0.8360 (mtpt) REVERT: N 66 HIS cc_start: 0.8193 (t-90) cc_final: 0.7573 (t-170) REVERT: N 72 ASP cc_start: 0.7349 (t70) cc_final: 0.6853 (t0) REVERT: g 217 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8595 (tmtt) REVERT: m 53 MET cc_start: 0.8045 (mmp) cc_final: 0.6883 (mtp) REVERT: o 593 GLN cc_start: 0.4731 (OUTLIER) cc_final: 0.3777 (mp10) REVERT: B 251 GLU cc_start: 0.7690 (tp30) cc_final: 0.7177 (tp30) REVERT: F 79 MET cc_start: 0.8382 (mmm) cc_final: 0.8166 (mmm) REVERT: O 194 TYR cc_start: 0.6414 (m-80) cc_final: 0.6120 (m-80) REVERT: R 116 GLN cc_start: 0.8021 (mt0) cc_final: 0.7742 (mt0) REVERT: b 113 ASP cc_start: 0.5251 (t0) cc_final: 0.4928 (t70) REVERT: f 173 LEU cc_start: 0.8226 (pt) cc_final: 0.7910 (pt) REVERT: z 147 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7050 (tt0) outliers start: 157 outliers final: 79 residues processed: 1159 average time/residue: 0.6356 time to fit residues: 1235.9255 Evaluate side-chains 915 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 831 time to evaluate : 4.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain P residue 19 ILE Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain Q residue 13 ILE Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 118 ILE Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 177 SER Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 167 LEU Chi-restraints excluded: chain e residue 123 ASP Chi-restraints excluded: chain e residue 143 THR Chi-restraints excluded: chain e residue 209 LEU Chi-restraints excluded: chain e residue 265 LYS Chi-restraints excluded: chain j residue 104 TYR Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain p residue 115 VAL Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 339 SER Chi-restraints excluded: chain I residue 344 ILE Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain g residue 217 LYS Chi-restraints excluded: chain g residue 333 PHE Chi-restraints excluded: chain i residue 38 SER Chi-restraints excluded: chain i residue 62 MET Chi-restraints excluded: chain k residue 115 HIS Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 159 ILE Chi-restraints excluded: chain k residue 209 ILE Chi-restraints excluded: chain k residue 252 GLU Chi-restraints excluded: chain m residue 3 THR Chi-restraints excluded: chain m residue 27 LEU Chi-restraints excluded: chain m residue 79 ARG Chi-restraints excluded: chain m residue 89 ILE Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain o residue 107 LEU Chi-restraints excluded: chain o residue 119 PHE Chi-restraints excluded: chain o residue 426 CYS Chi-restraints excluded: chain o residue 593 GLN Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain K residue 184 ILE Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 87 VAL Chi-restraints excluded: chain O residue 137 SER Chi-restraints excluded: chain O residue 163 GLN Chi-restraints excluded: chain O residue 181 CYS Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 212 VAL Chi-restraints excluded: chain R residue 101 CYS Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain b residue 96 CYS Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain n residue 149 ARG Chi-restraints excluded: chain z residue 146 MET Chi-restraints excluded: chain z residue 170 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 301 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 451 optimal weight: 8.9990 chunk 369 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 543 optimal weight: 3.9990 chunk 586 optimal weight: 0.0000 chunk 483 optimal weight: 6.9990 chunk 538 optimal weight: 0.1980 chunk 185 optimal weight: 4.9990 chunk 435 optimal weight: 2.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 HIS C 116 GLN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 GLN E 341 ASN E 351 GLN ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 HIS ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 336 GLN a 346 GLN c 18 GLN c 101 HIS ** c 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 83 HIS ** d 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 179 GLN e 245 HIS j 88 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 215 ASN G 227 HIS ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 320 HIS ** h 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 313 GLN o 492 HIS B 102 GLN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 HIS K 99 GLN K 149 HIS O 77 ASN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 107 HIS z 178 GLN z 211 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 69161 Z= 0.252 Angle : 0.645 16.847 97963 Z= 0.324 Chirality : 0.037 0.396 11544 Planarity : 0.006 0.111 9033 Dihedral : 18.328 175.148 19566 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.58 % Favored : 93.27 % Rotamer: Outliers : 3.92 % Allowed : 16.35 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.11), residues: 5437 helix: 0.87 (0.11), residues: 2393 sheet: -1.86 (0.23), residues: 444 loop : -2.03 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP G 242 HIS 0.014 0.002 HIS J 183 PHE 0.032 0.002 PHE m 73 TYR 0.030 0.002 TYR e 228 ARG 0.025 0.001 ARG i 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 995 time to evaluate : 4.587 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: E 174 GLN cc_start: 0.7840 (tp-100) cc_final: 0.7216 (pt0) REVERT: E 351 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: E 364 ASP cc_start: 0.8375 (m-30) cc_final: 0.7942 (m-30) REVERT: E 388 GLN cc_start: 0.7573 (pm20) cc_final: 0.7297 (pm20) REVERT: P 102 MET cc_start: 0.4936 (tpp) cc_final: 0.4143 (tpp) REVERT: P 106 ASN cc_start: 0.7524 (m-40) cc_final: 0.6576 (m110) REVERT: Q 1 MET cc_start: 0.1826 (mmm) cc_final: -0.0875 (pmm) REVERT: a 274 PHE cc_start: 0.7610 (m-10) cc_final: 0.5381 (m-80) REVERT: a 319 GLN cc_start: 0.8472 (tt0) cc_final: 0.8001 (mt0) REVERT: c 14 GLN cc_start: 0.8337 (tp40) cc_final: 0.8006 (tm-30) REVERT: c 99 MET cc_start: 0.8024 (tpp) cc_final: 0.7702 (tpt) REVERT: e 75 PHE cc_start: 0.7383 (t80) cc_final: 0.6968 (t80) REVERT: e 348 VAL cc_start: 0.4626 (OUTLIER) cc_final: 0.4291 (m) REVERT: e 397 MET cc_start: 0.4478 (mtt) cc_final: 0.4115 (ttt) REVERT: j 113 LYS cc_start: 0.8014 (ptpp) cc_final: 0.7801 (ptpt) REVERT: j 135 MET cc_start: 0.7229 (mpp) cc_final: 0.7001 (mtm) REVERT: j 190 MET cc_start: 0.8507 (mmt) cc_final: 0.8281 (mmt) REVERT: G 65 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7461 (pt0) REVERT: G 74 ILE cc_start: 0.5342 (mm) cc_final: 0.5005 (mm) REVERT: G 226 MET cc_start: 0.7807 (tpp) cc_final: 0.7383 (tmm) REVERT: I 79 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7699 (pp20) REVERT: I 162 MET cc_start: 0.7808 (ttm) cc_final: 0.7474 (ttm) REVERT: I 273 GLN cc_start: 0.7731 (pt0) cc_final: 0.7111 (tt0) REVERT: N 42 LYS cc_start: 0.8791 (mttt) cc_final: 0.8334 (mtpt) REVERT: N 50 GLU cc_start: 0.8704 (mp0) cc_final: 0.8131 (pm20) REVERT: N 66 HIS cc_start: 0.8284 (t-90) cc_final: 0.7835 (t-170) REVERT: N 69 GLU cc_start: 0.8209 (tp30) cc_final: 0.6668 (tp30) REVERT: N 72 ASP cc_start: 0.7700 (t70) cc_final: 0.7387 (t70) REVERT: g 179 GLN cc_start: 0.6572 (tp-100) cc_final: 0.6240 (tp-100) REVERT: g 217 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8750 (pptt) REVERT: h 309 GLU cc_start: 0.5266 (tm-30) cc_final: 0.5006 (tm-30) REVERT: h 313 ASP cc_start: 0.7057 (p0) cc_final: 0.6672 (p0) REVERT: m 53 MET cc_start: 0.7695 (mmp) cc_final: 0.6031 (mtp) REVERT: B 63 ASN cc_start: 0.7692 (t0) cc_final: 0.7456 (t0) REVERT: F 120 THR cc_start: 0.8362 (m) cc_final: 0.8140 (m) REVERT: K 75 SER cc_start: 0.8042 (m) cc_final: 0.7814 (p) REVERT: O 181 CYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7840 (m) REVERT: R 116 GLN cc_start: 0.8782 (mt0) cc_final: 0.8520 (mt0) REVERT: z 147 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7184 (tt0) REVERT: z 231 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6876 (pm20) outliers start: 189 outliers final: 94 residues processed: 1106 average time/residue: 0.6316 time to fit residues: 1183.6903 Evaluate side-chains 880 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 781 time to evaluate : 5.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 87 VAL Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 23 PHE Chi-restraints excluded: chain c residue 25 ASP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 71 THR Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain c residue 167 LEU Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 66 THR Chi-restraints excluded: chain e residue 141 ASN Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain e residue 348 VAL Chi-restraints excluded: chain j residue 60 ARG Chi-restraints excluded: chain j residue 68 LEU Chi-restraints excluded: chain j residue 104 TYR Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain j residue 173 MET Chi-restraints excluded: chain j residue 205 GLU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 156 GLN Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 301 LEU Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 339 SER Chi-restraints excluded: chain I residue 344 ILE Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 161 VAL Chi-restraints excluded: chain g residue 217 LYS Chi-restraints excluded: chain g residue 236 THR Chi-restraints excluded: chain h residue 338 ILE Chi-restraints excluded: chain i residue 56 ASN Chi-restraints excluded: chain i residue 62 MET Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 159 ILE Chi-restraints excluded: chain k residue 209 ILE Chi-restraints excluded: chain m residue 37 ARG Chi-restraints excluded: chain m residue 89 ILE Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain o residue 141 MET Chi-restraints excluded: chain o residue 426 CYS Chi-restraints excluded: chain o residue 497 ILE Chi-restraints excluded: chain o residue 580 ASN Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 87 VAL Chi-restraints excluded: chain O residue 112 SER Chi-restraints excluded: chain O residue 163 GLN Chi-restraints excluded: chain O residue 181 CYS Chi-restraints excluded: chain O residue 212 VAL Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 83 GLN Chi-restraints excluded: chain R residue 101 CYS Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain b residue 96 CYS Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 113 LEU Chi-restraints excluded: chain n residue 149 ARG Chi-restraints excluded: chain n residue 194 ILE Chi-restraints excluded: chain z residue 231 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 536 optimal weight: 2.9990 chunk 408 optimal weight: 8.9990 chunk 281 optimal weight: 6.9990 chunk 60 optimal weight: 40.0000 chunk 259 optimal weight: 4.9990 chunk 364 optimal weight: 2.9990 chunk 545 optimal weight: 0.5980 chunk 577 optimal weight: 40.0000 chunk 284 optimal weight: 4.9990 chunk 516 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 341 ASN ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 HIS a 116 GLN c 54 GLN c 59 ASN ** c 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN j 88 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS J 183 HIS ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 HIS g 325 GLN h 307 ASN ** h 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 167 ASN k 263 ASN B 255 GLN O 77 ASN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 215 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.6720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 69161 Z= 0.232 Angle : 0.590 13.369 97963 Z= 0.295 Chirality : 0.036 0.289 11544 Planarity : 0.005 0.063 9033 Dihedral : 18.339 177.506 19564 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.89 % Favored : 95.00 % Rotamer: Outliers : 3.78 % Allowed : 18.47 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.11), residues: 5437 helix: 1.02 (0.11), residues: 2395 sheet: -1.55 (0.24), residues: 437 loop : -1.87 (0.12), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP k 68 HIS 0.012 0.001 HIS J 183 PHE 0.032 0.002 PHE m 73 TYR 0.023 0.002 TYR e 228 ARG 0.031 0.001 ARG d 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 883 time to evaluate : 4.793 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: E 174 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7436 (pt0) REVERT: E 227 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8191 (m110) REVERT: E 306 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7907 (mttp) REVERT: E 388 GLN cc_start: 0.7711 (pm20) cc_final: 0.7407 (pm20) REVERT: E 408 TRP cc_start: 0.7554 (t-100) cc_final: 0.7214 (t-100) REVERT: Q 1 MET cc_start: 0.1869 (mmm) cc_final: -0.0781 (pmm) REVERT: a 217 MET cc_start: 0.7587 (ttt) cc_final: 0.7182 (ttt) REVERT: a 274 PHE cc_start: 0.8148 (m-10) cc_final: 0.7739 (m-80) REVERT: a 319 GLN cc_start: 0.8509 (tt0) cc_final: 0.8076 (mt0) REVERT: c 99 MET cc_start: 0.8128 (tpp) cc_final: 0.7889 (tpt) REVERT: e 57 MET cc_start: 0.8477 (ptp) cc_final: 0.8236 (ptp) REVERT: e 75 PHE cc_start: 0.7472 (t80) cc_final: 0.7214 (t80) REVERT: e 315 MET cc_start: 0.6146 (tpp) cc_final: 0.5875 (tpp) REVERT: j 80 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.7919 (m) REVERT: j 113 LYS cc_start: 0.8310 (ptpp) cc_final: 0.8094 (ptpt) REVERT: G 97 MET cc_start: 0.7642 (tmm) cc_final: 0.7232 (ttp) REVERT: G 98 MET cc_start: 0.8092 (mtm) cc_final: 0.7371 (mpp) REVERT: G 226 MET cc_start: 0.7846 (tpp) cc_final: 0.7493 (tmm) REVERT: I 79 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7751 (pp20) REVERT: I 273 GLN cc_start: 0.7758 (pt0) cc_final: 0.7151 (tt0) REVERT: N 30 VAL cc_start: 0.7844 (m) cc_final: 0.7558 (p) REVERT: N 50 GLU cc_start: 0.8435 (mp0) cc_final: 0.7871 (pm20) REVERT: N 66 HIS cc_start: 0.8181 (t-90) cc_final: 0.7846 (t-170) REVERT: N 72 ASP cc_start: 0.7881 (t70) cc_final: 0.7596 (t0) REVERT: N 87 ILE cc_start: 0.8383 (mt) cc_final: 0.8182 (mp) REVERT: N 124 GLN cc_start: 0.6768 (pt0) cc_final: 0.6552 (pt0) REVERT: g 217 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8801 (pptt) REVERT: h 297 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8566 (mttp) REVERT: m 53 MET cc_start: 0.7816 (mmp) cc_final: 0.6508 (mpp) REVERT: B 63 ASN cc_start: 0.8018 (t0) cc_final: 0.7707 (t0) REVERT: B 103 ASP cc_start: 0.8317 (m-30) cc_final: 0.7904 (m-30) REVERT: B 114 LEU cc_start: 0.8602 (tp) cc_final: 0.8280 (tt) REVERT: B 134 VAL cc_start: 0.8709 (p) cc_final: 0.8415 (p) REVERT: K 75 SER cc_start: 0.8203 (m) cc_final: 0.7938 (p) REVERT: O 70 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7490 (ttm) REVERT: O 81 ILE cc_start: 0.7306 (pt) cc_final: 0.7089 (mt) REVERT: R 79 GLN cc_start: 0.7458 (tt0) cc_final: 0.7241 (tt0) REVERT: b 101 GLU cc_start: 0.7928 (pp20) cc_final: 0.7719 (pp20) REVERT: b 106 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8391 (mp) REVERT: b 114 GLU cc_start: 0.8686 (mp0) cc_final: 0.8476 (pm20) REVERT: z 95 ASN cc_start: 0.6397 (m-40) cc_final: 0.6185 (p0) REVERT: z 147 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7031 (tt0) outliers start: 182 outliers final: 105 residues processed: 994 average time/residue: 0.6419 time to fit residues: 1091.1296 Evaluate side-chains 857 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 745 time to evaluate : 4.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain P residue 87 VAL Chi-restraints excluded: chain P residue 90 LEU Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 23 PHE Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 147 VAL Chi-restraints excluded: chain c residue 153 VAL Chi-restraints excluded: chain c residue 167 LEU Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain e residue 123 ASP Chi-restraints excluded: chain e residue 141 ASN Chi-restraints excluded: chain e residue 143 THR Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 60 ARG Chi-restraints excluded: chain j residue 80 VAL Chi-restraints excluded: chain j residue 88 GLN Chi-restraints excluded: chain j residue 104 TYR Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain j residue 173 MET Chi-restraints excluded: chain j residue 205 GLU Chi-restraints excluded: chain p residue 140 THR Chi-restraints excluded: chain p residue 145 LYS Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 227 HIS Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 312 GLN Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 339 SER Chi-restraints excluded: chain I residue 344 ILE Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain g residue 217 LYS Chi-restraints excluded: chain g residue 236 THR Chi-restraints excluded: chain g residue 336 LEU Chi-restraints excluded: chain h residue 297 LYS Chi-restraints excluded: chain h residue 307 ASN Chi-restraints excluded: chain h residue 329 LEU Chi-restraints excluded: chain h residue 338 ILE Chi-restraints excluded: chain i residue 62 MET Chi-restraints excluded: chain k residue 85 LEU Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 159 ILE Chi-restraints excluded: chain k residue 175 LEU Chi-restraints excluded: chain k residue 209 ILE Chi-restraints excluded: chain m residue 3 THR Chi-restraints excluded: chain m residue 89 ILE Chi-restraints excluded: chain o residue 79 HIS Chi-restraints excluded: chain o residue 119 PHE Chi-restraints excluded: chain o residue 580 ASN Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 70 MET Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 87 VAL Chi-restraints excluded: chain O residue 189 THR Chi-restraints excluded: chain O residue 212 VAL Chi-restraints excluded: chain R residue 66 CYS Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 101 CYS Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 93 MET Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain f residue 113 LEU Chi-restraints excluded: chain f residue 141 VAL Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain n residue 128 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 480 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 429 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 492 optimal weight: 7.9990 chunk 398 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 294 optimal weight: 2.9990 chunk 517 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 HIS C 130 HIS E 175 GLN E 277 HIS E 302 HIS E 341 ASN E 351 GLN E 360 GLN L 106 HIS P 16 HIS ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 HIS Q 23 GLN a 220 GLN ** c 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 122 GLN ** e 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 GLN ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 ASN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 125 HIS ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 80 HIS ** g 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 210 ASN g 325 GLN ** h 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 313 GLN o 376 HIS o 524 HIS B 186 HIS B 195 HIS O 127 GLN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN U 4 HIS U 53 GLN U 65 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.9416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 69161 Z= 0.452 Angle : 0.829 17.156 97963 Z= 0.419 Chirality : 0.045 0.338 11544 Planarity : 0.007 0.120 9033 Dihedral : 18.938 169.668 19564 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.25 % Favored : 92.59 % Rotamer: Outliers : 5.02 % Allowed : 19.22 % Favored : 75.76 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.11), residues: 5437 helix: 0.43 (0.10), residues: 2415 sheet: -1.59 (0.23), residues: 473 loop : -1.94 (0.12), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP I 363 HIS 0.087 0.003 HIS J 130 PHE 0.036 0.003 PHE e 138 TYR 0.034 0.003 TYR G 51 ARG 0.034 0.001 ARG J 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 773 time to evaluate : 4.631 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: C 164 TYR cc_start: 0.6123 (t80) cc_final: 0.5898 (t80) REVERT: E 174 GLN cc_start: 0.8124 (tp-100) cc_final: 0.7495 (pt0) REVERT: E 231 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6992 (mtp) REVERT: E 306 LYS cc_start: 0.8800 (mtpt) cc_final: 0.8532 (mttp) REVERT: E 312 TYR cc_start: 0.7553 (t80) cc_final: 0.6792 (t80) REVERT: E 315 ARG cc_start: 0.6150 (tpm170) cc_final: 0.4917 (tpm170) REVERT: E 351 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: L 48 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8642 (tppt) REVERT: L 101 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8369 (p0) REVERT: P 13 ARG cc_start: 0.5396 (ttm170) cc_final: 0.5139 (mtm180) REVERT: Q 1 MET cc_start: 0.1869 (mmm) cc_final: -0.0773 (pmm) REVERT: a 319 GLN cc_start: 0.8540 (tt0) cc_final: 0.8039 (mt0) REVERT: e 49 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.7477 (t-90) REVERT: e 397 MET cc_start: 0.4788 (mtt) cc_final: 0.4564 (ttt) REVERT: G 226 MET cc_start: 0.7866 (tpp) cc_final: 0.7616 (tmm) REVERT: I 294 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8202 (mm-30) REVERT: I 312 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8583 (mp10) REVERT: J 91 TYR cc_start: 0.8423 (t80) cc_final: 0.8204 (t80) REVERT: N 42 LYS cc_start: 0.8435 (mtpt) cc_final: 0.8126 (mtmm) REVERT: N 46 GLU cc_start: 0.8484 (mp0) cc_final: 0.8212 (mp0) REVERT: N 50 GLU cc_start: 0.8382 (mp0) cc_final: 0.7792 (pm20) REVERT: N 66 HIS cc_start: 0.8482 (t-90) cc_final: 0.8255 (t-170) REVERT: N 70 VAL cc_start: 0.7519 (t) cc_final: 0.7282 (t) REVERT: g 179 GLN cc_start: 0.6745 (tp-100) cc_final: 0.6282 (tp-100) REVERT: g 217 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8830 (pptt) REVERT: h 294 GLN cc_start: 0.8227 (tt0) cc_final: 0.7981 (tt0) REVERT: h 327 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7310 (mmtm) REVERT: h 385 PHE cc_start: 0.5166 (OUTLIER) cc_final: 0.4714 (m-10) REVERT: m 52 MET cc_start: 0.5950 (tpp) cc_final: 0.5689 (tpp) REVERT: m 53 MET cc_start: 0.8000 (mmp) cc_final: 0.6962 (mtp) REVERT: B 114 LEU cc_start: 0.8985 (tp) cc_final: 0.8642 (tt) REVERT: B 217 ASN cc_start: 0.8716 (t0) cc_final: 0.8470 (t0) REVERT: B 236 GLN cc_start: 0.8422 (mt0) cc_final: 0.8165 (mt0) REVERT: F 1 MET cc_start: 0.5790 (ttt) cc_final: 0.5259 (ttp) REVERT: K 163 SER cc_start: 0.8951 (m) cc_final: 0.8547 (t) REVERT: O 70 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8476 (ttm) REVERT: O 81 ILE cc_start: 0.8263 (pt) cc_final: 0.8051 (mm) REVERT: O 96 MET cc_start: 0.8920 (mmt) cc_final: 0.8639 (mmt) REVERT: b 106 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8728 (mp) REVERT: b 113 ASP cc_start: 0.6904 (t0) cc_final: 0.6439 (t0) REVERT: f 79 GLU cc_start: 0.8013 (tp30) cc_final: 0.7754 (tp30) outliers start: 242 outliers final: 131 residues processed: 935 average time/residue: 0.6251 time to fit residues: 996.9112 Evaluate side-chains 757 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 616 time to evaluate : 4.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 58 CYS Chi-restraints excluded: chain a residue 96 GLU Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain a residue 116 GLN Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain a residue 144 ASP Chi-restraints excluded: chain a residue 162 TYR Chi-restraints excluded: chain a residue 240 ASP Chi-restraints excluded: chain a residue 324 LEU Chi-restraints excluded: chain c residue 25 ASP Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 71 THR Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain c residue 153 VAL Chi-restraints excluded: chain c residue 167 LEU Chi-restraints excluded: chain d residue 81 LYS Chi-restraints excluded: chain d residue 189 TRP Chi-restraints excluded: chain e residue 49 HIS Chi-restraints excluded: chain e residue 123 ASP Chi-restraints excluded: chain e residue 143 THR Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain e residue 265 LYS Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 60 ARG Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain j residue 104 TYR Chi-restraints excluded: chain j residue 152 SER Chi-restraints excluded: chain j residue 173 MET Chi-restraints excluded: chain j residue 205 GLU Chi-restraints excluded: chain p residue 140 THR Chi-restraints excluded: chain p residue 145 LYS Chi-restraints excluded: chain p residue 184 VAL Chi-restraints excluded: chain p residue 194 VAL Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 213 PHE Chi-restraints excluded: chain G residue 224 HIS Chi-restraints excluded: chain G residue 227 HIS Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain I residue 156 GLN Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 301 LEU Chi-restraints excluded: chain I residue 312 GLN Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 339 SER Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 161 VAL Chi-restraints excluded: chain g residue 192 THR Chi-restraints excluded: chain g residue 217 LYS Chi-restraints excluded: chain g residue 236 THR Chi-restraints excluded: chain h residue 307 ASN Chi-restraints excluded: chain h residue 312 PHE Chi-restraints excluded: chain h residue 385 PHE Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 159 ILE Chi-restraints excluded: chain k residue 165 ILE Chi-restraints excluded: chain k residue 175 LEU Chi-restraints excluded: chain k residue 177 VAL Chi-restraints excluded: chain k residue 209 ILE Chi-restraints excluded: chain m residue 3 THR Chi-restraints excluded: chain m residue 5 SER Chi-restraints excluded: chain m residue 40 LYS Chi-restraints excluded: chain m residue 86 MET Chi-restraints excluded: chain m residue 89 ILE Chi-restraints excluded: chain o residue 79 HIS Chi-restraints excluded: chain o residue 92 ASP Chi-restraints excluded: chain o residue 433 GLU Chi-restraints excluded: chain o residue 497 ILE Chi-restraints excluded: chain o residue 580 ASN Chi-restraints excluded: chain o residue 618 MET Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 70 MET Chi-restraints excluded: chain O residue 212 VAL Chi-restraints excluded: chain O residue 214 GLN Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain R residue 66 CYS Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 101 CYS Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 33 ASP Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain f residue 141 VAL Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 149 GLU Chi-restraints excluded: chain n residue 128 ARG Chi-restraints excluded: chain z residue 109 MET Chi-restraints excluded: chain z residue 183 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 194 optimal weight: 9.9990 chunk 519 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 338 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 577 optimal weight: 30.0000 chunk 479 optimal weight: 0.6980 chunk 267 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 191 optimal weight: 0.9980 chunk 303 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS E 273 ASN E 359 HIS L 37 HIS ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 HIS a 266 HIS ** a 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 89 HIS ** j 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 111 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 GLN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 307 ASN h 359 GLN i 40 GLN k 263 ASN k 313 GLN o 122 ASN ** o 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 501 GLN ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 ASN ** z 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.9550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 69161 Z= 0.188 Angle : 0.588 11.970 97963 Z= 0.294 Chirality : 0.036 0.283 11544 Planarity : 0.004 0.060 9033 Dihedral : 18.687 176.001 19564 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.84 % Favored : 95.07 % Rotamer: Outliers : 3.28 % Allowed : 21.44 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.11), residues: 5437 helix: 0.97 (0.11), residues: 2395 sheet: -1.33 (0.24), residues: 470 loop : -1.74 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP I 363 HIS 0.011 0.001 HIS J 130 PHE 0.029 0.002 PHE J 94 TYR 0.026 0.002 TYR o 87 ARG 0.006 0.000 ARG I 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 703 time to evaluate : 4.533 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: E 174 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7457 (pt0) REVERT: E 231 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.6629 (mtp) REVERT: E 297 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8989 (t) REVERT: E 306 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8537 (mttp) REVERT: E 312 TYR cc_start: 0.7259 (t80) cc_final: 0.6544 (t80) REVERT: E 315 ARG cc_start: 0.5788 (tpm170) cc_final: 0.4349 (tpm170) REVERT: L 48 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8663 (tppt) REVERT: Q 1 MET cc_start: 0.1761 (mmm) cc_final: -0.0780 (pmm) REVERT: a 319 GLN cc_start: 0.8482 (tt0) cc_final: 0.8003 (mt0) REVERT: c 118 GLN cc_start: 0.8430 (pp30) cc_final: 0.8220 (pp30) REVERT: e 57 MET cc_start: 0.8207 (ptp) cc_final: 0.7973 (ptp) REVERT: e 75 PHE cc_start: 0.7734 (t80) cc_final: 0.7483 (t80) REVERT: j 139 TRP cc_start: 0.7267 (m100) cc_final: 0.6963 (m100) REVERT: G 97 MET cc_start: 0.7961 (tmm) cc_final: 0.7627 (ttp) REVERT: G 111 MET cc_start: 0.8579 (mmp) cc_final: 0.8234 (tmm) REVERT: G 226 MET cc_start: 0.7841 (tpp) cc_final: 0.7499 (tmm) REVERT: I 294 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8431 (mm-30) REVERT: I 348 MET cc_start: 0.8476 (ptp) cc_final: 0.8172 (mtm) REVERT: N 50 GLU cc_start: 0.8415 (mp0) cc_final: 0.7851 (pm20) REVERT: N 66 HIS cc_start: 0.8546 (t-90) cc_final: 0.8176 (t-170) REVERT: N 73 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7997 (mp0) REVERT: g 179 GLN cc_start: 0.6568 (tp-100) cc_final: 0.6207 (tp-100) REVERT: g 217 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8822 (pptt) REVERT: h 297 LYS cc_start: 0.8706 (pttm) cc_final: 0.8472 (mttp) REVERT: h 334 LYS cc_start: 0.7298 (tppt) cc_final: 0.7027 (tppt) REVERT: m 53 MET cc_start: 0.7769 (mmp) cc_final: 0.6657 (mpp) REVERT: o 593 GLN cc_start: 0.4788 (OUTLIER) cc_final: 0.3725 (mp10) REVERT: K 85 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7596 (pt0) REVERT: O 96 MET cc_start: 0.8902 (mmt) cc_final: 0.8639 (mmt) REVERT: b 106 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8618 (mp) REVERT: n 167 MET cc_start: 0.8215 (mmp) cc_final: 0.8004 (mmp) REVERT: z 162 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8056 (mp) outliers start: 158 outliers final: 93 residues processed: 821 average time/residue: 0.6637 time to fit residues: 940.5336 Evaluate side-chains 716 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 616 time to evaluate : 4.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain a residue 116 GLN Chi-restraints excluded: chain a residue 158 THR Chi-restraints excluded: chain a residue 162 TYR Chi-restraints excluded: chain a residue 324 LEU Chi-restraints excluded: chain c residue 23 PHE Chi-restraints excluded: chain c residue 25 ASP Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain c residue 167 LEU Chi-restraints excluded: chain d residue 98 ASP Chi-restraints excluded: chain e residue 143 THR Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain e residue 265 LYS Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain j residue 60 ARG Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 88 GLN Chi-restraints excluded: chain j residue 101 ARG Chi-restraints excluded: chain j residue 104 TYR Chi-restraints excluded: chain j residue 136 HIS Chi-restraints excluded: chain j residue 164 VAL Chi-restraints excluded: chain p residue 60 ASP Chi-restraints excluded: chain p residue 140 THR Chi-restraints excluded: chain p residue 145 LYS Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 227 HIS Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain I residue 156 GLN Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 339 SER Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 161 VAL Chi-restraints excluded: chain g residue 172 TYR Chi-restraints excluded: chain g residue 217 LYS Chi-restraints excluded: chain g residue 336 LEU Chi-restraints excluded: chain h residue 312 PHE Chi-restraints excluded: chain k residue 130 ASP Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 159 ILE Chi-restraints excluded: chain k residue 209 ILE Chi-restraints excluded: chain m residue 3 THR Chi-restraints excluded: chain m residue 40 LYS Chi-restraints excluded: chain m residue 89 ILE Chi-restraints excluded: chain o residue 79 HIS Chi-restraints excluded: chain o residue 433 GLU Chi-restraints excluded: chain o residue 580 ASN Chi-restraints excluded: chain o residue 593 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 212 VAL Chi-restraints excluded: chain O residue 214 GLN Chi-restraints excluded: chain O residue 216 VAL Chi-restraints excluded: chain R residue 66 CYS Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 101 CYS Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 64 TYR Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 149 GLU Chi-restraints excluded: chain f residue 153 ARG Chi-restraints excluded: chain z residue 162 ILE Chi-restraints excluded: chain z residue 217 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 556 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 329 optimal weight: 1.9990 chunk 421 optimal weight: 2.9990 chunk 326 optimal weight: 7.9990 chunk 486 optimal weight: 6.9990 chunk 322 optimal weight: 20.0000 chunk 575 optimal weight: 2.9990 chunk 360 optimal weight: 8.9990 chunk 350 optimal weight: 6.9990 chunk 265 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 HIS C 130 HIS ** E 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN L 74 ASN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 156 ASN e 188 GLN ** e 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 HIS ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 173 ASN ** h 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 ASN ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 199 HIS ** R 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 65 ASN b 66 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 1.0190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 69161 Z= 0.348 Angle : 0.673 13.034 97963 Z= 0.338 Chirality : 0.039 0.239 11544 Planarity : 0.005 0.076 9033 Dihedral : 18.759 176.975 19564 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.58 % Rotamer: Outliers : 3.82 % Allowed : 21.64 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.11), residues: 5437 helix: 0.86 (0.11), residues: 2408 sheet: -1.22 (0.23), residues: 485 loop : -1.70 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP I 363 HIS 0.011 0.001 HIS N 66 PHE 0.030 0.002 PHE J 94 TYR 0.032 0.002 TYR b 53 ARG 0.011 0.001 ARG j 195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 659 time to evaluate : 4.723 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: E 174 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7332 (pt0) REVERT: E 231 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6985 (mtp) REVERT: E 297 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.9024 (t) REVERT: E 306 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8553 (mttp) REVERT: E 312 TYR cc_start: 0.7467 (t80) cc_final: 0.6716 (t80) REVERT: E 315 ARG cc_start: 0.5701 (tpm170) cc_final: 0.4259 (tpm170) REVERT: Q 1 MET cc_start: 0.1727 (mmm) cc_final: -0.0887 (pmm) REVERT: a 81 MET cc_start: 0.7915 (ptm) cc_final: 0.7519 (ttm) REVERT: a 319 GLN cc_start: 0.8468 (tt0) cc_final: 0.8019 (mt0) REVERT: c 118 GLN cc_start: 0.8491 (pp30) cc_final: 0.8268 (pp30) REVERT: d 94 LYS cc_start: 0.8706 (tptt) cc_final: 0.8500 (mmmt) REVERT: j 190 MET cc_start: 0.8395 (mmt) cc_final: 0.8190 (mmt) REVERT: G 41 TYR cc_start: 0.7787 (m-80) cc_final: 0.7204 (m-80) REVERT: G 97 MET cc_start: 0.8123 (tmm) cc_final: 0.7817 (ttt) REVERT: G 111 MET cc_start: 0.8765 (mmp) cc_final: 0.8464 (tmm) REVERT: G 229 MET cc_start: 0.7682 (mmm) cc_final: 0.7389 (mpp) REVERT: I 294 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8419 (mm-30) REVERT: I 348 MET cc_start: 0.8509 (ptp) cc_final: 0.8246 (mtm) REVERT: N 50 GLU cc_start: 0.8375 (mp0) cc_final: 0.7840 (pm20) REVERT: N 66 HIS cc_start: 0.8619 (t-90) cc_final: 0.8170 (t-170) REVERT: N 69 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: g 179 GLN cc_start: 0.6724 (tp-100) cc_final: 0.6110 (tp-100) REVERT: g 217 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8836 (pptt) REVERT: h 334 LYS cc_start: 0.7316 (tppt) cc_final: 0.7075 (tppt) REVERT: i 93 LYS cc_start: 0.1791 (OUTLIER) cc_final: 0.1571 (tttm) REVERT: m 53 MET cc_start: 0.7898 (mmp) cc_final: 0.6744 (mtp) REVERT: o 593 GLN cc_start: 0.4729 (OUTLIER) cc_final: 0.3726 (mp10) REVERT: B 63 ASN cc_start: 0.8371 (t0) cc_final: 0.8026 (t0) REVERT: b 47 ARG cc_start: 0.7507 (tpt170) cc_final: 0.7239 (tpt170) REVERT: b 106 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8788 (mp) REVERT: n 138 MET cc_start: 0.8676 (tpp) cc_final: 0.8051 (tpt) outliers start: 184 outliers final: 129 residues processed: 791 average time/residue: 0.6238 time to fit residues: 842.6283 Evaluate side-chains 743 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 607 time to evaluate : 4.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 58 CYS Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain a residue 116 GLN Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 158 THR Chi-restraints excluded: chain a residue 162 TYR Chi-restraints excluded: chain a residue 240 ASP Chi-restraints excluded: chain a residue 324 LEU Chi-restraints excluded: chain c residue 25 ASP Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 167 LEU Chi-restraints excluded: chain d residue 98 ASP Chi-restraints excluded: chain d residue 189 TRP Chi-restraints excluded: chain e residue 143 THR Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain e residue 209 LEU Chi-restraints excluded: chain e residue 265 LYS Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 60 ARG Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 88 GLN Chi-restraints excluded: chain j residue 101 ARG Chi-restraints excluded: chain j residue 104 TYR Chi-restraints excluded: chain j residue 136 HIS Chi-restraints excluded: chain j residue 164 VAL Chi-restraints excluded: chain p residue 60 ASP Chi-restraints excluded: chain p residue 140 THR Chi-restraints excluded: chain p residue 145 LYS Chi-restraints excluded: chain p residue 194 VAL Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 227 HIS Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain I residue 156 GLN Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 339 SER Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 161 VAL Chi-restraints excluded: chain g residue 172 TYR Chi-restraints excluded: chain g residue 217 LYS Chi-restraints excluded: chain g residue 236 THR Chi-restraints excluded: chain g residue 360 LEU Chi-restraints excluded: chain h residue 297 LYS Chi-restraints excluded: chain h residue 312 PHE Chi-restraints excluded: chain h residue 329 LEU Chi-restraints excluded: chain i residue 59 PHE Chi-restraints excluded: chain i residue 93 LYS Chi-restraints excluded: chain k residue 116 LEU Chi-restraints excluded: chain k residue 130 ASP Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 159 ILE Chi-restraints excluded: chain k residue 177 VAL Chi-restraints excluded: chain k residue 209 ILE Chi-restraints excluded: chain k residue 214 CYS Chi-restraints excluded: chain k residue 228 LEU Chi-restraints excluded: chain k residue 237 LYS Chi-restraints excluded: chain m residue 3 THR Chi-restraints excluded: chain m residue 5 SER Chi-restraints excluded: chain m residue 40 LYS Chi-restraints excluded: chain m residue 79 ARG Chi-restraints excluded: chain m residue 86 MET Chi-restraints excluded: chain m residue 89 ILE Chi-restraints excluded: chain m residue 98 SER Chi-restraints excluded: chain o residue 119 PHE Chi-restraints excluded: chain o residue 141 MET Chi-restraints excluded: chain o residue 433 GLU Chi-restraints excluded: chain o residue 580 ASN Chi-restraints excluded: chain o residue 593 GLN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 212 VAL Chi-restraints excluded: chain O residue 214 GLN Chi-restraints excluded: chain O residue 216 VAL Chi-restraints excluded: chain R residue 66 CYS Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 101 CYS Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain b residue 33 ASP Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 64 TYR Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 149 GLU Chi-restraints excluded: chain f residue 151 THR Chi-restraints excluded: chain n residue 153 LEU Chi-restraints excluded: chain z residue 108 LEU Chi-restraints excluded: chain z residue 209 ILE Chi-restraints excluded: chain z residue 217 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 355 optimal weight: 10.0000 chunk 229 optimal weight: 30.0000 chunk 343 optimal weight: 8.9990 chunk 173 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 365 optimal weight: 6.9990 chunk 392 optimal weight: 8.9990 chunk 284 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 452 optimal weight: 0.9980 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN E 273 ASN E 351 GLN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 223 HIS ** a 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 188 ASN ** e 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 317 GLN ** e 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 GLN I 156 GLN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 HIS ** g 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 234 ASN g 367 HIS ** i 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 263 ASN m 109 GLN o 72 GLN ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 129 GLN z 264 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 1.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 69161 Z= 0.504 Angle : 0.819 15.319 97963 Z= 0.414 Chirality : 0.045 0.306 11544 Planarity : 0.006 0.062 9033 Dihedral : 19.089 175.596 19564 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.45 % Favored : 92.44 % Rotamer: Outliers : 4.23 % Allowed : 21.98 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.11), residues: 5437 helix: 0.38 (0.10), residues: 2404 sheet: -1.45 (0.23), residues: 490 loop : -1.81 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP I 363 HIS 0.012 0.002 HIS K 101 PHE 0.032 0.003 PHE e 151 TYR 0.029 0.003 TYR b 53 ARG 0.032 0.001 ARG e 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 613 time to evaluate : 4.623 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: E 174 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7400 (pt0) REVERT: E 231 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7151 (mtp) REVERT: E 234 LYS cc_start: 0.8006 (tttt) cc_final: 0.7061 (tptt) REVERT: E 262 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8716 (t) REVERT: E 297 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.8987 (t) REVERT: E 306 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8641 (mttm) REVERT: E 315 ARG cc_start: 0.5342 (OUTLIER) cc_final: 0.3445 (tpm170) REVERT: E 341 ASN cc_start: 0.6788 (m110) cc_final: 0.6425 (m-40) REVERT: E 415 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8969 (tp-100) REVERT: P 63 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7191 (mt-10) REVERT: Q 1 MET cc_start: 0.1363 (mmm) cc_final: -0.1521 (pmm) REVERT: a 81 MET cc_start: 0.8061 (ptm) cc_final: 0.7782 (ttm) REVERT: a 138 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8124 (p0) REVERT: j 73 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6947 (t80) REVERT: G 111 MET cc_start: 0.8824 (mmp) cc_final: 0.8467 (tmm) REVERT: I 294 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8508 (mm-30) REVERT: I 312 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8274 (mp10) REVERT: I 348 MET cc_start: 0.8535 (ptp) cc_final: 0.8322 (mtm) REVERT: N 42 LYS cc_start: 0.8282 (mttt) cc_final: 0.8037 (mtmm) REVERT: g 217 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8804 (pptt) REVERT: h 334 LYS cc_start: 0.7566 (tppt) cc_final: 0.7359 (tppt) REVERT: m 53 MET cc_start: 0.8045 (mmp) cc_final: 0.7266 (mtt) REVERT: o 593 GLN cc_start: 0.4554 (OUTLIER) cc_final: 0.3631 (mp10) REVERT: F 122 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7653 (mmtt) REVERT: K 163 SER cc_start: 0.9065 (m) cc_final: 0.8445 (t) REVERT: R 140 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7694 (mmm160) REVERT: U 8 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8888 (mt) REVERT: U 46 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: b 47 ARG cc_start: 0.7461 (tpt170) cc_final: 0.7256 (tpt170) REVERT: b 62 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8694 (p0) REVERT: f 84 MET cc_start: 0.8227 (ttm) cc_final: 0.8026 (ttm) outliers start: 204 outliers final: 146 residues processed: 765 average time/residue: 0.6215 time to fit residues: 813.3234 Evaluate side-chains 710 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 551 time to evaluate : 4.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 415 GLN Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 73 ILE Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 58 CYS Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain a residue 116 GLN Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 138 ASN Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 158 THR Chi-restraints excluded: chain a residue 162 TYR Chi-restraints excluded: chain a residue 240 ASP Chi-restraints excluded: chain a residue 324 LEU Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 25 ASP Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 160 THR Chi-restraints excluded: chain c residue 167 LEU Chi-restraints excluded: chain d residue 98 ASP Chi-restraints excluded: chain d residue 189 TRP Chi-restraints excluded: chain e residue 143 THR Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain e residue 209 LEU Chi-restraints excluded: chain e residue 265 LYS Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 73 PHE Chi-restraints excluded: chain j residue 80 VAL Chi-restraints excluded: chain j residue 88 GLN Chi-restraints excluded: chain j residue 93 CYS Chi-restraints excluded: chain j residue 101 ARG Chi-restraints excluded: chain j residue 104 TYR Chi-restraints excluded: chain j residue 136 HIS Chi-restraints excluded: chain j residue 152 SER Chi-restraints excluded: chain j residue 164 VAL Chi-restraints excluded: chain p residue 60 ASP Chi-restraints excluded: chain p residue 76 ASP Chi-restraints excluded: chain p residue 140 THR Chi-restraints excluded: chain p residue 145 LYS Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 227 HIS Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain I residue 156 GLN Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 312 GLN Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 333 SER Chi-restraints excluded: chain I residue 339 SER Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 142 CYS Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 161 VAL Chi-restraints excluded: chain g residue 172 TYR Chi-restraints excluded: chain g residue 217 LYS Chi-restraints excluded: chain g residue 236 THR Chi-restraints excluded: chain g residue 360 LEU Chi-restraints excluded: chain h residue 297 LYS Chi-restraints excluded: chain h residue 301 LEU Chi-restraints excluded: chain h residue 312 PHE Chi-restraints excluded: chain i residue 59 PHE Chi-restraints excluded: chain k residue 116 LEU Chi-restraints excluded: chain k residue 159 ILE Chi-restraints excluded: chain k residue 177 VAL Chi-restraints excluded: chain k residue 202 LYS Chi-restraints excluded: chain k residue 209 ILE Chi-restraints excluded: chain k residue 214 CYS Chi-restraints excluded: chain k residue 228 LEU Chi-restraints excluded: chain m residue 3 THR Chi-restraints excluded: chain m residue 5 SER Chi-restraints excluded: chain m residue 86 MET Chi-restraints excluded: chain m residue 89 ILE Chi-restraints excluded: chain m residue 98 SER Chi-restraints excluded: chain o residue 119 PHE Chi-restraints excluded: chain o residue 433 GLU Chi-restraints excluded: chain o residue 580 ASN Chi-restraints excluded: chain o residue 581 TYR Chi-restraints excluded: chain o residue 593 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain F residue 5 GLU Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain O residue 212 VAL Chi-restraints excluded: chain O residue 216 VAL Chi-restraints excluded: chain R residue 66 CYS Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 101 CYS Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 33 ASP Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 62 ASP Chi-restraints excluded: chain b residue 64 TYR Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain f residue 80 SER Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain f residue 141 VAL Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 149 GLU Chi-restraints excluded: chain f residue 151 THR Chi-restraints excluded: chain n residue 153 LEU Chi-restraints excluded: chain z residue 95 ASN Chi-restraints excluded: chain z residue 108 LEU Chi-restraints excluded: chain z residue 146 MET Chi-restraints excluded: chain z residue 217 MET Chi-restraints excluded: chain z residue 243 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 523 optimal weight: 0.8980 chunk 551 optimal weight: 0.7980 chunk 502 optimal weight: 0.5980 chunk 536 optimal weight: 0.9990 chunk 322 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 421 optimal weight: 0.0670 chunk 164 optimal weight: 1.9990 chunk 484 optimal weight: 0.9980 chunk 507 optimal weight: 0.9980 chunk 534 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS E 227 ASN ** E 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 75 GLN ** a 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 336 GLN e 188 GLN e 261 GLN p 207 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 312 GLN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 263 ASN k 313 GLN ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 HIS ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 120 ASN z 187 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 1.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 69161 Z= 0.170 Angle : 0.629 11.731 97963 Z= 0.314 Chirality : 0.036 0.219 11544 Planarity : 0.004 0.065 9033 Dihedral : 18.835 178.472 19564 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.97 % Favored : 94.96 % Rotamer: Outliers : 2.24 % Allowed : 24.28 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.11), residues: 5437 helix: 0.82 (0.11), residues: 2416 sheet: -1.17 (0.24), residues: 467 loop : -1.55 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP I 363 HIS 0.012 0.001 HIS k 124 PHE 0.037 0.002 PHE C 95 TYR 0.027 0.002 TYR e 184 ARG 0.009 0.001 ARG G 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 663 time to evaluate : 4.621 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: E 174 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7380 (pt0) REVERT: E 196 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8677 (p0) REVERT: E 234 LYS cc_start: 0.7945 (tttt) cc_final: 0.7060 (tptt) REVERT: E 297 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8881 (t) REVERT: E 306 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8653 (mttm) REVERT: E 315 ARG cc_start: 0.4748 (OUTLIER) cc_final: 0.3047 (tpm170) REVERT: E 415 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8883 (tp-100) REVERT: P 63 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7251 (mt-10) REVERT: Q 1 MET cc_start: 0.1660 (mmm) cc_final: -0.1056 (pmm) REVERT: a 319 GLN cc_start: 0.8462 (tt0) cc_final: 0.8193 (mt0) REVERT: G 111 MET cc_start: 0.8793 (mmp) cc_final: 0.8476 (tmm) REVERT: G 145 PHE cc_start: 0.9110 (t80) cc_final: 0.8904 (t80) REVERT: G 186 TRP cc_start: 0.7636 (m-10) cc_final: 0.7413 (m-10) REVERT: I 294 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8531 (mm-30) REVERT: I 312 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8252 (mp-120) REVERT: I 358 GLU cc_start: 0.8424 (tt0) cc_final: 0.8158 (tp30) REVERT: g 217 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8858 (pptt) REVERT: m 53 MET cc_start: 0.7773 (mmp) cc_final: 0.6863 (mtt) REVERT: o 141 MET cc_start: 0.3189 (mmm) cc_final: 0.2545 (mmm) REVERT: B 114 LEU cc_start: 0.9190 (tp) cc_final: 0.8960 (tt) REVERT: O 77 ASN cc_start: 0.8494 (m-40) cc_final: 0.8249 (p0) REVERT: U 8 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8797 (mt) REVERT: b 47 ARG cc_start: 0.7388 (tpt170) cc_final: 0.7029 (tpt170) REVERT: f 84 MET cc_start: 0.8140 (ttm) cc_final: 0.7862 (ttm) REVERT: z 85 ARG cc_start: 0.5805 (tpp80) cc_final: 0.5351 (tpp80) outliers start: 108 outliers final: 72 residues processed: 735 average time/residue: 0.6238 time to fit residues: 783.9106 Evaluate side-chains 675 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 596 time to evaluate : 4.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 415 GLN Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain P residue 41 CYS Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain a residue 116 GLN Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 158 THR Chi-restraints excluded: chain a residue 162 TYR Chi-restraints excluded: chain a residue 240 ASP Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain c residue 167 LEU Chi-restraints excluded: chain d residue 98 ASP Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain e residue 209 LEU Chi-restraints excluded: chain e residue 265 LYS Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 88 GLN Chi-restraints excluded: chain j residue 101 ARG Chi-restraints excluded: chain j residue 104 TYR Chi-restraints excluded: chain j residue 164 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 227 HIS Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 312 GLN Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 172 TYR Chi-restraints excluded: chain g residue 217 LYS Chi-restraints excluded: chain h residue 295 TRP Chi-restraints excluded: chain h residue 312 PHE Chi-restraints excluded: chain h residue 329 LEU Chi-restraints excluded: chain h residue 338 ILE Chi-restraints excluded: chain i residue 22 VAL Chi-restraints excluded: chain k residue 85 LEU Chi-restraints excluded: chain k residue 116 LEU Chi-restraints excluded: chain k residue 159 ILE Chi-restraints excluded: chain k residue 177 VAL Chi-restraints excluded: chain k residue 209 ILE Chi-restraints excluded: chain m residue 5 SER Chi-restraints excluded: chain o residue 79 HIS Chi-restraints excluded: chain o residue 580 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain F residue 5 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 212 VAL Chi-restraints excluded: chain O residue 216 VAL Chi-restraints excluded: chain R residue 66 CYS Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain b residue 64 TYR Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 149 GLU Chi-restraints excluded: chain f residue 151 THR Chi-restraints excluded: chain n residue 153 LEU Chi-restraints excluded: chain z residue 217 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 352 optimal weight: 0.7980 chunk 567 optimal weight: 3.9990 chunk 346 optimal weight: 7.9990 chunk 268 optimal weight: 8.9990 chunk 394 optimal weight: 7.9990 chunk 594 optimal weight: 10.0000 chunk 547 optimal weight: 0.2980 chunk 473 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 365 optimal weight: 5.9990 chunk 290 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS ** E 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 339 HIS j 179 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 GLN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 263 ASN ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 263 GLN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 1.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 69161 Z= 0.203 Angle : 0.620 13.589 97963 Z= 0.310 Chirality : 0.037 0.282 11544 Planarity : 0.004 0.054 9033 Dihedral : 18.744 178.988 19564 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.57 % Favored : 94.35 % Rotamer: Outliers : 1.83 % Allowed : 24.80 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.11), residues: 5437 helix: 0.95 (0.11), residues: 2414 sheet: -1.05 (0.24), residues: 466 loop : -1.48 (0.12), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP I 363 HIS 0.024 0.001 HIS e 339 PHE 0.055 0.002 PHE C 95 TYR 0.035 0.002 TYR G 41 ARG 0.008 0.001 ARG m 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 605 time to evaluate : 4.648 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: E 174 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7344 (pt0) REVERT: E 234 LYS cc_start: 0.8028 (tttt) cc_final: 0.7058 (tptt) REVERT: E 297 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8925 (t) REVERT: E 306 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8650 (mttm) REVERT: E 315 ARG cc_start: 0.4934 (OUTLIER) cc_final: 0.3202 (tpm170) REVERT: E 341 ASN cc_start: 0.5888 (m110) cc_final: 0.5663 (m-40) REVERT: E 415 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8873 (tp-100) REVERT: P 63 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7296 (mt-10) REVERT: Q 1 MET cc_start: 0.1643 (mmm) cc_final: -0.1156 (pmm) REVERT: a 319 GLN cc_start: 0.8477 (tt0) cc_final: 0.8215 (mt0) REVERT: j 139 TRP cc_start: 0.8019 (m100) cc_final: 0.7451 (m100) REVERT: G 111 MET cc_start: 0.8794 (mmp) cc_final: 0.8477 (tmm) REVERT: G 145 PHE cc_start: 0.9095 (t80) cc_final: 0.8848 (t80) REVERT: G 201 MET cc_start: 0.8559 (tpp) cc_final: 0.8344 (tpp) REVERT: I 294 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8514 (mm-30) REVERT: I 358 GLU cc_start: 0.8409 (tt0) cc_final: 0.8125 (tp30) REVERT: N 101 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8696 (mmmt) REVERT: g 217 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8857 (pptt) REVERT: h 363 HIS cc_start: 0.7503 (m-70) cc_final: 0.6955 (m-70) REVERT: m 53 MET cc_start: 0.7764 (mmp) cc_final: 0.6814 (mtt) REVERT: o 141 MET cc_start: 0.3145 (mmm) cc_final: 0.2580 (mmm) REVERT: B 114 LEU cc_start: 0.9239 (tp) cc_final: 0.8981 (tt) REVERT: F 122 LYS cc_start: 0.7774 (mmtt) cc_final: 0.7432 (mmtt) REVERT: O 77 ASN cc_start: 0.8634 (m-40) cc_final: 0.8332 (p0) REVERT: U 8 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8852 (mt) REVERT: b 47 ARG cc_start: 0.7415 (tpt170) cc_final: 0.7184 (tpt170) REVERT: f 84 MET cc_start: 0.8176 (ttm) cc_final: 0.7894 (ttm) outliers start: 88 outliers final: 68 residues processed: 669 average time/residue: 0.6152 time to fit residues: 705.5926 Evaluate side-chains 659 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 586 time to evaluate : 4.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 415 GLN Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain P residue 41 CYS Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain a residue 80 LYS Chi-restraints excluded: chain a residue 116 GLN Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 158 THR Chi-restraints excluded: chain a residue 162 TYR Chi-restraints excluded: chain a residue 240 ASP Chi-restraints excluded: chain a residue 324 LEU Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain c residue 167 LEU Chi-restraints excluded: chain d residue 98 ASP Chi-restraints excluded: chain e residue 209 LEU Chi-restraints excluded: chain e residue 265 LYS Chi-restraints excluded: chain e residue 339 HIS Chi-restraints excluded: chain j residue 88 GLN Chi-restraints excluded: chain j residue 104 TYR Chi-restraints excluded: chain j residue 164 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 227 HIS Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain J residue 142 CYS Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 172 TYR Chi-restraints excluded: chain g residue 217 LYS Chi-restraints excluded: chain h residue 312 PHE Chi-restraints excluded: chain k residue 85 LEU Chi-restraints excluded: chain k residue 116 LEU Chi-restraints excluded: chain k residue 159 ILE Chi-restraints excluded: chain k residue 177 VAL Chi-restraints excluded: chain k residue 209 ILE Chi-restraints excluded: chain o residue 79 HIS Chi-restraints excluded: chain o residue 580 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain F residue 5 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 212 VAL Chi-restraints excluded: chain R residue 66 CYS Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 84 TRP Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 64 TYR Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain f residue 98 ASP Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 149 GLU Chi-restraints excluded: chain f residue 151 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 376 optimal weight: 0.5980 chunk 504 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 436 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 131 optimal weight: 6.9990 chunk 474 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 487 optimal weight: 0.8980 chunk 60 optimal weight: 40.0000 chunk 87 optimal weight: 30.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS ** E 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 339 HIS j 108 ASN ** j 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 GLN I 156 GLN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 120 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.098779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.069389 restraints weight = 219339.773| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.77 r_work: 0.3154 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 1.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 69161 Z= 0.166 Angle : 0.605 14.155 97963 Z= 0.301 Chirality : 0.035 0.248 11544 Planarity : 0.004 0.066 9033 Dihedral : 18.672 178.549 19564 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.97 % Favored : 94.96 % Rotamer: Outliers : 1.74 % Allowed : 24.86 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.12), residues: 5437 helix: 1.02 (0.11), residues: 2412 sheet: -0.89 (0.24), residues: 470 loop : -1.40 (0.12), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP n 177 HIS 0.012 0.001 HIS k 124 PHE 0.030 0.001 PHE e 151 TYR 0.030 0.001 TYR e 91 ARG 0.011 0.000 ARG m 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17290.42 seconds wall clock time: 309 minutes 49.84 seconds (18589.84 seconds total)