Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 10:39:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf8_9362/07_2023/6nf8_9362.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf8_9362/07_2023/6nf8_9362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf8_9362/07_2023/6nf8_9362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf8_9362/07_2023/6nf8_9362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf8_9362/07_2023/6nf8_9362.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf8_9362/07_2023/6nf8_9362.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.067 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 ARG 252": "NH1" <-> "NH2" Residue "e ARG 277": "NH1" <-> "NH2" Residue "e ARG 330": "NH1" <-> "NH2" Residue "e GLU 399": "OE1" <-> "OE2" Residue "G ARG 69": "NH1" <-> "NH2" 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 GLU 142": "OE1" <-> "OE2" 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 ARG 196": "NH1" <-> "NH2" Residue "g ARG 256": "NH1" <-> "NH2" Residue "g GLU 326": "OE1" <-> "OE2" Residue "g GLU 374": "OE1" <-> "OE2" Residue "o ARG 80": "NH1" <-> "NH2" Residue "f PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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': 91, 'rna2p_pyr': 67, 'rna3p_pur': 431, 'rna3p_pyr': 363} 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: {'PTRANS': 19, 'TRANS': 193} 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: 22.80, per 1000 atoms: 0.35 Number of scatterers: 65776 At special positions: 0 Unit cell: (207.58, 193.67, 264.29, 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: 25.37 Conformation dependent library (CDL) restraints added in 5.4 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: 222 helices and 36 sheets defined 49.0% alpha, 8.3% beta 200 base pairs and 399 stacking pairs defined. Time for finding SS restraints: 14.72 Creating SS restraints... Processing helix chain 'C' and resid 58 through 62 removed outlier: 3.601A pdb=" N ILE C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 100 removed outlier: 3.673A pdb=" N ASP C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'E' and resid 164 through 185 Processing helix chain 'E' and resid 263 through 276 removed outlier: 3.741A 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: 3.689A 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 removed outlier: 3.502A pdb=" N VAL E 414 " --> pdb=" O ASP E 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 40 removed outlier: 3.616A pdb=" N LEU L 36 " --> pdb=" O THR L 32 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS L 37 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG L 38 " --> pdb=" O ASN L 34 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG L 39 " --> pdb=" O GLN L 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 78 Processing helix chain 'P' and resid 84 through 95 Processing helix chain 'P' and resid 100 through 125 removed outlier: 3.535A pdb=" N ILE P 104 " --> pdb=" O HIS P 100 " (cutoff:3.500A) Processing helix chain 'a' and resid 71 through 83 removed outlier: 3.827A pdb=" N ILE a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS a 80 " --> pdb=" O SER a 76 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY a 83 " --> pdb=" O ILE a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 90 Processing helix chain 'a' and resid 106 through 125 removed outlier: 3.573A pdb=" N VAL a 123 " --> pdb=" O GLU a 119 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG a 124 " --> pdb=" O ALA a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 149 removed outlier: 3.783A pdb=" N GLU a 148 " --> pdb=" O ASP a 144 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY a 149 " --> pdb=" O LYS a 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 144 through 149' Processing helix chain 'a' and resid 185 through 196 removed outlier: 3.565A pdb=" N ARG a 190 " --> pdb=" O GLU a 186 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR a 195 " --> pdb=" O MET a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 210 through 220 removed outlier: 3.717A pdb=" N GLN a 215 " --> pdb=" O GLU a 211 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR a 216 " --> pdb=" O GLU a 212 " (cutoff:3.500A) Processing helix chain 'a' and resid 222 through 234 removed outlier: 3.600A pdb=" N VAL a 226 " --> pdb=" O ARG a 222 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU a 227 " --> pdb=" O HIS a 223 " (cutoff:3.500A) Processing helix chain 'a' and resid 238 through 256 removed outlier: 3.759A pdb=" N ILE a 242 " --> pdb=" O SER a 238 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS a 254 " --> pdb=" O GLU a 250 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR a 255 " --> pdb=" O ASP a 251 " (cutoff:3.500A) Processing helix chain 'a' and resid 265 through 277 removed outlier: 4.343A pdb=" N GLY a 269 " --> pdb=" O ARG a 265 " (cutoff:3.500A) Processing helix chain 'a' and resid 280 through 290 removed outlier: 3.611A pdb=" N ASP a 286 " --> pdb=" O GLY a 282 " (cutoff:3.500A) Processing helix chain 'a' and resid 292 through 307 removed outlier: 3.529A pdb=" N SER a 298 " --> pdb=" O ASP a 294 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU a 299 " --> pdb=" O ASP a 295 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL a 300 " --> pdb=" O ALA a 296 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN a 301 " --> pdb=" O ALA a 297 " (cutoff:3.500A) Processing helix chain 'a' and resid 310 through 320 removed outlier: 4.442A pdb=" N ALA a 316 " --> pdb=" O SER a 312 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA a 320 " --> pdb=" O ALA a 316 " (cutoff:3.500A) Processing helix chain 'a' and resid 326 through 334 removed outlier: 3.675A pdb=" N PHE a 330 " --> pdb=" O LEU a 326 " (cutoff:3.500A) Processing helix chain 'a' and resid 337 through 353 removed outlier: 4.067A pdb=" N ILE a 341 " --> pdb=" O LYS a 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU a 342 " --> pdb=" O GLY a 338 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU a 343 " --> pdb=" O ALA a 339 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU a 350 " --> pdb=" O GLN a 346 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE a 353 " --> pdb=" O GLN a 349 " (cutoff:3.500A) Processing helix chain 'c' and resid 7 through 11 Processing helix chain 'c' and resid 12 through 17 Processing helix chain 'c' and resid 41 through 51 Processing helix chain 'c' and resid 51 through 58 removed outlier: 3.569A 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: 3.928A pdb=" N SER c 124 " --> pdb=" O ARG c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 139 through 143 removed outlier: 3.522A pdb=" N GLU c 142 " --> pdb=" O CYS c 139 " (cutoff:3.500A) Processing helix chain 'c' and resid 160 through 168 removed outlier: 3.528A pdb=" N GLN c 164 " --> pdb=" O THR c 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 39 removed outlier: 3.750A pdb=" N ILE d 39 " --> pdb=" O LYS d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 87 removed outlier: 3.953A pdb=" N PHE d 54 " --> pdb=" O PRO d 50 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL d 55 " --> pdb=" O ALA d 51 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU d 56 " --> pdb=" O GLU d 52 " (cutoff:3.500A) Processing helix chain 'd' and resid 88 through 164 removed outlier: 3.552A pdb=" N GLU d 92 " --> pdb=" O GLY d 88 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN d 126 " --> pdb=" O ALA d 122 " (cutoff:3.500A) removed outlier: 3.607A 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 174 removed outlier: 3.864A pdb=" N LEU d 173 " --> pdb=" O ARG d 170 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU d 174 " --> pdb=" O GLU d 171 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 182 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: 3.931A 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: 3.722A pdb=" N LEU e 104 " --> pdb=" O CYS e 101 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 119 removed outlier: 3.828A pdb=" N TYR e 119 " --> pdb=" O GLN e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 123 through 132 removed outlier: 3.644A 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: 3.534A pdb=" N GLU e 201 " --> pdb=" O SER e 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 217 through 238 removed outlier: 4.308A pdb=" N LEU e 221 " --> pdb=" O ASN e 217 " (cutoff:3.500A) Processing helix chain 'e' and resid 240 through 245 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: 3.505A pdb=" N GLU e 333 " --> pdb=" O PRO e 329 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS e 341 " --> pdb=" O ALA e 337 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN e 343 " --> pdb=" O HIS e 339 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA e 344 " --> pdb=" O SER e 340 " (cutoff:3.500A) Processing helix chain 'e' and resid 352 through 364 removed outlier: 3.538A pdb=" N LYS e 362 " --> pdb=" O THR e 358 " (cutoff:3.500A) Processing helix chain 'e' and resid 364 through 406 removed outlier: 3.907A pdb=" N CYS e 368 " --> pdb=" O GLN e 364 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU e 369 " --> pdb=" O LEU e 365 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA e 370 " --> pdb=" O PRO e 366 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU e 371 " --> pdb=" O THR e 367 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA e 374 " --> pdb=" O ALA e 370 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU e 392 " --> pdb=" O VAL e 388 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG e 393 " --> pdb=" O ASN e 389 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU e 394 " --> pdb=" O LEU e 390 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG e 398 " --> pdb=" O GLU e 394 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA e 401 " --> pdb=" O MET e 397 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS e 404 " --> pdb=" O LYS e 400 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 27 removed outlier: 3.953A pdb=" N GLU j 13 " --> pdb=" O ARG j 9 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU j 14 " --> pdb=" O LEU j 10 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG j 16 " --> pdb=" O ALA j 12 " (cutoff:3.500A) removed outlier: 3.727A 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 55 removed outlier: 3.771A pdb=" N TRP j 55 " --> pdb=" O LEU j 52 " (cutoff:3.500A) Processing helix chain 'j' and resid 63 through 69 removed outlier: 3.665A pdb=" N LEU j 67 " --> pdb=" O ARG j 63 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 87 Processing helix chain 'j' and resid 147 through 153 removed outlier: 4.051A pdb=" N THR j 151 " --> pdb=" O GLU j 147 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE j 153 " --> pdb=" O ALA j 149 " (cutoff:3.500A) Processing helix chain 'j' and resid 167 through 182 Processing helix chain 'p' and resid 54 through 58 removed outlier: 3.899A pdb=" N TYR p 58 " --> pdb=" O PRO p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 61 through 68 removed outlier: 3.619A pdb=" N HIS p 65 " --> pdb=" O SER p 61 " (cutoff:3.500A) Processing helix chain 'p' and resid 119 through 125 removed outlier: 3.965A pdb=" N LEU p 123 " --> pdb=" O ASN p 119 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN p 125 " --> pdb=" O LYS p 121 " (cutoff:3.500A) Processing helix chain 'p' and resid 136 through 141 Processing helix chain 'p' and resid 143 through 161 removed outlier: 3.562A pdb=" N ASP p 159 " --> pdb=" O GLN p 155 " (cutoff:3.500A) Processing helix chain 'p' and resid 190 through 195 removed outlier: 3.694A pdb=" N VAL p 194 " --> pdb=" O ALA p 190 " (cutoff:3.500A) Processing helix chain 'p' and resid 200 through 204 removed outlier: 3.675A pdb=" N TYR p 203 " --> pdb=" O TYR p 200 " (cutoff:3.500A) removed outlier: 3.758A 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 209 through 220 removed outlier: 3.752A pdb=" N LEU p 213 " --> pdb=" O PRO p 209 " (cutoff:3.500A) 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 Processing helix chain 'G' and resid 130 through 137 removed outlier: 3.508A pdb=" N GLN G 134 " --> pdb=" O SER G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 152 removed outlier: 3.510A pdb=" N ILE G 144 " --> pdb=" O ASN G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 194 Processing helix chain 'G' and resid 200 through 214 removed outlier: 3.540A pdb=" N LYS G 204 " --> pdb=" O LEU G 200 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS G 214 " --> pdb=" O LEU G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 233 removed outlier: 3.520A pdb=" N LYS G 221 " --> pdb=" O GLY G 217 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASN G 233 " --> pdb=" O MET G 229 " (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: 3.648A pdb=" N THR I 153 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 3.965A 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 removed outlier: 3.515A pdb=" N PHE I 221 " --> pdb=" O ASP I 217 " (cutoff:3.500A) 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: 3.837A pdb=" N LEU I 313 " --> pdb=" O ASP I 309 " (cutoff:3.500A) Proline residue: I 316 - end of helix Processing helix chain 'I' and resid 337 through 353 removed outlier: 3.522A pdb=" N ALA I 341 " --> pdb=" O ARG I 337 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA I 351 " --> pdb=" O ALA I 347 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS I 353 " --> pdb=" O SER I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 357 through 366 removed outlier: 3.726A pdb=" N GLU I 362 " --> pdb=" O GLU I 358 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TRP I 363 " --> pdb=" O ASP I 359 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG I 365 " --> pdb=" O VAL I 361 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN I 366 " --> pdb=" O GLU I 362 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 103 removed outlier: 4.484A pdb=" N LEU J 88 " --> pdb=" O ASP J 84 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP J 89 " --> pdb=" O LYS J 85 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 162 removed outlier: 3.547A pdb=" N VAL J 155 " --> pdb=" O SER J 151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU J 158 " --> pdb=" O ASP J 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 55 removed outlier: 3.945A pdb=" N LEU N 35 " --> pdb=" O ASP N 31 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASP N 49 " --> pdb=" O TYR N 45 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU N 50 " --> pdb=" O GLU N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 58 No H-bonds generated for 'chain 'N' and resid 56 through 58' Processing helix chain 'N' and resid 64 through 78 removed outlier: 3.774A pdb=" N GLN N 68 " --> pdb=" O PRO N 64 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU N 69 " --> pdb=" O LYS N 65 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.693A pdb=" N ARG N 86 " --> pdb=" O CYS N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 117 removed outlier: 3.752A pdb=" N ARG N 112 " --> pdb=" O ARG N 108 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS N 117 " --> pdb=" O HIS N 113 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 58 removed outlier: 3.777A 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: 3.593A pdb=" N ASN g 113 " --> pdb=" O HIS g 109 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 147 removed outlier: 3.851A pdb=" N SER g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) Processing helix chain 'g' and resid 157 through 162 removed outlier: 3.724A pdb=" N VAL g 161 " --> pdb=" O ALA g 157 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 174 removed outlier: 3.770A 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: 3.739A pdb=" N THR g 192 " --> pdb=" O LYS g 188 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN g 194 " --> pdb=" O PHE g 190 " (cutoff:3.500A) Processing helix chain 'g' and resid 220 through 231 removed outlier: 3.502A 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 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: 7.472A pdb=" N LYS g 330 " --> pdb=" O GLU g 326 " (cutoff:3.500A) removed outlier: 8.111A 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 368 through 371 removed outlier: 3.609A pdb=" N HIS g 371 " --> pdb=" O GLU g 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 368 through 371' Processing helix chain 'g' and resid 372 through 384 removed outlier: 3.597A pdb=" N LYS g 376 " --> pdb=" O THR g 372 " (cutoff:3.500A) Processing helix chain 'g' and resid 386 through 391 Processing helix chain 'h' and resid 287 through 298 Processing helix chain 'h' and resid 325 through 330 removed outlier: 3.931A pdb=" N GLU h 330 " --> pdb=" O LYS h 327 " (cutoff:3.500A) Processing helix chain 'h' and resid 336 through 351 Processing helix chain 'h' and resid 356 through 372 removed outlier: 3.522A pdb=" N LYS h 360 " --> pdb=" O SER h 356 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE h 367 " --> pdb=" O HIS h 363 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG h 368 " --> pdb=" O ILE h 364 " (cutoff:3.500A) Processing helix chain 'h' and resid 375 through 381 removed outlier: 3.839A pdb=" N LYS h 379 " --> pdb=" O GLN h 375 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 20 removed outlier: 3.678A pdb=" N LEU i 9 " --> pdb=" O SER i 5 " (cutoff:3.500A) Processing helix chain 'i' and resid 30 through 39 removed outlier: 3.984A pdb=" N VAL i 34 " --> pdb=" O SER i 30 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU i 39 " --> pdb=" O LYS i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 67 removed outlier: 3.676A pdb=" N PHE i 59 " --> pdb=" O HIS i 55 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA i 60 " --> pdb=" O ASN i 56 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU i 61 " --> pdb=" O THR i 57 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 87 removed outlier: 3.639A pdb=" N LYS i 87 " --> pdb=" O LEU i 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 62 removed outlier: 3.968A pdb=" N LYS k 61 " --> pdb=" O PRO k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 105 through 110 removed outlier: 3.534A 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 128 removed outlier: 3.772A pdb=" N CYS k 125 " --> pdb=" O ILE k 121 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU k 126 " --> pdb=" O LYS k 122 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA k 127 " --> pdb=" O LYS k 123 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU k 128 " --> pdb=" O HIS k 124 " (cutoff:3.500A) Processing helix chain 'k' and resid 129 through 131 No H-bonds generated for 'chain 'k' and resid 129 through 131' Processing helix chain 'k' and resid 141 through 149 Processing helix chain 'k' and resid 185 through 197 removed outlier: 3.950A pdb=" N LYS k 190 " --> pdb=" O ASP k 186 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE k 193 " --> pdb=" O LYS k 189 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS k 194 " --> pdb=" O LYS k 190 " (cutoff:3.500A) Processing helix chain 'k' and resid 216 through 231 removed outlier: 3.513A pdb=" N THR k 229 " --> pdb=" O MET k 225 " (cutoff:3.500A) Processing helix chain 'k' and resid 232 through 235 removed outlier: 3.676A pdb=" N SER k 235 " --> pdb=" O TYR k 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 232 through 235' Processing helix chain 'k' and resid 239 through 243 removed outlier: 3.672A pdb=" N GLU k 242 " --> pdb=" O GLU k 239 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS k 243 " --> pdb=" O GLU k 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 239 through 243' Processing helix chain 'k' and resid 258 through 275 removed outlier: 4.246A pdb=" N LYS k 262 " --> pdb=" O SER k 258 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN k 263 " --> pdb=" O ALA k 259 " (cutoff:3.500A) Processing helix chain 'k' and resid 282 through 288 removed outlier: 3.527A pdb=" N THR k 288 " --> pdb=" O GLU k 284 " (cutoff:3.500A) Processing helix chain 'k' and resid 289 through 303 removed outlier: 3.766A pdb=" N ASP k 293 " --> pdb=" O LYS k 289 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR k 294 " --> pdb=" O GLU k 290 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER k 300 " --> pdb=" O ASN k 296 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU k 301 " --> pdb=" O SER k 297 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS k 302 " --> pdb=" O VAL k 298 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN k 303 " --> pdb=" O VAL k 299 " (cutoff:3.500A) Processing helix chain 'k' and resid 307 through 320 removed outlier: 3.765A pdb=" N ILE k 311 " --> pdb=" O ASN k 307 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER k 312 " --> pdb=" O GLU k 308 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS k 315 " --> pdb=" O ILE k 311 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 58 removed outlier: 3.815A pdb=" N ALA m 54 " --> pdb=" O SER m 50 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS m 55 " --> pdb=" O ILE m 51 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TRP m 56 " --> pdb=" O MET m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 88 Processing helix chain 'm' and resid 100 through 109 Processing helix chain 'o' and resid 69 through 78 removed outlier: 3.631A pdb=" N ALA o 73 " --> pdb=" O ALA o 69 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL o 78 " --> pdb=" O LEU o 74 " (cutoff:3.500A) Processing helix chain 'o' and resid 99 through 124 removed outlier: 3.555A pdb=" N TYR o 124 " --> pdb=" O ILE o 120 " (cutoff:3.500A) Processing helix chain 'o' and resid 146 through 156 removed outlier: 4.404A pdb=" N UNK o 150 " --> pdb=" O UNK o 146 " (cutoff:3.500A) Processing helix chain 'o' and resid 166 through 171 removed outlier: 4.328A pdb=" N UNK o 171 " --> pdb=" O UNK o 167 " (cutoff:3.500A) Processing helix chain 'o' and resid 221 through 230 Processing helix chain 'o' and resid 238 through 249 Processing helix chain 'o' and resid 256 through 267 removed outlier: 4.294A pdb=" N UNK o 260 " --> pdb=" O UNK o 256 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N UNK o 261 " --> pdb=" O UNK o 257 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N UNK o 267 " --> pdb=" O UNK o 263 " (cutoff:3.500A) Processing helix chain 'o' and resid 273 through 285 removed outlier: 4.370A pdb=" N UNK o 277 " --> pdb=" O UNK o 273 " (cutoff:3.500A) Processing helix chain 'o' and resid 291 through 296 removed outlier: 3.614A pdb=" N UNK o 296 " --> pdb=" O UNK o 292 " (cutoff:3.500A) Processing helix chain 'o' and resid 312 through 325 removed outlier: 3.560A pdb=" N UNK o 316 " --> pdb=" O UNK o 312 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N UNK o 317 " --> pdb=" O UNK o 313 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N UNK o 319 " --> pdb=" O UNK o 315 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N UNK o 320 " --> pdb=" O UNK o 316 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N UNK o 323 " --> pdb=" O UNK o 319 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N UNK o 325 " --> pdb=" O UNK o 321 " (cutoff:3.500A) Processing helix chain 'o' and resid 332 through 341 removed outlier: 4.146A pdb=" N UNK o 336 " --> pdb=" O UNK o 332 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N UNK o 337 " --> pdb=" O UNK o 333 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N UNK o 339 " --> pdb=" O UNK o 335 " (cutoff:3.500A) Processing helix chain 'o' and resid 372 through 382 removed outlier: 3.636A pdb=" N HIS o 376 " --> pdb=" O LEU o 372 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N HIS o 377 " --> pdb=" O ALA o 373 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE o 378 " --> pdb=" O THR o 374 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE o 379 " --> pdb=" O TYR o 375 " (cutoff:3.500A) Processing helix chain 'o' and resid 387 through 398 removed outlier: 3.588A pdb=" N UNK o 392 " --> pdb=" O UNK o 388 " (cutoff:3.500A) Processing helix chain 'o' and resid 420 through 430 Processing helix chain 'o' and resid 432 through 440 removed outlier: 3.556A pdb=" N TYR o 436 " --> pdb=" O LEU o 432 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN o 437 " --> pdb=" O GLU o 433 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL o 438 " --> pdb=" O LEU o 434 " (cutoff:3.500A) Processing helix chain 'o' and resid 460 through 469 removed outlier: 3.833A pdb=" N PHE o 464 " --> pdb=" O TYR o 460 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU o 467 " --> pdb=" O LYS o 463 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU o 468 " --> pdb=" O PHE o 464 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS o 469 " --> pdb=" O PHE o 465 " (cutoff:3.500A) Processing helix chain 'o' and resid 473 through 485 Processing helix chain 'o' and resid 492 through 504 removed outlier: 3.586A pdb=" N LEU o 496 " --> pdb=" O HIS o 492 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP o 504 " --> pdb=" O LEU o 500 " (cutoff:3.500A) Processing helix chain 'o' and resid 511 through 522 Processing helix chain 'o' and resid 530 through 537 removed outlier: 3.626A pdb=" N LEU o 537 " --> pdb=" O GLU o 533 " (cutoff:3.500A) Processing helix chain 'o' and resid 546 through 557 removed outlier: 4.151A pdb=" N ALA o 550 " --> pdb=" O GLU o 546 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP o 557 " --> pdb=" O ASP o 553 " (cutoff:3.500A) Processing helix chain 'o' and resid 580 through 590 removed outlier: 3.902A pdb=" N ILE o 584 " --> pdb=" O ASN o 580 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU o 585 " --> pdb=" O TYR o 581 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY o 590 " --> pdb=" O PHE o 586 " (cutoff:3.500A) Processing helix chain 'o' and resid 597 through 602 removed outlier: 4.259A pdb=" N LEU o 601 " --> pdb=" O LYS o 597 " (cutoff:3.500A) Processing helix chain 'o' and resid 610 through 616 removed outlier: 3.707A pdb=" N LEU o 614 " --> pdb=" O ARG o 610 " (cutoff:3.500A) Processing helix chain 'o' and resid 617 through 619 No H-bonds generated for 'chain 'o' and resid 617 through 619' Processing helix chain 'o' and resid 625 through 639 removed outlier: 3.980A pdb=" N GLN o 629 " --> pdb=" O SER o 625 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA o 630 " --> pdb=" O SER o 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.615A pdb=" N PHE B 68 " --> pdb=" O LYS B 65 " (cutoff:3.500A) 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: 3.741A pdb=" N THR B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 139 No H-bonds generated for 'chain 'B' and resid 137 through 139' Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 167 through 172 removed outlier: 3.638A pdb=" N LEU B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 204 removed outlier: 3.637A pdb=" N ARG B 199 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 202 " --> pdb=" O VAL B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 261 removed outlier: 3.591A 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 72 through 84 removed outlier: 4.205A pdb=" N ALA F 76 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET F 79 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 4.280A 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 128 through 144 removed outlier: 3.910A pdb=" N GLN K 132 " --> pdb=" O GLY K 128 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR K 133 " --> pdb=" O ILE K 129 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA K 134 " --> pdb=" O ALA K 130 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY K 144 " --> pdb=" O ALA K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 171 removed outlier: 4.010A pdb=" N LEU K 168 " --> pdb=" O ALA K 164 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR K 169 " --> pdb=" O ILE K 165 " (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 111 removed outlier: 3.882A pdb=" N MET O 102 " --> pdb=" O ASN O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 145 removed outlier: 3.984A pdb=" N GLN O 127 " --> pdb=" O SER O 123 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE O 128 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL O 129 " --> pdb=" O GLU O 125 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU O 140 " --> pdb=" O ARG O 136 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS O 141 " --> pdb=" O SER O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 171 Processing helix chain 'O' and resid 173 through 185 removed outlier: 3.544A pdb=" N PHE O 177 " --> pdb=" O ASN O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 199 through 233 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 103 through 119 removed outlier: 3.547A pdb=" N GLU R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE R 117 " --> pdb=" O LYS R 113 " (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 34 through 43 Processing helix chain 'U' and resid 47 through 75 removed outlier: 3.708A pdb=" N ARG U 52 " --> pdb=" O PRO U 48 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN U 53 " --> pdb=" O CYS U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 4.136A pdb=" N ARG U 80 " --> pdb=" O ARG U 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 22 Processing helix chain 'b' and resid 31 through 38 Processing helix chain 'b' and resid 66 through 79 removed outlier: 3.747A pdb=" N ILE b 70 " --> pdb=" O HIS b 66 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS b 73 " --> pdb=" O GLN b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 94 through 110 removed outlier: 3.720A pdb=" N GLY b 110 " --> pdb=" O LEU b 106 " (cutoff:3.500A) Processing helix chain 'b' and resid 113 through 129 removed outlier: 3.502A pdb=" N GLY b 122 " --> pdb=" O PHE b 118 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU b 125 " --> pdb=" O ALA b 121 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA b 127 " --> pdb=" O LYS b 123 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU b 128 " --> pdb=" O ALA b 124 " (cutoff:3.500A) Processing helix chain 'f' and resid 80 through 86 removed outlier: 3.581A pdb=" N LEU f 85 " --> pdb=" O PHE f 81 " (cutoff:3.500A) removed outlier: 4.024A 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 Processing helix chain 'n' and resid 153 through 181 removed outlier: 3.582A pdb=" N TRP n 177 " --> pdb=" O LEU n 173 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY n 181 " --> pdb=" O TRP n 177 " (cutoff:3.500A) Processing helix chain 'z' and resid 101 through 113 removed outlier: 3.776A pdb=" N VAL z 105 " --> pdb=" O HIS z 101 " (cutoff:3.500A) Processing helix chain 'z' and resid 132 through 149 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: 4.137A 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: 6.427A pdb=" N VAL C 117 " --> pdb=" O ARG C 152 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N HIS C 154 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE C 119 " --> pdb=" O HIS C 154 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N GLN C 156 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ALA C 121 " --> pdb=" O GLN C 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 221 through 228 removed outlier: 5.449A pdb=" N ILE E 222 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA E 246 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA E 261 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY E 255 " --> pdb=" O VAL E 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 231 through 232 Processing sheet with id=AA4, first strand: chain 'E' and resid 294 through 298 Processing sheet with id=AA5, first strand: chain 'E' and resid 382 through 385 removed outlier: 3.683A pdb=" N VAL E 384 " --> pdb=" O VAL E 370 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL E 370 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS a 103 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR a 101 " --> pdb=" O PHE E 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 57 through 68 removed outlier: 6.784A pdb=" N ARG L 82 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N THR L 65 " --> pdb=" O CYS L 80 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N CYS L 80 " --> pdb=" O THR L 65 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE L 67 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ARG L 78 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS L 81 " --> pdb=" O CYS L 93 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N VAL L 125 " --> pdb=" O VAL L 92 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE L 94 " --> pdb=" O VAL L 125 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS L 124 " --> pdb=" O GLN L 111 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY L 60 " --> pdb=" O VAL L 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 49 through 50 removed outlier: 3.856A pdb=" N GLU P 49 " --> pdb=" O ALA P 36 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA P 36 " --> pdb=" O GLU P 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 52 through 54 Processing sheet with id=AA9, first strand: chain 'Q' and resid 15 through 19 removed outlier: 6.749A pdb=" N LYS Q 27 " --> pdb=" O ILE Q 18 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL Q 34 " --> pdb=" O PHE Q 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 63 through 68 removed outlier: 6.993A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 85 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU Q 83 " --> pdb=" O LEU Q 65 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LYS Q 67 " --> pdb=" O LEU Q 81 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU Q 81 " --> pdb=" O LYS Q 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 91 through 93 removed outlier: 4.118A pdb=" N VAL Q 91 " --> pdb=" O CYS Q 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 140 through 143 removed outlier: 6.791A pdb=" N LEU a 180 " --> pdb=" O LEU a 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 27 through 29 removed outlier: 6.849A pdb=" N TYR c 79 " --> pdb=" O LYS c 28 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 66 through 68 removed outlier: 3.702A pdb=" N ASN c 33 " --> pdb=" O PHE c 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'd' and resid 190 through 191 removed outlier: 4.183A pdb=" N ALA d 190 " --> pdb=" O VAL d 198 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL d 198 " --> pdb=" O ALA d 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'j' and resid 123 through 130 removed outlier: 3.615A pdb=" N LEU j 118 " --> pdb=" O GLU j 125 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU j 127 " --> pdb=" O GLY j 116 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY j 116 " --> pdb=" O GLU j 127 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ARG j 129 " --> pdb=" O ALA j 114 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ALA j 114 " --> pdb=" O ARG j 129 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG j 99 " --> pdb=" O TRP j 115 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ILE j 117 " --> pdb=" O LEU j 97 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU j 97 " --> pdb=" O ILE j 117 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR j 119 " --> pdb=" O TRP j 95 " (cutoff:3.500A) removed outlier: 5.682A 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: 3.636A 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: 3.712A 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: 3.762A pdb=" N ASN I 280 " --> pdb=" O SER I 333 " (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 64 through 65 removed outlier: 4.243A pdb=" N THR J 64 " --> pdb=" O THR o 64 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR o 64 " --> pdb=" O THR J 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'J' and resid 108 through 109 removed outlier: 3.920A pdb=" N HIS J 109 " --> pdb=" O CYS J 142 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY J 82 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL J 80 " --> pdb=" O ARG J 141 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS J 74 " --> pdb=" O HIS J 147 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR J 149 " --> pdb=" O LEU J 72 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU J 72 " --> pdb=" O THR J 149 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR J 73 " --> pdb=" O LEU J 177 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU J 177 " --> pdb=" O TYR J 73 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ARG J 75 " --> pdb=" O THR J 175 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR J 175 " --> pdb=" O ARG J 75 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER J 77 " --> pdb=" O THR J 173 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET J 170 " --> pdb=" O ILE k 159 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 117 through 121 removed outlier: 4.031A pdb=" N PHE J 118 " --> pdb=" O TYR J 134 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR J 134 " --> pdb=" O PHE J 118 " (cutoff:3.500A) removed outlier: 3.652A 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: 3.507A pdb=" N TYR g 67 " --> pdb=" O LEU g 98 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU g 98 " --> pdb=" O TYR g 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'g' and resid 150 through 154 removed outlier: 6.914A pdb=" N LEU g 257 " --> pdb=" O ALA g 304 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL g 306 " --> pdb=" O LEU g 257 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL g 259 " --> pdb=" O VAL g 306 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR g 308 " --> pdb=" O VAL g 259 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL g 261 " --> pdb=" O THR g 308 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL g 121 " --> pdb=" O ILE g 305 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU g 307 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR g 123 " --> pdb=" O LEU g 307 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG g 122 " --> pdb=" O ILE g 340 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE g 342 " --> pdb=" O ARG g 122 " (cutoff:3.500A) removed outlier: 5.684A 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: 3.987A pdb=" N TYR g 207 " --> pdb=" O THR g 215 " (cutoff:3.500A) removed outlier: 4.016A 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 'k' and resid 175 through 178 Processing sheet with id=AD2, first strand: chain 'B' and resid 95 through 99 Processing sheet with id=AD3, first strand: chain 'B' and resid 154 through 156 removed outlier: 5.946A pdb=" N ILE B 131 " --> pdb=" O TYR B 154 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N HIS B 156 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE B 133 " --> pdb=" O HIS B 156 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE B 182 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL B 211 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N PHE B 184 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL B 225 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLY B 210 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 35 through 52 removed outlier: 6.699A pdb=" N ASP F 67 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU F 39 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU F 65 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ASN F 41 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR F 63 " --> pdb=" O ASN F 41 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLY F 43 " --> pdb=" O GLY F 61 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLY F 61 " --> pdb=" O GLY F 43 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ARG F 45 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR F 59 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 10.453A pdb=" N LEU F 47 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 12.696A pdb=" N ARG F 57 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE F 68 " --> pdb=" O TYR F 4 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR F 4 " --> pdb=" O PHE F 68 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 98 through 103 removed outlier: 3.881A pdb=" N GLN K 99 " --> pdb=" O LYS K 92 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA K 89 " --> pdb=" O VAL K 153 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL K 150 " --> pdb=" O VAL K 175 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER K 177 " --> pdb=" O VAL K 150 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'f' and resid 123 through 126 removed outlier: 7.653A pdb=" N ASP f 112 " --> pdb=" O ILE f 108 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE f 108 " --> pdb=" O ASP f 112 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR f 114 " --> pdb=" O PHE f 106 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY f 172 " --> pdb=" O ARG f 142 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG f 144 " --> pdb=" O LEU f 170 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU f 170 " --> pdb=" O ARG f 144 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU f 146 " --> pdb=" O ALA f 168 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA f 168 " --> pdb=" O LEU f 146 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'f' and resid 151 through 152 removed outlier: 4.219A pdb=" N SER f 152 " --> pdb=" O THR f 161 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR f 161 " --> pdb=" O SER f 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'z' and resid 88 through 90 removed outlier: 5.846A pdb=" N HIS z 88 " --> pdb=" O TYR z 128 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU z 130 " --> pdb=" O HIS z 88 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE z 90 " --> pdb=" O LEU z 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'z' and resid 159 through 164 removed outlier: 3.592A pdb=" N LYS z 194 " --> pdb=" O LEU z 163 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL z 189 " --> pdb=" O LEU z 240 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL z 239 " --> pdb=" O SER z 224 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG z 241 " --> pdb=" O THR z 222 " (cutoff:3.500A) 1782 hydrogen bonds defined for protein. 5166 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 495 hydrogen bonds 862 hydrogen bond angles 0 basepair planarities 200 basepair parallelities 399 stacking parallelities Total time for adding SS restraints: 25.46 Time building geometry restraints manager: 27.97 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: 17076 1.34 - 1.45: 16847 1.45 - 1.57: 32993 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 3.20e+00 bond pdb=" N MET U 1 " pdb=" CA MET U 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 3.09e+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 3.04e+00 bond pdb=" N MET b 1 " pdb=" CA MET b 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 ... (remaining 69156 not shown) Histogram of bond angle deviations from ideal: 81.82 - 92.26: 2 92.26 - 102.69: 1663 102.69 - 113.13: 43537 113.13 - 123.56: 47335 123.56 - 134.00: 5426 Bond angle restraints: 97963 Sorted by residual: angle pdb=" O3' C A 569 " pdb=" P C A 570 " pdb=" OP1 C A 570 " ideal model delta sigma weight residual 108.00 81.82 26.18 3.00e+00 1.11e-01 7.61e+01 angle pdb=" O3' C A 569 " pdb=" P C A 570 " pdb=" OP2 C A 570 " ideal model delta sigma weight residual 108.00 81.90 26.10 3.00e+00 1.11e-01 7.57e+01 angle pdb=" N VAL j 32 " pdb=" CA VAL j 32 " pdb=" C VAL j 32 " ideal model delta sigma weight residual 111.90 108.88 3.02 8.10e-01 1.52e+00 1.39e+01 angle pdb=" OP1 C A 570 " pdb=" P C A 570 " pdb=" OP2 C A 570 " ideal model delta sigma weight residual 119.60 130.57 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" N VAL i 68 " pdb=" CA VAL i 68 " pdb=" C VAL i 68 " ideal model delta sigma weight residual 112.12 109.26 2.86 8.40e-01 1.42e+00 1.16e+01 ... (remaining 97958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 39130 35.14 - 70.27: 820 70.27 - 105.41: 62 105.41 - 140.54: 8 140.54 - 175.68: 3 Dihedral angle restraints: 40023 sinusoidal: 23490 harmonic: 16533 Sorted by residual: 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 46.44 -174.44 1 1.70e+01 3.46e-03 6.63e+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 12.42 -140.42 1 1.70e+01 3.46e-03 5.88e+01 dihedral pdb=" CB CYS m 55 " pdb=" SG CYS m 55 " pdb=" SG CYS m 66 " pdb=" CB CYS m 66 " ideal model delta sinusoidal sigma weight residual -86.00 -146.06 60.06 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 40020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.380: 11543 0.380 - 0.760: 0 0.760 - 1.140: 0 1.140 - 1.520: 0 1.520 - 1.900: 1 Chirality restraints: 11544 Sorted by residual: chirality pdb=" P C A 570 " pdb=" OP1 C A 570 " pdb=" OP2 C A 570 " pdb=" O5' C A 570 " both_signs ideal model delta sigma weight residual True 2.41 0.51 1.90 2.00e-01 2.50e+01 9.03e+01 chirality pdb=" CA ILE o 96 " pdb=" N ILE o 96 " pdb=" C ILE o 96 " pdb=" CB ILE o 96 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ILE k 110 " pdb=" N ILE k 110 " pdb=" C ILE k 110 " pdb=" CB ILE k 110 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 11541 not shown) Planarity restraints: 9033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER e 269 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO e 270 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO e 270 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO e 270 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U A 478 " 0.022 2.00e-02 2.50e+03 1.10e-02 2.70e+00 pdb=" N1 U A 478 " -0.019 2.00e-02 2.50e+03 pdb=" C2 U A 478 " -0.008 2.00e-02 2.50e+03 pdb=" O2 U A 478 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U A 478 " 0.007 2.00e-02 2.50e+03 pdb=" C4 U A 478 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U A 478 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U A 478 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U A 478 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 556 " 0.016 2.00e-02 2.50e+03 9.80e-03 2.16e+00 pdb=" N1 U A 556 " -0.023 2.00e-02 2.50e+03 pdb=" C2 U A 556 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U A 556 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U A 556 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U A 556 " 0.007 2.00e-02 2.50e+03 pdb=" O4 U A 556 " -0.000 2.00e-02 2.50e+03 pdb=" C5 U A 556 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U A 556 " -0.001 2.00e-02 2.50e+03 ... (remaining 9030 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 349 2.51 - 3.11: 46024 3.11 - 3.71: 102035 3.71 - 4.30: 146122 4.30 - 4.90: 226620 Nonbonded interactions: 521150 Sorted by model distance: nonbonded pdb=" O2 U A 607 " pdb=" O6 G A 686 " model vdw 1.916 2.432 nonbonded pdb=" O2' C A 391 " pdb=" O2 U A 478 " model vdw 1.919 2.440 nonbonded pdb=" O2' G A 782 " pdb=" O2 U A 786 " model vdw 1.926 2.440 nonbonded pdb=" O2' U A 363 " pdb=" OP1 A A 364 " model vdw 1.935 2.440 nonbonded pdb=" O2' A A 188 " pdb=" O5' U A 189 " model vdw 1.957 2.440 ... (remaining 521145 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: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 16.860 Check model and map are aligned: 0.730 Set scattering table: 0.440 Process input model: 140.470 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 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 0.034 69161 Z= 0.094 Angle : 0.389 26.175 97963 Z= 0.213 Chirality : 0.034 1.900 11544 Planarity : 0.002 0.061 9033 Dihedral : 12.763 175.678 29287 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 1.31 % Allowed : 10.41 % Favored : 88.28 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -2.53 (0.11), residues: 5437 helix: -0.02 (0.11), residues: 2276 sheet: -3.31 (0.20), residues: 427 loop : -2.98 (0.11), residues: 2734 *********************** 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 1752 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1724 time to evaluate : 4.520 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 8 residues processed: 1745 average time/residue: 0.7099 time to fit residues: 1990.7322 Evaluate side-chains 770 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 762 time to evaluate : 4.555 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.6747 time to fit residues: 14.6652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 504 optimal weight: 0.0070 chunk 452 optimal weight: 9.9990 chunk 251 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 305 optimal weight: 7.9990 chunk 241 optimal weight: 20.0000 chunk 467 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 348 optimal weight: 6.9990 chunk 542 optimal weight: 4.9990 overall best weight: 2.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 HIS E 292 HIS E 302 HIS ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 HIS L 103 GLN Q 44 ASN ** c 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 117 HIS e 131 ASN e 238 GLN e 317 GLN e 405 HIS j 24 GLN j 45 HIS ** p 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN G 96 ASN ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 HIS J 183 HIS N 113 HIS g 62 HIS g 291 ASN g 367 HIS h 322 HIS ** h 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 124 HIS m 15 ASN o 420 GLN B 75 ASN B 79 HIS B 119 ASN O 127 GLN O 143 GLN O 145 HIS U 4 HIS U 53 GLN z 264 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 69161 Z= 0.298 Angle : 0.689 26.825 97963 Z= 0.341 Chirality : 0.042 1.916 11544 Planarity : 0.006 0.102 9033 Dihedral : 12.900 177.457 17672 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.61 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -1.58 (0.11), residues: 5437 helix: 0.64 (0.11), residues: 2342 sheet: -2.53 (0.22), residues: 471 loop : -2.43 (0.11), residues: 2624 *********************** 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 1010 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 837 time to evaluate : 4.739 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 outliers start: 173 outliers final: 99 residues processed: 952 average time/residue: 0.6379 time to fit residues: 1027.0775 Evaluate side-chains 767 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 668 time to evaluate : 4.547 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 0 residues processed: 99 average time/residue: 0.4765 time to fit residues: 95.7325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 301 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 451 optimal weight: 5.9990 chunk 369 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 543 optimal weight: 4.9990 chunk 586 optimal weight: 0.9980 chunk 483 optimal weight: 6.9990 chunk 538 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 435 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 HIS a 166 HIS ** a 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 18 GLN c 63 GLN c 146 GLN d 102 HIS e 131 ASN e 317 GLN G 113 GLN ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 HIS ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 ASN ** h 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 420 GLN B 82 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** K 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 136 GLN n 139 ASN n 166 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 69161 Z= 0.228 Angle : 0.583 26.493 97963 Z= 0.288 Chirality : 0.039 1.914 11544 Planarity : 0.004 0.056 9033 Dihedral : 12.894 177.788 17672 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.62 % Favored : 93.34 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -1.07 (0.11), residues: 5437 helix: 0.99 (0.11), residues: 2352 sheet: -2.22 (0.22), residues: 489 loop : -2.08 (0.12), residues: 2596 *********************** 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 830 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 734 time to evaluate : 4.544 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 outliers start: 96 outliers final: 43 residues processed: 797 average time/residue: 0.6254 time to fit residues: 853.4909 Evaluate side-chains 662 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 619 time to evaluate : 4.659 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4807 time to fit residues: 45.8700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 536 optimal weight: 0.5980 chunk 408 optimal weight: 0.0470 chunk 281 optimal weight: 7.9990 chunk 60 optimal weight: 40.0000 chunk 259 optimal weight: 20.0000 chunk 364 optimal weight: 2.9990 chunk 545 optimal weight: 0.9990 chunk 577 optimal weight: 40.0000 chunk 284 optimal weight: 0.9980 chunk 516 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 146 GLN e 317 GLN p 111 GLN p 125 GLN G 113 GLN G 146 HIS ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 375 GLN k 124 HIS ** m 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 109 GLN B 243 GLN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 69161 Z= 0.140 Angle : 0.537 26.628 97963 Z= 0.260 Chirality : 0.037 1.906 11544 Planarity : 0.004 0.057 9033 Dihedral : 12.820 178.505 17672 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.26 % Favored : 94.72 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -0.77 (0.12), residues: 5437 helix: 1.18 (0.11), residues: 2346 sheet: -1.79 (0.23), residues: 480 loop : -1.90 (0.12), residues: 2611 *********************** 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 787 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 708 time to evaluate : 4.603 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 outliers start: 79 outliers final: 39 residues processed: 752 average time/residue: 0.6177 time to fit residues: 800.1456 Evaluate side-chains 653 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 614 time to evaluate : 4.577 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.5010 time to fit residues: 42.3944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 480 optimal weight: 0.0170 chunk 327 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 429 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 492 optimal weight: 1.9990 chunk 398 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 294 optimal weight: 3.9990 chunk 517 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 overall best weight: 1.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 GLN L 100 HIS L 101 ASN ** a 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 HIS ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 ASN ** h 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.5055 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= 0.198 Angle : 0.565 26.412 97963 Z= 0.278 Chirality : 0.039 1.912 11544 Planarity : 0.004 0.069 9033 Dihedral : 12.956 178.482 17672 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -0.61 (0.12), residues: 5437 helix: 1.22 (0.11), residues: 2361 sheet: -1.56 (0.23), residues: 487 loop : -1.78 (0.12), residues: 2589 *********************** 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 729 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 660 time to evaluate : 4.700 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 outliers start: 69 outliers final: 35 residues processed: 707 average time/residue: 0.6182 time to fit residues: 752.6251 Evaluate side-chains 637 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 602 time to evaluate : 4.604 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4806 time to fit residues: 37.8774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 194 optimal weight: 10.0000 chunk 519 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 338 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 577 optimal weight: 50.0000 chunk 479 optimal weight: 5.9990 chunk 267 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 303 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 359 HIS Q 52 HIS Q 79 HIS a 75 GLN ** a 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 59 ASN d 72 GLN d 135 GLN e 131 ASN e 224 GLN e 317 GLN G 72 GLN ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 HIS ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 325 GLN ** h 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 40 GLN k 124 HIS m 15 ASN ** m 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 69161 Z= 0.322 Angle : 0.700 26.218 97963 Z= 0.348 Chirality : 0.043 1.916 11544 Planarity : 0.005 0.059 9033 Dihedral : 13.561 177.485 17672 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.71 % Favored : 93.27 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -0.80 (0.11), residues: 5437 helix: 0.85 (0.11), residues: 2401 sheet: -1.23 (0.24), residues: 470 loop : -1.78 (0.12), residues: 2566 *********************** 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 751 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 639 time to evaluate : 4.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 63 residues processed: 707 average time/residue: 0.6237 time to fit residues: 760.3693 Evaluate side-chains 644 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 581 time to evaluate : 4.606 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.5273 time to fit residues: 67.1019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 556 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 329 optimal weight: 4.9990 chunk 421 optimal weight: 2.9990 chunk 326 optimal weight: 6.9990 chunk 486 optimal weight: 1.9990 chunk 322 optimal weight: 0.0370 chunk 575 optimal weight: 0.9990 chunk 360 optimal weight: 9.9990 chunk 350 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN E 175 GLN a 75 GLN a 314 GLN p 81 HIS G 96 ASN G 113 GLN ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 143 GLN ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 69161 Z= 0.212 Angle : 0.612 26.325 97963 Z= 0.300 Chirality : 0.040 1.910 11544 Planarity : 0.004 0.074 9033 Dihedral : 13.419 177.813 17672 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -0.57 (0.12), residues: 5437 helix: 1.05 (0.11), residues: 2386 sheet: -1.23 (0.23), residues: 497 loop : -1.62 (0.12), residues: 2554 *********************** 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 685 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 636 time to evaluate : 4.642 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 outliers start: 49 outliers final: 24 residues processed: 672 average time/residue: 0.6338 time to fit residues: 737.9581 Evaluate side-chains 606 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 582 time to evaluate : 4.713 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4973 time to fit residues: 28.5350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 355 optimal weight: 0.8980 chunk 229 optimal weight: 20.0000 chunk 343 optimal weight: 8.9990 chunk 173 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 365 optimal weight: 8.9990 chunk 392 optimal weight: 6.9990 chunk 284 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 452 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN p 81 HIS G 45 GLN ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 GLN ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 124 HIS m 15 ASN ** m 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN F 92 ASN ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 166 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.6382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 69161 Z= 0.235 Angle : 0.628 26.291 97963 Z= 0.308 Chirality : 0.041 1.909 11544 Planarity : 0.004 0.085 9033 Dihedral : 13.461 178.149 17672 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -0.53 (0.12), residues: 5437 helix: 1.04 (0.11), residues: 2401 sheet: -1.16 (0.24), residues: 481 loop : -1.58 (0.12), residues: 2555 *********************** 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 652 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 608 time to evaluate : 4.700 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 outliers start: 44 outliers final: 29 residues processed: 634 average time/residue: 0.6169 time to fit residues: 681.1159 Evaluate side-chains 603 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 574 time to evaluate : 4.684 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4771 time to fit residues: 32.9267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 523 optimal weight: 3.9990 chunk 551 optimal weight: 0.2980 chunk 502 optimal weight: 8.9990 chunk 536 optimal weight: 0.1980 chunk 322 optimal weight: 0.0970 chunk 233 optimal weight: 9.9990 chunk 421 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 484 optimal weight: 0.9990 chunk 507 optimal weight: 10.0000 chunk 534 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 GLN P 69 ASN e 131 ASN j 108 ASN G 96 ASN ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 194 ASN i 75 HIS ** m 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 69161 Z= 0.159 Angle : 0.589 26.349 97963 Z= 0.287 Chirality : 0.039 1.907 11544 Planarity : 0.004 0.063 9033 Dihedral : 13.338 177.936 17672 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -0.40 (0.12), residues: 5437 helix: 1.13 (0.11), residues: 2403 sheet: -1.00 (0.24), residues: 491 loop : -1.52 (0.12), residues: 2543 *********************** 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 669 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 636 time to evaluate : 4.641 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 outliers start: 33 outliers final: 15 residues processed: 652 average time/residue: 0.6289 time to fit residues: 714.2259 Evaluate side-chains 600 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 585 time to evaluate : 4.550 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.6042 time to fit residues: 21.6976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 352 optimal weight: 1.9990 chunk 567 optimal weight: 8.9990 chunk 346 optimal weight: 9.9990 chunk 268 optimal weight: 0.9990 chunk 394 optimal weight: 20.0000 chunk 594 optimal weight: 0.0980 chunk 547 optimal weight: 0.2980 chunk 473 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 365 optimal weight: 8.9990 chunk 290 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 131 ASN ** p 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 HIS ** k 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 124 HIS m 15 ASN ** m 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.6378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.063 69161 Z= 0.153 Angle : 0.592 26.354 97963 Z= 0.287 Chirality : 0.039 1.907 11544 Planarity : 0.004 0.065 9033 Dihedral : 13.262 177.603 17672 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -0.31 (0.12), residues: 5437 helix: 1.22 (0.11), residues: 2387 sheet: -0.93 (0.24), residues: 489 loop : -1.47 (0.12), residues: 2561 ********************** 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 619 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 604 time to evaluate : 4.717 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 outliers start: 15 outliers final: 9 residues processed: 611 average time/residue: 0.6514 time to fit residues: 693.7806 Evaluate side-chains 588 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 579 time to evaluate : 4.633 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.6327 time to fit residues: 15.6347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 376 optimal weight: 10.0000 chunk 504 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 436 optimal weight: 0.9980 chunk 69 optimal weight: 30.0000 chunk 131 optimal weight: 0.5980 chunk 474 optimal weight: 3.9990 chunk 198 optimal weight: 0.6980 chunk 487 optimal weight: 0.8980 chunk 60 optimal weight: 40.0000 chunk 87 optimal weight: 30.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 172 ASN e 131 ASN ** j 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 81 HIS ** p 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN G 113 GLN G 166 HIS ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 HIS ** m 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 127 GLN ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 135 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.104041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.075007 restraints weight = 216245.693| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.25 r_work: 0.3311 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.6411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 69161 Z= 0.147 Angle : 0.579 26.347 97963 Z= 0.281 Chirality : 0.038 1.908 11544 Planarity : 0.004 0.064 9033 Dihedral : 13.196 177.168 17672 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -0.24 (0.12), residues: 5437 helix: 1.25 (0.11), residues: 2389 sheet: -0.89 (0.24), residues: 482 loop : -1.40 (0.12), residues: 2566 =============================================================================== Job complete usr+sys time: 15669.15 seconds wall clock time: 276 minutes 2.37 seconds (16562.37 seconds total)