Starting phenix.real_space_refine on Sun Dec 10 00:27:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/12_2023/6neq_9358.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/12_2023/6neq_9358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/12_2023/6neq_9358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/12_2023/6neq_9358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/12_2023/6neq_9358.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/12_2023/6neq_9358.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 952 5.49 5 S 212 5.16 5 C 37974 2.51 5 N 11974 2.21 5 O 14664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ARG 315": "NH1" <-> "NH2" Residue "e ARG 38": "NH1" <-> "NH2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e ARG 82": "NH1" <-> "NH2" Residue "e ARG 202": "NH1" <-> "NH2" Residue "e TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 252": "NH1" <-> "NH2" Residue "e ARG 277": "NH1" <-> "NH2" Residue "e ARG 330": "NH1" <-> "NH2" Residue "e GLU 399": "OE1" <-> "OE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G ARG 216": "NH1" <-> "NH2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I GLU 102": "OE1" <-> "OE2" Residue "I PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "I TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 173": "OE1" <-> "OE2" Residue "I ARG 175": "NH1" <-> "NH2" Residue "I GLU 206": "OE1" <-> "OE2" Residue "I GLU 207": "OE1" <-> "OE2" Residue "I GLU 239": "OE1" <-> "OE2" Residue "I GLU 282": "OE1" <-> "OE2" Residue "I GLU 294": "OE1" <-> "OE2" Residue "I GLU 358": "OE1" <-> "OE2" Residue "I GLU 385": "OE1" <-> "OE2" Residue "g TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 196": "NH1" <-> "NH2" Residue "g ARG 256": "NH1" <-> "NH2" Residue "g GLU 326": "OE1" <-> "OE2" Residue "g PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 374": "OE1" <-> "OE2" Residue "i TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 80": "NH1" <-> "NH2" Residue "o TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 65776 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 20256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 20256 Classifications: {'RNA': 952} Modifications used: {'rna2p_pur': 90, 'rna2p_pyr': 68, 'rna3p_pur': 432, 'rna3p_pyr': 362} Link IDs: {'rna2p': 158, 'rna3p': 793} Chain: "C" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 998 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "E" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2464 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 13, 'TRANS': 295} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 853 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 11, 'TRANS': 97} Chain: "P" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 916 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 857 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "a" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2356 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 13, 'TRANS': 275} Chain: "c" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1374 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 11, 'TRANS': 156} Chain: "d" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1463 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "e" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2950 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 10, 'TRANS': 347} Chain breaks: 1 Chain: "j" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1792 Classifications: {'peptide': 213} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 192} Chain: "p" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1531 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 20, 'TRANS': 166} Chain: "G" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1721 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 194} Chain: "I" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2541 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 12, 'TRANS': 298} Chain breaks: 1 Chain: "J" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1049 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "N" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 861 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "g" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2855 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 17, 'TRANS': 333} Chain: "h" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 871 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 98} Chain: "i" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 818 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "k" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2227 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 17, 'TRANS': 257} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 9, 'TRANS': 108} Chain: "o" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3273 Classifications: {'peptide': 461} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 145} Link IDs: {'PTRANS': 18, 'TRANS': 442} Chain breaks: 14 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 147} Unresolved non-hydrogen planarities: 147 Chain: "B" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1726 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain: "F" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 991 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain: "K" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1001 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "O" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1421 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain: "R" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 8, 'TRANS': 88} Chain: "U" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 737 Classifications: {'peptide': 86} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 82} Chain: "b" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1108 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "f" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 775 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "n" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 642 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "z" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1616 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 201} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 25.53, per 1000 atoms: 0.39 Number of scatterers: 65776 At special positions: 0 Unit cell: (206.064, 192.112, 266.166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 212 16.00 P 952 15.00 O 14664 8.00 N 11974 7.00 C 37974 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 76 " distance=2.03 Simple disulfide: pdb=" SG CYS m 55 " - pdb=" SG CYS m 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 24.76 Conformation dependent library (CDL) restraints added in 6.1 seconds 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10730 Finding SS restraints... Secondary structure from input PDB file: 225 helices and 37 sheets defined 50.3% alpha, 8.6% beta 232 base pairs and 391 stacking pairs defined. Time for finding SS restraints: 18.17 Creating SS restraints... Processing helix chain 'C' and resid 58 through 62 removed outlier: 3.664A pdb=" N ILE C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 100 removed outlier: 3.700A pdb=" N ASP C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.570A pdb=" N SER C 144 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR C 147 " --> pdb=" O LEU C 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 185 Processing helix chain 'E' and resid 263 through 276 removed outlier: 3.535A pdb=" N ALA E 267 " --> pdb=" O GLU E 263 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL E 276 " --> pdb=" O LYS E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 328 Processing helix chain 'E' and resid 341 through 355 removed outlier: 3.568A pdb=" N ARG E 355 " --> pdb=" O GLN E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 367 Processing helix chain 'E' and resid 408 through 414 Processing helix chain 'L' and resid 32 through 40 Processing helix chain 'L' and resid 71 through 75 removed outlier: 3.505A pdb=" N SER L 75 " --> pdb=" O LYS L 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 78 removed outlier: 3.858A pdb=" N HIS P 75 " --> pdb=" O ASP P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 95 Processing helix chain 'P' and resid 100 through 124 Processing helix chain 'a' and resid 71 through 83 removed outlier: 4.128A pdb=" N ILE a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS a 80 " --> pdb=" O SER a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 90 Processing helix chain 'a' and resid 106 through 125 removed outlier: 3.651A pdb=" N VAL a 123 " --> pdb=" O GLU a 119 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG a 124 " --> pdb=" O ALA a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 148 Processing helix chain 'a' and resid 165 through 169 removed outlier: 3.649A pdb=" N GLU a 168 " --> pdb=" O PRO a 165 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG a 169 " --> pdb=" O HIS a 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 165 through 169' Processing helix chain 'a' and resid 184 through 196 removed outlier: 3.598A pdb=" N ARG a 190 " --> pdb=" O GLU a 186 " (cutoff:3.500A) Processing helix chain 'a' and resid 210 through 220 removed outlier: 4.641A pdb=" N THR a 216 " --> pdb=" O GLU a 212 " (cutoff:3.500A) Processing helix chain 'a' and resid 222 through 234 removed outlier: 3.848A pdb=" N LEU a 227 " --> pdb=" O HIS a 223 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN a 228 " --> pdb=" O VAL a 224 " (cutoff:3.500A) Processing helix chain 'a' and resid 238 through 256 removed outlier: 3.791A pdb=" N ILE a 242 " --> pdb=" O SER a 238 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS a 254 " --> pdb=" O GLU a 250 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR a 255 " --> pdb=" O ASP a 251 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 278 Processing helix chain 'a' and resid 280 through 290 Processing helix chain 'a' and resid 292 through 306 removed outlier: 3.513A pdb=" N ALA a 296 " --> pdb=" O LEU a 292 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL a 300 " --> pdb=" O ALA a 296 " (cutoff:3.500A) Processing helix chain 'a' and resid 310 through 319 removed outlier: 3.772A pdb=" N GLN a 314 " --> pdb=" O GLY a 310 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU a 315 " --> pdb=" O GLN a 311 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS a 317 " --> pdb=" O ALA a 313 " (cutoff:3.500A) Processing helix chain 'a' and resid 324 through 333 removed outlier: 3.869A pdb=" N PHE a 330 " --> pdb=" O LEU a 326 " (cutoff:3.500A) Processing helix chain 'a' and resid 337 through 353 removed outlier: 4.085A pdb=" N ILE a 341 " --> pdb=" O LYS a 337 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU a 343 " --> pdb=" O ALA a 339 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN a 346 " --> pdb=" O GLU a 342 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE a 353 " --> pdb=" O GLN a 349 " (cutoff:3.500A) Processing helix chain 'c' and resid 12 through 17 Processing helix chain 'c' and resid 41 through 58 removed outlier: 4.318A pdb=" N ILE c 52 " --> pdb=" O VAL c 48 " (cutoff:3.500A) Proline residue: c 53 - end of helix removed outlier: 3.616A pdb=" N LYS c 58 " --> pdb=" O GLN c 54 " (cutoff:3.500A) Processing helix chain 'c' and resid 94 through 106 Processing helix chain 'c' and resid 109 through 124 removed outlier: 3.559A pdb=" N LEU c 123 " --> pdb=" O GLU c 119 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER c 124 " --> pdb=" O ARG c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 139 through 143 Processing helix chain 'c' and resid 160 through 168 Processing helix chain 'd' and resid 35 through 39 removed outlier: 3.685A pdb=" N ILE d 39 " --> pdb=" O LYS d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 87 removed outlier: 3.683A pdb=" N PHE d 54 " --> pdb=" O PRO d 50 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU d 56 " --> pdb=" O GLU d 52 " (cutoff:3.500A) Processing helix chain 'd' and resid 88 through 164 removed outlier: 3.761A pdb=" N GLN d 126 " --> pdb=" O ALA d 122 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU d 137 " --> pdb=" O GLN d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 167 No H-bonds generated for 'chain 'd' and resid 165 through 167' Processing helix chain 'd' and resid 169 through 173 removed outlier: 3.545A pdb=" N LEU d 173 " --> pdb=" O ARG d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 182 removed outlier: 3.827A pdb=" N GLU d 178 " --> pdb=" O GLU d 174 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 33 Processing helix chain 'e' and resid 35 through 41 Processing helix chain 'e' and resid 42 through 44 No H-bonds generated for 'chain 'e' and resid 42 through 44' Processing helix chain 'e' and resid 49 through 63 Processing helix chain 'e' and resid 68 through 77 removed outlier: 3.941A pdb=" N ILE e 72 " --> pdb=" O SER e 68 " (cutoff:3.500A) Processing helix chain 'e' and resid 81 through 96 Processing helix chain 'e' and resid 100 through 104 removed outlier: 3.637A pdb=" N LEU e 104 " --> pdb=" O CYS e 101 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 119 removed outlier: 3.803A pdb=" N TYR e 119 " --> pdb=" O GLN e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 123 through 132 removed outlier: 3.585A pdb=" N LYS e 132 " --> pdb=" O THR e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 154 Processing helix chain 'e' and resid 157 through 169 Processing helix chain 'e' and resid 177 through 192 Processing helix chain 'e' and resid 197 through 210 removed outlier: 3.565A pdb=" N GLU e 201 " --> pdb=" O SER e 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 217 through 238 removed outlier: 4.303A pdb=" N LEU e 221 " --> pdb=" O ASN e 217 " (cutoff:3.500A) Processing helix chain 'e' and resid 239 through 245 removed outlier: 3.843A pdb=" N VAL e 243 " --> pdb=" O GLY e 239 " (cutoff:3.500A) Processing helix chain 'e' and resid 255 through 265 Processing helix chain 'e' and resid 266 through 268 No H-bonds generated for 'chain 'e' and resid 266 through 268' Processing helix chain 'e' and resid 275 through 291 Processing helix chain 'e' and resid 327 through 345 removed outlier: 3.522A pdb=" N GLU e 333 " --> pdb=" O PRO e 329 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS e 341 " --> pdb=" O ALA e 337 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN e 343 " --> pdb=" O HIS e 339 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA e 344 " --> pdb=" O SER e 340 " (cutoff:3.500A) Processing helix chain 'e' and resid 352 through 364 Processing helix chain 'e' and resid 364 through 406 removed outlier: 3.909A pdb=" N CYS e 368 " --> pdb=" O GLN e 364 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU e 369 " --> pdb=" O LEU e 365 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA e 370 " --> pdb=" O PRO e 366 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU e 371 " --> pdb=" O THR e 367 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA e 374 " --> pdb=" O ALA e 370 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG e 393 " --> pdb=" O ASN e 389 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU e 394 " --> pdb=" O LEU e 390 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG e 398 " --> pdb=" O GLU e 394 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA e 401 " --> pdb=" O MET e 397 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS e 404 " --> pdb=" O LYS e 400 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 27 removed outlier: 4.069A pdb=" N GLU j 13 " --> pdb=" O ARG j 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU j 14 " --> pdb=" O LEU j 10 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG j 16 " --> pdb=" O ALA j 12 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG j 17 " --> pdb=" O GLU j 13 " (cutoff:3.500A) Processing helix chain 'j' and resid 29 through 34 Processing helix chain 'j' and resid 51 through 53 No H-bonds generated for 'chain 'j' and resid 51 through 53' Processing helix chain 'j' and resid 54 through 61 removed outlier: 3.699A pdb=" N VAL j 58 " --> pdb=" O ALA j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 63 through 69 removed outlier: 3.575A pdb=" N LEU j 67 " --> pdb=" O ARG j 63 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 89 removed outlier: 3.504A pdb=" N GLN j 88 " --> pdb=" O SER j 84 " (cutoff:3.500A) Processing helix chain 'j' and resid 167 through 182 Processing helix chain 'p' and resid 55 through 61 removed outlier: 4.234A pdb=" N LEU p 59 " --> pdb=" O PRO p 55 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP p 60 " --> pdb=" O TRP p 56 " (cutoff:3.500A) Processing helix chain 'p' and resid 61 through 68 removed outlier: 3.695A pdb=" N HIS p 65 " --> pdb=" O SER p 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN p 68 " --> pdb=" O TYR p 64 " (cutoff:3.500A) Processing helix chain 'p' and resid 119 through 124 Processing helix chain 'p' and resid 125 through 127 No H-bonds generated for 'chain 'p' and resid 125 through 127' Processing helix chain 'p' and resid 136 through 141 Processing helix chain 'p' and resid 143 through 161 Processing helix chain 'p' and resid 190 through 196 Processing helix chain 'p' and resid 200 through 204 removed outlier: 3.606A pdb=" N TYR p 203 " --> pdb=" O TYR p 200 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER p 204 " --> pdb=" O PRO p 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 200 through 204' Processing helix chain 'p' and resid 210 through 220 Processing helix chain 'G' and resid 58 through 69 Processing helix chain 'G' and resid 88 through 99 Processing helix chain 'G' and resid 103 through 128 removed outlier: 3.619A pdb=" N ALA G 107 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 137 Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 175 through 194 Processing helix chain 'G' and resid 200 through 214 removed outlier: 3.715A pdb=" N LYS G 204 " --> pdb=" O LEU G 200 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS G 214 " --> pdb=" O LEU G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 232 Processing helix chain 'G' and resid 233 through 240 removed outlier: 4.458A pdb=" N HIS G 238 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR G 239 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG G 240 " --> pdb=" O ALA G 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 93 Processing helix chain 'I' and resid 100 through 112 Processing helix chain 'I' and resid 127 through 132 Processing helix chain 'I' and resid 150 through 154 removed outlier: 3.599A pdb=" N THR I 153 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY I 154 " --> pdb=" O PHE I 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 150 through 154' Processing helix chain 'I' and resid 155 through 178 Processing helix chain 'I' and resid 201 through 209 Processing helix chain 'I' and resid 214 through 230 Processing helix chain 'I' and resid 235 through 243 Processing helix chain 'I' and resid 300 through 304 Processing helix chain 'I' and resid 306 through 321 removed outlier: 3.509A pdb=" N GLN I 312 " --> pdb=" O GLN I 308 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU I 313 " --> pdb=" O ASP I 309 " (cutoff:3.500A) Proline residue: I 316 - end of helix removed outlier: 3.639A pdb=" N LEU I 320 " --> pdb=" O PRO I 316 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 353 removed outlier: 3.529A pdb=" N ALA I 341 " --> pdb=" O ARG I 337 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA I 351 " --> pdb=" O ALA I 347 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS I 353 " --> pdb=" O SER I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 357 through 366 removed outlier: 3.680A pdb=" N GLU I 362 " --> pdb=" O GLU I 358 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP I 363 " --> pdb=" O ASP I 359 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN I 366 " --> pdb=" O GLU I 362 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 103 Processing helix chain 'J' and resid 150 through 162 Processing helix chain 'N' and resid 31 through 59 removed outlier: 3.868A pdb=" N LEU N 35 " --> pdb=" O ASP N 31 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASP N 49 " --> pdb=" O TYR N 45 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLU N 50 " --> pdb=" O GLU N 46 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN N 55 " --> pdb=" O ARG N 51 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER N 56 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU N 57 " --> pdb=" O ARG N 53 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG N 58 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS N 59 " --> pdb=" O ASN N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 78 removed outlier: 4.074A pdb=" N GLN N 68 " --> pdb=" O PRO N 64 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU N 69 " --> pdb=" O LYS N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 107 through 116 Processing helix chain 'g' and resid 54 through 58 removed outlier: 3.816A pdb=" N HIS g 58 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 63 Processing helix chain 'g' and resid 70 through 78 Processing helix chain 'g' and resid 83 through 94 Processing helix chain 'g' and resid 101 through 113 removed outlier: 3.603A pdb=" N ASN g 113 " --> pdb=" O HIS g 109 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 147 removed outlier: 3.814A pdb=" N SER g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) Processing helix chain 'g' and resid 157 through 161 Processing helix chain 'g' and resid 171 through 174 removed outlier: 3.754A pdb=" N LYS g 174 " --> pdb=" O THR g 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 171 through 174' Processing helix chain 'g' and resid 179 through 194 removed outlier: 3.719A pdb=" N THR g 192 " --> pdb=" O LYS g 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN g 194 " --> pdb=" O PHE g 190 " (cutoff:3.500A) Processing helix chain 'g' and resid 220 through 231 removed outlier: 3.514A pdb=" N VAL g 224 " --> pdb=" O PRO g 220 " (cutoff:3.500A) Processing helix chain 'g' and resid 234 through 250 Processing helix chain 'g' and resid 264 through 269 removed outlier: 3.505A pdb=" N GLY g 269 " --> pdb=" O ALA g 266 " (cutoff:3.500A) Processing helix chain 'g' and resid 282 through 285 Processing helix chain 'g' and resid 286 through 293 Processing helix chain 'g' and resid 294 through 296 No H-bonds generated for 'chain 'g' and resid 294 through 296' Processing helix chain 'g' and resid 323 through 336 removed outlier: 3.521A pdb=" N LEU g 327 " --> pdb=" O LEU g 323 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LYS g 330 " --> pdb=" O GLU g 326 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLU g 331 " --> pdb=" O LEU g 327 " (cutoff:3.500A) Processing helix chain 'g' and resid 348 through 362 Processing helix chain 'g' and resid 367 through 371 removed outlier: 3.554A pdb=" N HIS g 371 " --> pdb=" O GLU g 368 " (cutoff:3.500A) Processing helix chain 'g' and resid 372 through 384 removed outlier: 3.631A pdb=" N LYS g 376 " --> pdb=" O THR g 372 " (cutoff:3.500A) Processing helix chain 'g' and resid 386 through 397 removed outlier: 3.916A pdb=" N TYR g 396 " --> pdb=" O ARG g 392 " (cutoff:3.500A) Processing helix chain 'h' and resid 287 through 299 removed outlier: 3.687A pdb=" N GLU h 291 " --> pdb=" O ASN h 287 " (cutoff:3.500A) Processing helix chain 'h' and resid 313 through 317 Processing helix chain 'h' and resid 326 through 330 removed outlier: 3.602A pdb=" N GLU h 330 " --> pdb=" O LYS h 327 " (cutoff:3.500A) Processing helix chain 'h' and resid 336 through 351 removed outlier: 3.569A pdb=" N LYS h 351 " --> pdb=" O CYS h 347 " (cutoff:3.500A) Processing helix chain 'h' and resid 356 through 374 removed outlier: 3.903A pdb=" N PHE h 367 " --> pdb=" O HIS h 363 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG h 368 " --> pdb=" O ILE h 364 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU h 373 " --> pdb=" O ASN h 369 " (cutoff:3.500A) Processing helix chain 'h' and resid 375 through 382 Processing helix chain 'i' and resid 5 through 20 removed outlier: 3.660A pdb=" N LEU i 9 " --> pdb=" O SER i 5 " (cutoff:3.500A) Processing helix chain 'i' and resid 30 through 39 removed outlier: 4.059A pdb=" N VAL i 34 " --> pdb=" O SER i 30 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU i 39 " --> pdb=" O LYS i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 69 removed outlier: 3.753A pdb=" N PHE i 59 " --> pdb=" O HIS i 55 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA i 60 " --> pdb=" O ASN i 56 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU i 61 " --> pdb=" O THR i 57 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET i 62 " --> pdb=" O TYR i 58 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER i 67 " --> pdb=" O GLY i 63 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 87 removed outlier: 3.671A pdb=" N LYS i 87 " --> pdb=" O LEU i 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 62 removed outlier: 4.117A pdb=" N LYS k 61 " --> pdb=" O PRO k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 72 removed outlier: 4.063A pdb=" N VAL k 71 " --> pdb=" O ASP k 67 " (cutoff:3.500A) Processing helix chain 'k' and resid 105 through 110 removed outlier: 3.500A pdb=" N LYS k 109 " --> pdb=" O LEU k 105 " (cutoff:3.500A) Processing helix chain 'k' and resid 113 through 116 Processing helix chain 'k' and resid 117 through 125 Processing helix chain 'k' and resid 126 through 130 removed outlier: 3.639A pdb=" N LYS k 129 " --> pdb=" O GLU k 126 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP k 130 " --> pdb=" O ALA k 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 126 through 130' Processing helix chain 'k' and resid 141 through 149 removed outlier: 3.557A pdb=" N CYS k 145 " --> pdb=" O SER k 141 " (cutoff:3.500A) Processing helix chain 'k' and resid 185 through 197 removed outlier: 3.965A pdb=" N LYS k 190 " --> pdb=" O ASP k 186 " (cutoff:3.500A) Processing helix chain 'k' and resid 216 through 233 removed outlier: 3.641A pdb=" N THR k 229 " --> pdb=" O MET k 225 " (cutoff:3.500A) Processing helix chain 'k' and resid 258 through 275 removed outlier: 4.205A pdb=" N LYS k 262 " --> pdb=" O SER k 258 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN k 263 " --> pdb=" O ALA k 259 " (cutoff:3.500A) Processing helix chain 'k' and resid 282 through 288 removed outlier: 3.526A pdb=" N THR k 288 " --> pdb=" O GLU k 284 " (cutoff:3.500A) Processing helix chain 'k' and resid 289 through 303 removed outlier: 3.686A pdb=" N ASP k 293 " --> pdb=" O LYS k 289 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR k 294 " --> pdb=" O GLU k 290 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL k 299 " --> pdb=" O LYS k 295 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER k 300 " --> pdb=" O ASN k 296 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU k 301 " --> pdb=" O SER k 297 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN k 303 " --> pdb=" O VAL k 299 " (cutoff:3.500A) Processing helix chain 'k' and resid 307 through 322 removed outlier: 3.970A pdb=" N ILE k 311 " --> pdb=" O ASN k 307 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER k 312 " --> pdb=" O GLU k 308 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG k 320 " --> pdb=" O GLU k 316 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU k 322 " --> pdb=" O VAL k 318 " (cutoff:3.500A) Processing helix chain 'm' and resid 45 through 53 Processing helix chain 'm' and resid 67 through 88 Processing helix chain 'm' and resid 100 through 111 removed outlier: 3.681A pdb=" N LYS m 106 " --> pdb=" O ARG m 102 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG m 110 " --> pdb=" O LYS m 106 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE m 111 " --> pdb=" O LEU m 107 " (cutoff:3.500A) Processing helix chain 'o' and resid 69 through 78 removed outlier: 3.603A pdb=" N ALA o 73 " --> pdb=" O ALA o 69 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL o 78 " --> pdb=" O LEU o 74 " (cutoff:3.500A) Processing helix chain 'o' and resid 99 through 123 Processing helix chain 'o' and resid 124 through 129 removed outlier: 4.037A pdb=" N GLN o 129 " --> pdb=" O LYS o 126 " (cutoff:3.500A) Processing helix chain 'o' and resid 146 through 156 removed outlier: 3.535A pdb=" N UNK o 150 " --> pdb=" O UNK o 146 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N UNK o 151 " --> pdb=" O UNK o 147 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N UNK o 152 " --> pdb=" O UNK o 148 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N UNK o 153 " --> pdb=" O UNK o 149 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N UNK o 154 " --> pdb=" O UNK o 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 162 through 173 removed outlier: 3.562A pdb=" N UNK o 166 " --> pdb=" O UNK o 162 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N UNK o 167 " --> pdb=" O UNK o 163 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N UNK o 168 " --> pdb=" O UNK o 164 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N UNK o 169 " --> pdb=" O UNK o 165 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N UNK o 170 " --> pdb=" O UNK o 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N UNK o 171 " --> pdb=" O UNK o 167 " (cutoff:3.500A) Processing helix chain 'o' and resid 221 through 232 removed outlier: 3.816A pdb=" N UNK o 225 " --> pdb=" O UNK o 221 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N UNK o 226 " --> pdb=" O UNK o 222 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N UNK o 227 " --> pdb=" O UNK o 223 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N UNK o 228 " --> pdb=" O UNK o 224 " (cutoff:3.500A) Processing helix chain 'o' and resid 238 through 250 removed outlier: 3.586A pdb=" N UNK o 242 " --> pdb=" O UNK o 238 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N UNK o 243 " --> pdb=" O UNK o 239 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N UNK o 244 " --> pdb=" O UNK o 240 " (cutoff:3.500A) Processing helix chain 'o' and resid 256 through 269 removed outlier: 3.788A pdb=" N UNK o 260 " --> pdb=" O UNK o 256 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N UNK o 261 " --> pdb=" O UNK o 257 " (cutoff:3.500A) Processing helix chain 'o' and resid 273 through 285 removed outlier: 3.604A pdb=" N UNK o 277 " --> pdb=" O UNK o 273 " (cutoff:3.500A) Processing helix chain 'o' and resid 291 through 299 removed outlier: 3.534A pdb=" N UNK o 295 " --> pdb=" O UNK o 291 " (cutoff:3.500A) Processing helix chain 'o' and resid 316 through 326 removed outlier: 3.653A pdb=" N UNK o 320 " --> pdb=" O UNK o 316 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N UNK o 321 " --> pdb=" O UNK o 317 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNK o 322 " --> pdb=" O UNK o 318 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N UNK o 323 " --> pdb=" O UNK o 319 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N UNK o 324 " --> pdb=" O UNK o 320 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N UNK o 325 " --> pdb=" O UNK o 321 " (cutoff:3.500A) Processing helix chain 'o' and resid 332 through 341 removed outlier: 3.832A pdb=" N UNK o 336 " --> pdb=" O UNK o 332 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N UNK o 337 " --> pdb=" O UNK o 333 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N UNK o 338 " --> pdb=" O UNK o 334 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N UNK o 339 " --> pdb=" O UNK o 335 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK o 341 " --> pdb=" O UNK o 337 " (cutoff:3.500A) Processing helix chain 'o' and resid 354 through 362 removed outlier: 3.626A pdb=" N UNK o 358 " --> pdb=" O UNK o 354 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N UNK o 359 " --> pdb=" O UNK o 355 " (cutoff:3.500A) Processing helix chain 'o' and resid 375 through 383 removed outlier: 3.801A pdb=" N ILE o 379 " --> pdb=" O TYR o 375 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN o 380 " --> pdb=" O HIS o 376 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU o 381 " --> pdb=" O HIS o 377 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE o 382 " --> pdb=" O ILE o 378 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR o 383 " --> pdb=" O ILE o 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 375 through 383' Processing helix chain 'o' and resid 387 through 399 Processing helix chain 'o' and resid 418 through 430 removed outlier: 3.546A pdb=" N ALA o 422 " --> pdb=" O PHE o 418 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET o 423 " --> pdb=" O PHE o 419 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG o 424 " --> pdb=" O GLN o 420 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL o 425 " --> pdb=" O SER o 421 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS o 426 " --> pdb=" O ALA o 422 " (cutoff:3.500A) Processing helix chain 'o' and resid 432 through 440 removed outlier: 3.774A pdb=" N TYR o 436 " --> pdb=" O LEU o 432 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN o 437 " --> pdb=" O GLU o 433 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL o 438 " --> pdb=" O LEU o 434 " (cutoff:3.500A) Processing helix chain 'o' and resid 460 through 467 removed outlier: 3.857A pdb=" N PHE o 464 " --> pdb=" O TYR o 460 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE o 465 " --> pdb=" O TYR o 461 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU o 467 " --> pdb=" O LYS o 463 " (cutoff:3.500A) Processing helix chain 'o' and resid 468 through 471 removed outlier: 3.909A pdb=" N MET o 471 " --> pdb=" O LEU o 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 468 through 471' Processing helix chain 'o' and resid 473 through 485 removed outlier: 3.654A pdb=" N ASP o 483 " --> pdb=" O LYS o 479 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE o 485 " --> pdb=" O TYR o 481 " (cutoff:3.500A) Processing helix chain 'o' and resid 492 through 507 removed outlier: 4.405A pdb=" N LEU o 496 " --> pdb=" O HIS o 492 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE o 497 " --> pdb=" O SER o 493 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP o 498 " --> pdb=" O GLN o 494 " (cutoff:3.500A) Processing helix chain 'o' and resid 511 through 522 Processing helix chain 'o' and resid 530 through 537 Processing helix chain 'o' and resid 544 through 548 removed outlier: 3.760A pdb=" N GLN o 548 " --> pdb=" O PRO o 545 " (cutoff:3.500A) Processing helix chain 'o' and resid 549 through 560 removed outlier: 3.745A pdb=" N ASP o 553 " --> pdb=" O ALA o 549 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP o 557 " --> pdb=" O ASP o 553 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE o 558 " --> pdb=" O CYS o 554 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS o 559 " --> pdb=" O ALA o 555 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER o 560 " --> pdb=" O ALA o 556 " (cutoff:3.500A) Processing helix chain 'o' and resid 581 through 588 removed outlier: 4.249A pdb=" N LEU o 585 " --> pdb=" O TYR o 581 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE o 586 " --> pdb=" O ILE o 582 " (cutoff:3.500A) Processing helix chain 'o' and resid 592 through 602 removed outlier: 3.998A pdb=" N LYS o 597 " --> pdb=" O GLN o 593 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N MET o 598 " --> pdb=" O GLU o 594 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU o 599 " --> pdb=" O ALA o 595 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY o 600 " --> pdb=" O TRP o 596 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU o 601 " --> pdb=" O LYS o 597 " (cutoff:3.500A) Processing helix chain 'o' and resid 627 through 641 removed outlier: 3.825A pdb=" N VAL o 631 " --> pdb=" O PRO o 627 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU o 632 " --> pdb=" O ALA o 628 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL o 633 " --> pdb=" O GLN o 629 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL o 634 " --> pdb=" O ALA o 630 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER o 639 " --> pdb=" O LYS o 635 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE o 640 " --> pdb=" O LEU o 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 106 through 127 removed outlier: 3.681A pdb=" N THR B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 127 " --> pdb=" O HIS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 152 removed outlier: 3.689A pdb=" N CYS B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 195 through 204 removed outlier: 3.528A pdb=" N ARG B 199 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA B 202 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS B 203 " --> pdb=" O ARG B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 261 removed outlier: 3.705A pdb=" N ARG B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 31 Processing helix chain 'F' and resid 73 through 84 removed outlier: 3.506A pdb=" N SER F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG F 84 " --> pdb=" O GLU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 100 Processing helix chain 'K' and resid 114 through 119 Processing helix chain 'K' and resid 123 through 126 removed outlier: 3.829A pdb=" N GLY K 126 " --> pdb=" O ALA K 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 123 through 126' Processing helix chain 'K' and resid 127 through 144 removed outlier: 3.550A pdb=" N ALA K 131 " --> pdb=" O THR K 127 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY K 144 " --> pdb=" O ALA K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 171 removed outlier: 3.573A pdb=" N ILE K 165 " --> pdb=" O ARG K 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 76 removed outlier: 4.172A pdb=" N GLN O 76 " --> pdb=" O LYS O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 92 Processing helix chain 'O' and resid 93 through 97 Processing helix chain 'O' and resid 98 through 112 removed outlier: 3.911A pdb=" N MET O 102 " --> pdb=" O ASN O 98 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER O 112 " --> pdb=" O GLU O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 145 removed outlier: 3.923A pdb=" N GLN O 127 " --> pdb=" O SER O 123 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE O 128 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL O 129 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 171 removed outlier: 3.590A pdb=" N LYS O 152 " --> pdb=" O ASP O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 184 Processing helix chain 'O' and resid 199 through 235 removed outlier: 3.518A pdb=" N ALA O 229 " --> pdb=" O ALA O 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 82 Processing helix chain 'R' and resid 83 through 85 No H-bonds generated for 'chain 'R' and resid 83 through 85' Processing helix chain 'R' and resid 94 through 99 Processing helix chain 'R' and resid 101 through 118 removed outlier: 4.465A pdb=" N ARG R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 131 Processing helix chain 'U' and resid 19 through 34 Processing helix chain 'U' and resid 35 through 44 removed outlier: 4.172A pdb=" N TYR U 44 " --> pdb=" O LYS U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 75 removed outlier: 3.549A pdb=" N GLN U 53 " --> pdb=" O CYS U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 4.116A pdb=" N ARG U 80 " --> pdb=" O ARG U 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 22 removed outlier: 3.536A pdb=" N ALA b 22 " --> pdb=" O ASP b 18 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 38 removed outlier: 3.776A pdb=" N VAL b 34 " --> pdb=" O LEU b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 66 through 79 removed outlier: 3.972A pdb=" N ILE b 70 " --> pdb=" O HIS b 66 " (cutoff:3.500A) Processing helix chain 'b' and resid 94 through 110 removed outlier: 3.933A pdb=" N GLY b 110 " --> pdb=" O LEU b 106 " (cutoff:3.500A) Processing helix chain 'b' and resid 113 through 127 Processing helix chain 'f' and resid 80 through 87 removed outlier: 3.808A pdb=" N ARG f 86 " --> pdb=" O ALA f 82 " (cutoff:3.500A) Processing helix chain 'f' and resid 88 through 94 Processing helix chain 'n' and resid 129 through 150 removed outlier: 4.429A pdb=" N ARG n 134 " --> pdb=" O VAL n 130 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG n 135 " --> pdb=" O LEU n 131 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 181 Processing helix chain 'z' and resid 101 through 113 removed outlier: 3.833A pdb=" N VAL z 105 " --> pdb=" O HIS z 101 " (cutoff:3.500A) Processing helix chain 'z' and resid 132 through 150 Processing helix chain 'z' and resid 169 through 184 Processing helix chain 'z' and resid 202 through 216 Processing helix chain 'z' and resid 246 through 263 removed outlier: 4.054A pdb=" N ALA z 250 " --> pdb=" O ASN z 246 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 110 through 112 removed outlier: 6.936A pdb=" N VAL C 117 " --> pdb=" O ARG C 152 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N HIS C 154 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE C 119 " --> pdb=" O HIS C 154 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N GLN C 156 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA C 121 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N VAL C 158 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 123 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 221 through 228 removed outlier: 5.413A pdb=" N ILE E 222 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA E 246 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA E 261 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 253 through 254 Processing sheet with id=AA4, first strand: chain 'E' and resid 294 through 295 Processing sheet with id=AA5, first strand: chain 'E' and resid 301 through 302 removed outlier: 3.619A pdb=" N SER E 337 " --> pdb=" O HIS E 302 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 382 through 385 removed outlier: 3.695A pdb=" N VAL E 384 " --> pdb=" O VAL E 370 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL E 370 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL E 371 " --> pdb=" O LYS a 103 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS a 103 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR a 101 " --> pdb=" O PHE E 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 57 through 68 removed outlier: 4.045A pdb=" N ARG L 64 " --> pdb=" O ARG L 82 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS L 81 " --> pdb=" O CYS L 93 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE L 94 " --> pdb=" O VAL L 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 18 through 19 Processing sheet with id=AA9, first strand: chain 'P' and resid 52 through 54 removed outlier: 3.532A pdb=" N SER P 53 " --> pdb=" O ALA P 67 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR a 179 " --> pdb=" O GLU a 175 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA a 142 " --> pdb=" O LEU a 180 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS a 182 " --> pdb=" O VAL a 140 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL a 140 " --> pdb=" O LYS a 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 12 through 14 removed outlier: 7.390A pdb=" N ILE Q 63 " --> pdb=" O ILE Q 84 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE Q 84 " --> pdb=" O ILE Q 63 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU Q 65 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 16 through 19 removed outlier: 6.648A pdb=" N LYS Q 27 " --> pdb=" O ILE Q 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 92 through 93 Processing sheet with id=AB4, first strand: chain 'c' and resid 63 through 68 removed outlier: 3.744A pdb=" N VAL c 29 " --> pdb=" O TYR c 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN c 33 " --> pdb=" O PHE c 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 190 through 191 removed outlier: 3.538A pdb=" N ALA d 190 " --> pdb=" O VAL d 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 42 through 43 Processing sheet with id=AB7, first strand: chain 'j' and resid 123 through 130 removed outlier: 3.641A pdb=" N LEU j 118 " --> pdb=" O GLU j 125 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU j 127 " --> pdb=" O GLY j 116 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLY j 116 " --> pdb=" O GLU j 127 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ARG j 129 " --> pdb=" O ALA j 114 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA j 114 " --> pdb=" O ARG j 129 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG j 99 " --> pdb=" O TRP j 115 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE j 117 " --> pdb=" O LEU j 97 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU j 97 " --> pdb=" O ILE j 117 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR j 119 " --> pdb=" O TRP j 95 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N TRP j 95 " --> pdb=" O THR j 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 156 through 162 removed outlier: 3.535A pdb=" N TYR G 168 " --> pdb=" O ILE G 161 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 260 through 261 removed outlier: 3.664A pdb=" N ASP I 327 " --> pdb=" O TYR I 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 260 through 261 removed outlier: 3.709A pdb=" N ASN I 280 " --> pdb=" O SER I 333 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 333 " --> pdb=" O ASN I 280 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 294 through 295 Processing sheet with id=AC3, first strand: chain 'J' and resid 143 through 149 removed outlier: 6.599A pdb=" N GLU J 144 " --> pdb=" O SER J 77 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER J 77 " --> pdb=" O GLU J 144 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU J 146 " --> pdb=" O ARG J 75 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG J 75 " --> pdb=" O GLU J 146 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR J 73 " --> pdb=" O LEU J 177 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU J 177 " --> pdb=" O TYR J 73 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG J 75 " --> pdb=" O THR J 175 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR J 175 " --> pdb=" O ARG J 75 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET J 170 " --> pdb=" O ILE k 159 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU J 178 " --> pdb=" O ILE k 151 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU k 152 " --> pdb=" O ARG k 176 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG k 176 " --> pdb=" O GLU k 152 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR k 174 " --> pdb=" O ASP k 154 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 81 through 82 Processing sheet with id=AC5, first strand: chain 'J' and resid 118 through 121 removed outlier: 3.840A pdb=" N PHE J 118 " --> pdb=" O TYR J 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR J 134 " --> pdb=" O PHE J 118 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN N 124 " --> pdb=" O GLU J 135 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 66 through 68 removed outlier: 3.817A pdb=" N LEU g 98 " --> pdb=" O TYR g 67 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 150 through 154 removed outlier: 7.053A pdb=" N LEU g 257 " --> pdb=" O ALA g 304 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL g 306 " --> pdb=" O LEU g 257 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL g 259 " --> pdb=" O VAL g 306 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR g 308 " --> pdb=" O VAL g 259 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL g 261 " --> pdb=" O THR g 308 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL g 121 " --> pdb=" O ILE g 305 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU g 307 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR g 123 " --> pdb=" O LEU g 307 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARG g 122 " --> pdb=" O ILE g 340 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE g 342 " --> pdb=" O ARG g 122 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL g 124 " --> pdb=" O ILE g 342 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'g' and resid 168 through 170 Processing sheet with id=AC9, first strand: chain 'g' and resid 207 through 208 removed outlier: 3.942A pdb=" N TYR g 207 " --> pdb=" O THR g 215 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR g 215 " --> pdb=" O TYR g 207 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.871A pdb=" N ILE B 104 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER B 98 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLN B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 154 through 156 removed outlier: 6.312A pdb=" N ILE B 131 " --> pdb=" O TYR B 154 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N HIS B 156 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE B 133 " --> pdb=" O HIS B 156 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU B 132 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 182 " --> pdb=" O VAL B 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 35 through 52 removed outlier: 6.774A pdb=" N ASP F 67 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU F 39 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU F 65 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASN F 41 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N TYR F 63 " --> pdb=" O ASN F 41 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLY F 43 " --> pdb=" O GLY F 61 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY F 61 " --> pdb=" O GLY F 43 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ARG F 45 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR F 59 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 10.698A pdb=" N LEU F 47 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 13.025A pdb=" N ARG F 57 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE F 68 " --> pdb=" O TYR F 4 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR F 4 " --> pdb=" O PHE F 68 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 98 through 103 removed outlier: 6.813A pdb=" N ALA K 89 " --> pdb=" O VAL K 153 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 177 through 179 Processing sheet with id=AD6, first strand: chain 'f' and resid 123 through 126 removed outlier: 7.465A pdb=" N ASP f 112 " --> pdb=" O ILE f 108 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE f 108 " --> pdb=" O ASP f 112 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR f 114 " --> pdb=" O PHE f 106 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLU f 167 " --> pdb=" O LEU f 146 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'f' and resid 123 through 126 removed outlier: 7.465A pdb=" N ASP f 112 " --> pdb=" O ILE f 108 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE f 108 " --> pdb=" O ASP f 112 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR f 114 " --> pdb=" O PHE f 106 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY f 172 " --> pdb=" O ARG f 142 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'f' and resid 151 through 152 removed outlier: 4.173A pdb=" N SER f 152 " --> pdb=" O THR f 161 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR f 161 " --> pdb=" O SER f 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'z' and resid 88 through 90 removed outlier: 6.313A pdb=" N HIS z 88 " --> pdb=" O TYR z 128 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N LEU z 130 " --> pdb=" O HIS z 88 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N PHE z 90 " --> pdb=" O LEU z 130 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU z 127 " --> pdb=" O ARG z 119 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'z' and resid 159 through 164 removed outlier: 3.686A pdb=" N VAL z 189 " --> pdb=" O LEU z 240 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL z 239 " --> pdb=" O SER z 224 " (cutoff:3.500A) 1847 hydrogen bonds defined for protein. 5331 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 571 hydrogen bonds 1006 hydrogen bond angles 0 basepair planarities 232 basepair parallelities 391 stacking parallelities Total time for adding SS restraints: 25.09 Time building geometry restraints manager: 26.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 17445 1.34 - 1.45: 16738 1.45 - 1.57: 32733 1.57 - 1.69: 1903 1.69 - 1.81: 342 Bond restraints: 69161 Sorted by residual: bond pdb=" N MET F 1 " pdb=" CA MET F 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" N MET U 1 " pdb=" CA MET U 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 bond pdb=" N MET Q 1 " pdb=" CA MET Q 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N MET m 1 " pdb=" CA MET m 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N MET j 1 " pdb=" CA MET j 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 ... (remaining 69156 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.14: 7110 107.14 - 113.85: 40330 113.85 - 120.56: 26319 120.56 - 127.27: 21664 127.27 - 133.98: 2540 Bond angle restraints: 97963 Sorted by residual: angle pdb=" N ILE p 107 " pdb=" CA ILE p 107 " pdb=" C ILE p 107 " ideal model delta sigma weight residual 111.81 108.96 2.85 8.60e-01 1.35e+00 1.10e+01 angle pdb=" N LYS R 104 " pdb=" CA LYS R 104 " pdb=" C LYS R 104 " ideal model delta sigma weight residual 114.62 111.06 3.56 1.14e+00 7.69e-01 9.74e+00 angle pdb=" C LYS j 5 " pdb=" N VAL j 6 " pdb=" CA VAL j 6 " ideal model delta sigma weight residual 121.70 127.22 -5.52 1.80e+00 3.09e-01 9.41e+00 angle pdb=" N VAL k 64 " pdb=" CA VAL k 64 " pdb=" C VAL k 64 " ideal model delta sigma weight residual 111.81 109.31 2.50 8.60e-01 1.35e+00 8.43e+00 angle pdb=" N VAL B 191 " pdb=" CA VAL B 191 " pdb=" C VAL B 191 " ideal model delta sigma weight residual 111.91 109.41 2.50 8.90e-01 1.26e+00 7.91e+00 ... (remaining 97958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 40001 35.40 - 70.79: 1627 70.79 - 106.19: 273 106.19 - 141.58: 10 141.58 - 176.98: 4 Dihedral angle restraints: 41915 sinusoidal: 25382 harmonic: 16533 Sorted by residual: dihedral pdb=" O4' C A 499 " pdb=" C1' C A 499 " pdb=" N1 C A 499 " pdb=" C2 C A 499 " ideal model delta sinusoidal sigma weight residual -128.00 48.98 -176.98 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A 620 " pdb=" C1' U A 620 " pdb=" N1 U A 620 " pdb=" C2 U A 620 " ideal model delta sinusoidal sigma weight residual -128.00 32.51 -160.51 1 1.70e+01 3.46e-03 6.45e+01 dihedral pdb=" O4' U A 881 " pdb=" C1' U A 881 " pdb=" N1 U A 881 " pdb=" C2 U A 881 " ideal model delta sinusoidal sigma weight residual -128.00 -21.32 -106.68 1 1.70e+01 3.46e-03 4.28e+01 ... (remaining 41912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 8597 0.028 - 0.057: 2209 0.057 - 0.085: 394 0.085 - 0.114: 296 0.114 - 0.142: 48 Chirality restraints: 11544 Sorted by residual: chirality pdb=" CA ILE g 340 " pdb=" N ILE g 340 " pdb=" C ILE g 340 " pdb=" CB ILE g 340 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE K 69 " pdb=" N ILE K 69 " pdb=" C ILE K 69 " pdb=" CB ILE K 69 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE g 208 " pdb=" N ILE g 208 " pdb=" C ILE g 208 " pdb=" CB ILE g 208 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 11541 not shown) Planarity restraints: 9033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER e 269 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO e 270 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO e 270 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO e 270 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G A 683 " -0.009 2.00e-02 2.50e+03 7.69e-03 1.78e+00 pdb=" N9 G A 683 " 0.008 2.00e-02 2.50e+03 pdb=" C8 G A 683 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G A 683 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 683 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 683 " -0.017 2.00e-02 2.50e+03 pdb=" O6 G A 683 " 0.005 2.00e-02 2.50e+03 pdb=" N1 G A 683 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 683 " -0.011 2.00e-02 2.50e+03 pdb=" N2 G A 683 " 0.010 2.00e-02 2.50e+03 pdb=" N3 G A 683 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G A 683 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 946 " 0.017 2.00e-02 2.50e+03 8.55e-03 1.64e+00 pdb=" N1 U A 946 " -0.016 2.00e-02 2.50e+03 pdb=" C2 U A 946 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U A 946 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U A 946 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U A 946 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U A 946 " 0.008 2.00e-02 2.50e+03 pdb=" C5 U A 946 " -0.004 2.00e-02 2.50e+03 pdb=" C6 U A 946 " -0.002 2.00e-02 2.50e+03 ... (remaining 9030 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 434 2.54 - 3.13: 48818 3.13 - 3.72: 105272 3.72 - 4.31: 145505 4.31 - 4.90: 225793 Nonbonded interactions: 525822 Sorted by model distance: nonbonded pdb=" O2' C A 580 " pdb=" OP1 U A 581 " model vdw 1.949 2.440 nonbonded pdb=" O TYR e 157 " pdb=" OH TYR e 184 " model vdw 1.983 2.440 nonbonded pdb=" O2' G A 242 " pdb=" O2' C A 257 " model vdw 2.024 2.440 nonbonded pdb=" OH TYR G 37 " pdb=" OD1 ASP I 373 " model vdw 2.031 2.440 nonbonded pdb=" O2' A A 865 " pdb=" O4' G A 866 " model vdw 2.032 2.440 ... (remaining 525817 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 15.130 Check model and map are aligned: 0.710 Set scattering table: 0.460 Process input model: 146.720 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.210 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5134 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.037 69161 Z= 0.096 Angle : 0.371 5.523 97963 Z= 0.209 Chirality : 0.029 0.142 11544 Planarity : 0.002 0.043 9033 Dihedral : 16.684 176.977 31179 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 1.60 % Allowed : 10.28 % Favored : 88.12 % Rotamer: Outliers : 0.35 % Allowed : 3.03 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.11), residues: 5437 helix: -0.07 (0.10), residues: 2279 sheet: -3.11 (0.22), residues: 413 loop : -2.81 (0.11), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP e 107 HIS 0.003 0.000 HIS e 97 PHE 0.019 0.000 PHE G 123 TYR 0.005 0.000 TYR G 64 ARG 0.002 0.000 ARG I 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10874 Ramachandran restraints generated. 5437 Oldfield, 0 Emsley, 5437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1912 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1895 time to evaluate : 4.483 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 outliers start: 17 outliers final: 2 residues processed: 1910 average time/residue: 0.7226 time to fit residues: 2217.6397 Evaluate side-chains 953 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 951 time to evaluate : 4.491 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4970 time to fit residues: 7.6453 ------------------------------------------------------------------------------- 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: 5.9990 chunk 452 optimal weight: 8.9990 chunk 251 optimal weight: 0.6980 chunk 154 optimal weight: 0.5980 chunk 305 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 chunk 467 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 chunk 348 optimal weight: 10.0000 chunk 542 optimal weight: 0.6980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS C 116 GLN E 175 GLN E 341 ASN E 369 HIS P 16 HIS ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 23 GLN ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 223 HIS ** c 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 83 HIS d 133 GLN ** d 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 100 ASN ** e 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 179 GLN e 245 HIS j 66 GLN p 68 ASN p 146 GLN ** p 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 HIS G 147 GLN G 151 ASN G 224 HIS I 127 HIS I 366 GLN J 83 HIS J 183 HIS N 55 ASN ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 HIS g 163 ASN h 322 HIS ** h 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 359 GLN h 363 HIS o 494 GLN B 75 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 HIS B 167 ASN B 255 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 116 GLN U 65 ASN U 79 ASN f 92 GLN f 107 HIS z 211 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 69161 Z= 0.321 Angle : 0.723 14.974 97963 Z= 0.369 Chirality : 0.041 0.413 11544 Planarity : 0.006 0.081 9033 Dihedral : 18.367 175.434 19564 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.44 % Favored : 94.35 % Rotamer: Outliers : 4.17 % Allowed : 14.36 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.11), residues: 5437 helix: 0.30 (0.10), residues: 2377 sheet: -2.59 (0.22), residues: 423 loop : -2.29 (0.11), residues: 2637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP j 95 HIS 0.013 0.002 HIS z 211 PHE 0.026 0.002 PHE F 64 TYR 0.059 0.003 TYR e 228 ARG 0.044 0.001 ARG j 101 *********************** 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 1296 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1095 time to evaluate : 4.680 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 outliers start: 201 outliers final: 93 residues processed: 1215 average time/residue: 0.6475 time to fit residues: 1330.1887 Evaluate side-chains 919 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 826 time to evaluate : 4.515 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 0 residues processed: 93 average time/residue: 0.4982 time to fit residues: 92.8533 ------------------------------------------------------------------------------- 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: 1.9990 chunk 168 optimal weight: 5.9990 chunk 451 optimal weight: 8.9990 chunk 369 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 543 optimal weight: 1.9990 chunk 586 optimal weight: 20.0000 chunk 483 optimal weight: 6.9990 chunk 538 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 435 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 HIS C 116 GLN C 130 HIS E 174 GLN E 302 HIS E 341 ASN P 28 ASN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 213 ASN a 336 GLN c 59 ASN c 101 HIS ** c 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 66 GLN p 146 GLN ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 HIS N 113 HIS N 124 GLN ** g 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 263 ASN o 494 GLN B 58 HIS ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN f 107 HIS z 178 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 69161 Z= 0.186 Angle : 0.551 10.626 97963 Z= 0.273 Chirality : 0.034 0.248 11544 Planarity : 0.004 0.059 9033 Dihedral : 18.281 177.744 19564 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.09 % Favored : 93.76 % Rotamer: Outliers : 2.12 % Allowed : 17.74 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.11), residues: 5437 helix: 0.94 (0.11), residues: 2389 sheet: -1.97 (0.23), residues: 433 loop : -2.01 (0.12), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 140 HIS 0.014 0.001 HIS N 66 PHE 0.022 0.002 PHE j 73 TYR 0.035 0.002 TYR e 335 ARG 0.014 0.001 ARG e 330 *********************** 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 993 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 891 time to evaluate : 4.586 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 outliers start: 102 outliers final: 54 residues processed: 950 average time/residue: 0.6437 time to fit residues: 1045.2783 Evaluate side-chains 809 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 755 time to evaluate : 4.567 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.5173 time to fit residues: 57.8831 ------------------------------------------------------------------------------- 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: 5.9990 chunk 408 optimal weight: 20.0000 chunk 281 optimal weight: 0.9990 chunk 60 optimal weight: 40.0000 chunk 259 optimal weight: 0.2980 chunk 364 optimal weight: 9.9990 chunk 545 optimal weight: 2.9990 chunk 577 optimal weight: 10.0000 chunk 284 optimal weight: 5.9990 chunk 516 optimal weight: 0.1980 chunk 155 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 HIS a 116 GLN c 54 GLN ** c 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 172 ASN ** d 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 GLN j 89 HIS ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 HIS ** g 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 325 GLN h 307 ASN h 320 HIS ** h 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 313 GLN o 501 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 178 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.6927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 69161 Z= 0.204 Angle : 0.585 17.539 97963 Z= 0.291 Chirality : 0.035 0.218 11544 Planarity : 0.005 0.079 9033 Dihedral : 18.341 176.140 19564 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.09 % Favored : 94.79 % Rotamer: Outliers : 2.51 % Allowed : 18.34 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.11), residues: 5437 helix: 1.08 (0.11), residues: 2354 sheet: -1.54 (0.24), residues: 427 loop : -1.80 (0.12), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP z 182 HIS 0.026 0.001 HIS N 66 PHE 0.043 0.002 PHE m 73 TYR 0.035 0.002 TYR e 335 ARG 0.016 0.001 ARG m 79 *********************** 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 970 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 849 time to evaluate : 4.539 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: 121 outliers final: 60 residues processed: 922 average time/residue: 0.6577 time to fit residues: 1030.9027 Evaluate side-chains 775 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 715 time to evaluate : 4.549 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.4947 time to fit residues: 62.2109 ------------------------------------------------------------------------------- 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: 0.1980 chunk 327 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 429 optimal weight: 6.9990 chunk 238 optimal weight: 8.9990 chunk 492 optimal weight: 5.9990 chunk 398 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 294 optimal weight: 4.9990 chunk 517 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS E 277 HIS E 341 ASN E 360 GLN P 38 HIS c 54 GLN ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 122 GLN ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN e 339 HIS j 24 GLN ** p 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 GLN I 296 ASN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS J 183 HIS g 80 HIS g 210 ASN g 325 GLN k 263 ASN k 313 GLN o 79 HIS o 376 HIS o 524 HIS B 58 HIS ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS K 99 GLN ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 127 GLN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 4 HIS U 53 GLN z 178 GLN z 212 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.9304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 69161 Z= 0.384 Angle : 0.745 12.916 97963 Z= 0.378 Chirality : 0.042 0.262 11544 Planarity : 0.006 0.088 9033 Dihedral : 18.809 172.379 19564 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.86 % Favored : 92.99 % Rotamer: Outliers : 3.03 % Allowed : 19.24 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.11), residues: 5437 helix: 0.56 (0.10), residues: 2416 sheet: -1.52 (0.24), residues: 448 loop : -1.93 (0.12), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP j 87 HIS 0.021 0.002 HIS j 145 PHE 0.041 0.003 PHE o 459 TYR 0.036 0.003 TYR e 335 ARG 0.025 0.001 ARG d 144 *********************** 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 943 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 797 time to evaluate : 4.606 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: 146 outliers final: 76 residues processed: 898 average time/residue: 0.6400 time to fit residues: 982.7604 Evaluate side-chains 693 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 617 time to evaluate : 4.610 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 0 residues processed: 76 average time/residue: 0.4958 time to fit residues: 76.5441 ------------------------------------------------------------------------------- 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: 4.9990 chunk 519 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 338 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 577 optimal weight: 20.0000 chunk 479 optimal weight: 2.9990 chunk 267 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 303 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS L 74 ASN L 101 ASN a 287 GLN ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 188 ASN e 188 GLN ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 261 GLN ** j 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 GLN I 366 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 HIS N 124 GLN h 359 GLN k 263 ASN k 313 GLN o 501 GLN o 593 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN K 132 GLN ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 127 GLN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.9652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 69161 Z= 0.237 Angle : 0.603 11.052 97963 Z= 0.302 Chirality : 0.037 0.235 11544 Planarity : 0.004 0.068 9033 Dihedral : 18.675 175.953 19564 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 1.64 % Allowed : 21.50 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.11), residues: 5437 helix: 0.92 (0.11), residues: 2402 sheet: -1.44 (0.24), residues: 469 loop : -1.80 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP I 363 HIS 0.011 0.001 HIS a 246 PHE 0.033 0.002 PHE J 94 TYR 0.030 0.002 TYR e 335 ARG 0.010 0.001 ARG R 142 *********************** 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 778 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 699 time to evaluate : 4.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 31 residues processed: 752 average time/residue: 0.6288 time to fit residues: 813.7223 Evaluate side-chains 635 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 604 time to evaluate : 4.561 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4965 time to fit residues: 34.8383 ------------------------------------------------------------------------------- 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: 6.9990 chunk 421 optimal weight: 6.9990 chunk 326 optimal weight: 5.9990 chunk 486 optimal weight: 0.7980 chunk 322 optimal weight: 5.9990 chunk 575 optimal weight: 0.9990 chunk 360 optimal weight: 8.9990 chunk 350 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS ** E 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 GLN L 37 HIS L 74 ASN a 287 GLN ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 188 GLN ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 221 GLN ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 HIS ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 125 HIS J 130 HIS g 173 ASN g 179 GLN ** h 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 ASN k 233 HIS k 263 ASN o 72 GLN o 501 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS K 132 GLN ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 1.0480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 69161 Z= 0.361 Angle : 0.701 12.933 97963 Z= 0.353 Chirality : 0.040 0.279 11544 Planarity : 0.005 0.118 9033 Dihedral : 18.794 178.829 19564 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.73 % Favored : 93.18 % Rotamer: Outliers : 1.87 % Allowed : 22.10 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.11), residues: 5437 helix: 0.76 (0.11), residues: 2413 sheet: -1.30 (0.24), residues: 467 loop : -1.79 (0.12), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.003 TRP G 186 HIS 0.014 0.002 HIS G 227 PHE 0.031 0.002 PHE J 94 TYR 0.069 0.002 TYR b 53 ARG 0.012 0.001 ARG a 174 *********************** 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 733 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 643 time to evaluate : 4.679 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 outliers start: 90 outliers final: 51 residues processed: 698 average time/residue: 0.6561 time to fit residues: 786.1731 Evaluate side-chains 631 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 580 time to evaluate : 4.610 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.4952 time to fit residues: 54.3475 ------------------------------------------------------------------------------- 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: 4.9990 chunk 229 optimal weight: 20.0000 chunk 343 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 365 optimal weight: 5.9990 chunk 392 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 452 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS E 174 GLN E 273 ASN E 415 GLN a 75 GLN ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 221 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 GLN I 156 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 263 ASN ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 501 GLN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 GLN K 149 HIS ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 199 HIS U 65 ASN b 66 HIS z 129 GLN ** z 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 264 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 1.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 69161 Z= 0.438 Angle : 0.752 16.459 97963 Z= 0.380 Chirality : 0.042 0.257 11544 Planarity : 0.005 0.072 9033 Dihedral : 18.931 176.429 19564 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.42 % Favored : 93.49 % Rotamer: Outliers : 1.62 % Allowed : 22.95 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.34 % 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: -1.01 (0.11), residues: 5437 helix: 0.57 (0.10), residues: 2410 sheet: -1.29 (0.23), residues: 487 loop : -1.79 (0.12), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.003 TRP G 186 HIS 0.012 0.002 HIS a 246 PHE 0.034 0.002 PHE J 94 TYR 0.032 0.002 TYR i 7 ARG 0.015 0.001 ARG E 315 *********************** 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 693 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 615 time to evaluate : 4.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 39 residues processed: 660 average time/residue: 0.6234 time to fit residues: 710.0809 Evaluate side-chains 594 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 555 time to evaluate : 4.517 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.5010 time to fit residues: 42.5616 ------------------------------------------------------------------------------- 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: 0.9980 chunk 551 optimal weight: 0.4980 chunk 502 optimal weight: 0.5980 chunk 536 optimal weight: 0.6980 chunk 322 optimal weight: 20.0000 chunk 233 optimal weight: 7.9990 chunk 421 optimal weight: 0.0470 chunk 164 optimal weight: 0.5980 chunk 484 optimal weight: 3.9990 chunk 507 optimal weight: 0.9990 chunk 534 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS E 341 ASN E 369 HIS a 223 HIS a 245 HIS a 266 HIS ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 336 GLN c 101 HIS ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 146 GLN ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 GLN I 156 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS ** g 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 234 ASN ** h 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 359 GLN k 233 HIS k 313 GLN ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 501 GLN B 88 HIS ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN K 132 GLN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 120 ASN z 178 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 1.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 69161 Z= 0.170 Angle : 0.618 12.557 97963 Z= 0.309 Chirality : 0.036 0.329 11544 Planarity : 0.004 0.071 9033 Dihedral : 18.744 179.587 19564 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 0.73 % Allowed : 24.11 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.11), residues: 5437 helix: 0.97 (0.11), residues: 2387 sheet: -1.10 (0.24), residues: 486 loop : -1.58 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.132 0.003 TRP G 186 HIS 0.012 0.001 HIS k 124 PHE 0.056 0.002 PHE C 95 TYR 0.029 0.002 TYR e 335 ARG 0.013 0.001 ARG G 180 *********************** 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 701 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 666 time to evaluate : 5.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 14 residues processed: 684 average time/residue: 0.6404 time to fit residues: 749.9488 Evaluate side-chains 598 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 584 time to evaluate : 4.631 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.5232 time to fit residues: 19.3902 ------------------------------------------------------------------------------- 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: 3.9990 chunk 567 optimal weight: 0.2980 chunk 346 optimal weight: 8.9990 chunk 268 optimal weight: 0.9990 chunk 394 optimal weight: 0.9980 chunk 594 optimal weight: 20.0000 chunk 547 optimal weight: 0.5980 chunk 473 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 365 optimal weight: 10.0000 chunk 290 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS E 292 HIS P 75 HIS Q 44 ASN a 276 ASN ** a 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 156 ASN ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 108 ASN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN F 56 GLN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 1.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 69161 Z= 0.163 Angle : 0.593 13.251 97963 Z= 0.297 Chirality : 0.035 0.261 11544 Planarity : 0.004 0.068 9033 Dihedral : 18.621 178.009 19564 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 0.12 % Allowed : 24.67 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.38 (0.12), residues: 5437 helix: 1.11 (0.11), residues: 2402 sheet: -0.84 (0.25), residues: 465 loop : -1.50 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.117 0.002 TRP G 186 HIS 0.012 0.001 HIS j 89 PHE 0.046 0.001 PHE C 95 TYR 0.028 0.001 TYR G 41 ARG 0.006 0.000 ARG a 190 ********************** 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 626 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 620 time to evaluate : 4.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 624 average time/residue: 0.6605 time to fit residues: 699.2296 Evaluate side-chains 582 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 579 time to evaluate : 4.582 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.5659 time to fit residues: 9.0313 ------------------------------------------------------------------------------- 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: 3.9990 chunk 504 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 436 optimal weight: 0.0980 chunk 69 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 474 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 487 optimal weight: 0.5980 chunk 60 optimal weight: 40.0000 chunk 87 optimal weight: 30.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS E 273 ASN ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 109 GLN ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 501 GLN B 102 GLN F 56 GLN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.099270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.069869 restraints weight = 221020.324| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.84 r_work: 0.3168 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 1.1262 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= 0.170 Angle : 0.589 13.256 97963 Z= 0.293 Chirality : 0.035 0.221 11544 Planarity : 0.004 0.064 9033 Dihedral : 18.580 177.900 19564 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.04 % Favored : 94.87 % Rotamer: Outliers : 0.33 % Allowed : 24.74 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.29 (0.12), residues: 5437 helix: 1.18 (0.11), residues: 2408 sheet: -0.73 (0.25), residues: 452 loop : -1.46 (0.12), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.120 0.002 TRP G 186 HIS 0.012 0.001 HIS N 66 PHE 0.033 0.001 PHE e 151 TYR 0.027 0.001 TYR e 335 ARG 0.006 0.000 ARG d 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17051.58 seconds wall clock time: 299 minutes 10.01 seconds (17950.01 seconds total)