Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 11:25:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/07_2023/6neq_9358.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/07_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_9358/07_2023/6neq_9358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/07_2023/6neq_9358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/07_2023/6neq_9358.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6neq_9358/07_2023/6neq_9358.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.077 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 65776 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 20256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 20256 Classifications: {'RNA': 952} Modifications used: {'rna2p_pur': 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: 23.17, per 1000 atoms: 0.35 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: 27.16 Conformation dependent library (CDL) restraints added in 5.5 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: 16.08 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: 26.46 Time building geometry restraints manager: 29.63 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: 39164 35.40 - 70.79: 787 70.79 - 106.19: 58 106.19 - 141.58: 10 141.58 - 176.98: 4 Dihedral angle restraints: 40023 sinusoidal: 23490 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 40020 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: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 17.020 Check model and map are aligned: 0.740 Set scattering table: 0.470 Process input model: 146.490 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.770 ------------------------------------------------------------------------------- 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 : 12.814 176.977 29287 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 % 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 *********************** 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 : 4.542 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: 0.7209 time to fit residues: 2208.5752 Evaluate side-chains 953 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 951 time to evaluate : 4.536 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5130 time to fit residues: 7.8159 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 z 211 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.175 69161 Z= 0.315 Angle : 0.737 15.493 97963 Z= 0.370 Chirality : 0.040 0.317 11544 Planarity : 0.006 0.090 9033 Dihedral : 13.006 175.348 17672 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.06 % Favored : 94.76 % Rotamer Outliers : 4.27 % 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: -1.69 (0.11), residues: 5437 helix: 0.32 (0.10), residues: 2377 sheet: -2.63 (0.22), residues: 431 loop : -2.27 (0.11), residues: 2629 *********************** 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 1298 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1092 time to evaluate : 4.503 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 outliers start: 206 outliers final: 97 residues processed: 1213 average time/residue: 0.6882 time to fit residues: 1416.3015 Evaluate side-chains 916 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 819 time to evaluate : 4.663 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 0 residues processed: 97 average time/residue: 0.5279 time to fit residues: 101.3575 ------------------------------------------------------------------------------- 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: 2.9990 chunk 168 optimal weight: 5.9990 chunk 451 optimal weight: 5.9990 chunk 369 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 543 optimal weight: 2.9990 chunk 586 optimal weight: 20.0000 chunk 483 optimal weight: 5.9990 chunk 538 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 435 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 HIS C 130 HIS E 159 GLN E 174 GLN E 302 HIS E 341 ASN E 351 GLN L 100 HIS ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 HIS ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 100 HIS P 106 ASN Q 23 GLN ** a 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 59 ASN c 101 HIS ** c 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 172 ASN ** d 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** i 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 313 GLN o 376 HIS o 492 HIS o 494 GLN o 501 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 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 ** z 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.7128 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= 0.294 Angle : 0.671 12.970 97963 Z= 0.339 Chirality : 0.039 0.314 11544 Planarity : 0.006 0.079 9033 Dihedral : 13.263 175.858 17672 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.04 % Favored : 92.79 % Rotamer Outliers : 3.26 % 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: -1.13 (0.11), residues: 5437 helix: 0.68 (0.10), residues: 2392 sheet: -1.95 (0.23), residues: 445 loop : -1.96 (0.12), residues: 2600 *********************** 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 1061 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 904 time to evaluate : 4.614 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 outliers start: 157 outliers final: 72 residues processed: 996 average time/residue: 0.6866 time to fit residues: 1128.7525 Evaluate side-chains 780 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 708 time to evaluate : 4.643 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 0 residues processed: 72 average time/residue: 0.5435 time to fit residues: 78.3339 ------------------------------------------------------------------------------- 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: 1.9990 chunk 408 optimal weight: 20.0000 chunk 281 optimal weight: 5.9990 chunk 60 optimal weight: 40.0000 chunk 259 optimal weight: 9.9990 chunk 364 optimal weight: 3.9990 chunk 545 optimal weight: 2.9990 chunk 577 optimal weight: 40.0000 chunk 284 optimal weight: 6.9990 chunk 516 optimal weight: 3.9990 chunk 155 optimal weight: 0.3980 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 ASN E 341 ASN ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 100 HIS a 116 GLN ** a 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 336 GLN a 346 GLN ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN ** e 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 GLN ** 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** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS J 183 HIS ** g 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 210 ASN h 307 ASN ** h 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 148 HIS k 263 ASN k 313 GLN o 494 GLN o 593 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS B 255 GLN K 99 GLN ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 127 GLN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 217 GLN U 4 HIS ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.8502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 69161 Z= 0.279 Angle : 0.651 16.508 97963 Z= 0.326 Chirality : 0.038 0.214 11544 Planarity : 0.006 0.099 9033 Dihedral : 13.383 175.114 17672 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.98 % Favored : 94.91 % Rotamer Outliers : 3.11 % 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: -0.97 (0.11), residues: 5437 helix: 0.74 (0.11), residues: 2381 sheet: -1.68 (0.24), residues: 441 loop : -1.82 (0.12), residues: 2615 *********************** 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 942 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 792 time to evaluate : 4.611 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: 150 outliers final: 67 residues processed: 889 average time/residue: 0.6542 time to fit residues: 995.8456 Evaluate side-chains 715 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 648 time to evaluate : 4.577 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.5032 time to fit residues: 69.3949 ------------------------------------------------------------------------------- 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: 7.9990 chunk 8 optimal weight: 9.9990 chunk 429 optimal weight: 0.6980 chunk 238 optimal weight: 5.9990 chunk 492 optimal weight: 6.9990 chunk 398 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 294 optimal weight: 0.9990 chunk 517 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN E 277 HIS ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN ** a 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 188 GLN ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 339 HIS j 89 HIS p 111 GLN ** p 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 221 GLN ** 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 183 HIS N 89 ASN ** g 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 320 HIS k 263 ASN k 313 GLN m 31 ASN o 122 ASN ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 501 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 53 GLN ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.9154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 69161 Z= 0.254 Angle : 0.598 11.524 97963 Z= 0.300 Chirality : 0.036 0.231 11544 Planarity : 0.004 0.057 9033 Dihedral : 13.322 175.548 17672 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Rotamer Outliers : 1.89 % 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: -0.72 (0.11), residues: 5437 helix: 1.03 (0.11), residues: 2368 sheet: -1.55 (0.24), residues: 455 loop : -1.75 (0.12), residues: 2614 *********************** 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 781 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 690 time to evaluate : 5.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 48 residues processed: 749 average time/residue: 0.6251 time to fit residues: 801.3365 Evaluate side-chains 668 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 620 time to evaluate : 4.630 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.5087 time to fit residues: 51.4208 ------------------------------------------------------------------------------- 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: 1.9990 chunk 519 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 338 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 577 optimal weight: 40.0000 chunk 479 optimal weight: 4.9990 chunk 267 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 303 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 359 HIS ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 188 GLN ** 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** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 125 HIS g 173 ASN k 112 ASN k 233 HIS ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 501 GLN B 58 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.9612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 69161 Z= 0.223 Angle : 0.577 11.210 97963 Z= 0.289 Chirality : 0.035 0.210 11544 Planarity : 0.004 0.061 9033 Dihedral : 13.295 176.660 17672 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.06 % Favored : 94.85 % Rotamer Outliers : 1.56 % 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 (0.12), residues: 5437 helix: 1.10 (0.11), residues: 2376 sheet: -1.48 (0.23), residues: 476 loop : -1.63 (0.12), residues: 2585 *********************** 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 741 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 666 time to evaluate : 4.671 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 outliers start: 75 outliers final: 36 residues processed: 713 average time/residue: 0.6571 time to fit residues: 799.3462 Evaluate side-chains 631 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 595 time to evaluate : 4.617 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4882 time to fit residues: 39.2871 ------------------------------------------------------------------------------- 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: 0.0020 chunk 421 optimal weight: 6.9990 chunk 326 optimal weight: 3.9990 chunk 486 optimal weight: 2.9990 chunk 322 optimal weight: 20.0000 chunk 575 optimal weight: 5.9990 chunk 360 optimal weight: 8.9990 chunk 350 optimal weight: 8.9990 chunk 265 optimal weight: 8.9990 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 GLN L 37 HIS L 101 ASN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 228 ASN d 72 GLN ** d 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 122 GLN e 188 GLN e 238 GLN e 261 GLN ** p 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 HIS ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 80 HIS h 375 GLN o 72 GLN ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 501 GLN o 524 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 195 HIS K 149 HIS O 77 ASN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 1.0477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 69161 Z= 0.348 Angle : 0.682 12.886 97963 Z= 0.343 Chirality : 0.039 0.234 11544 Planarity : 0.005 0.061 9033 Dihedral : 13.597 177.224 17672 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.75 % Favored : 93.14 % Rotamer Outliers : 1.62 % 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: -0.74 (0.11), residues: 5437 helix: 0.85 (0.11), residues: 2395 sheet: -1.36 (0.23), residues: 476 loop : -1.65 (0.12), residues: 2566 *********************** 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 724 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 646 time to evaluate : 4.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 38 residues processed: 689 average time/residue: 0.6517 time to fit residues: 767.0571 Evaluate side-chains 616 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 578 time to evaluate : 4.576 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 38 outliers final: 1 residues processed: 38 average time/residue: 0.5510 time to fit residues: 44.5751 ------------------------------------------------------------------------------- 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: 6.9990 chunk 229 optimal weight: 30.0000 chunk 343 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 365 optimal weight: 5.9990 chunk 392 optimal weight: 6.9990 chunk 284 optimal weight: 0.3980 chunk 53 optimal weight: 10.0000 chunk 452 optimal weight: 5.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 273 ASN ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 GLN L 101 ASN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 188 GLN ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 179 GLN ** p 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 313 GLN m 109 GLN ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 501 GLN B 75 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 65 ASN U 79 ASN b 66 HIS ** z 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 1.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 69161 Z= 0.351 Angle : 0.674 10.965 97963 Z= 0.340 Chirality : 0.039 0.240 11544 Planarity : 0.005 0.062 9033 Dihedral : 13.684 178.649 17672 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.63 % Favored : 94.28 % Rotamer Outliers : 1.33 % 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: -0.77 (0.11), residues: 5437 helix: 0.84 (0.11), residues: 2396 sheet: -1.24 (0.23), residues: 480 loop : -1.70 (0.12), residues: 2561 *********************** 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 684 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 620 time to evaluate : 4.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 33 residues processed: 656 average time/residue: 0.6325 time to fit residues: 713.9596 Evaluate side-chains 588 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 555 time to evaluate : 4.589 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 1 residues processed: 33 average time/residue: 0.5080 time to fit residues: 37.1859 ------------------------------------------------------------------------------- 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: 0.7980 chunk 551 optimal weight: 0.6980 chunk 502 optimal weight: 0.0270 chunk 536 optimal weight: 0.9990 chunk 322 optimal weight: 6.9990 chunk 233 optimal weight: 20.0000 chunk 421 optimal weight: 0.0770 chunk 164 optimal weight: 0.6980 chunk 484 optimal weight: 0.7980 chunk 507 optimal weight: 0.8980 chunk 534 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 341 ASN ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 108 ASN ** 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 366 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 307 ASN ** h 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 363 HIS ** k 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 501 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 199 HIS ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 1.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.101 69161 Z= 0.162 Angle : 0.594 12.587 97963 Z= 0.295 Chirality : 0.035 0.342 11544 Planarity : 0.004 0.060 9033 Dihedral : 13.450 179.806 17672 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.93 % Favored : 95.00 % Rotamer Outliers : 0.56 % 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: -0.44 (0.12), residues: 5437 helix: 1.10 (0.11), residues: 2388 sheet: -1.13 (0.24), residues: 488 loop : -1.50 (0.12), residues: 2561 *********************** 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 691 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 664 time to evaluate : 4.637 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: 27 outliers final: 10 residues processed: 677 average time/residue: 0.6255 time to fit residues: 729.7533 Evaluate side-chains 583 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 573 time to evaluate : 4.586 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.5941 time to fit residues: 16.1548 ------------------------------------------------------------------------------- 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: 10.0000 chunk 567 optimal weight: 4.9990 chunk 346 optimal weight: 0.3980 chunk 268 optimal weight: 7.9990 chunk 394 optimal weight: 10.0000 chunk 594 optimal weight: 4.9990 chunk 547 optimal weight: 2.9990 chunk 473 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 365 optimal weight: 10.0000 chunk 290 optimal weight: 0.0980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 108 ASN ** p 146 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** ** N 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 233 HIS k 313 GLN ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 102 GLN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 ASN z 129 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 1.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 69161 Z= 0.262 Angle : 0.632 13.258 97963 Z= 0.315 Chirality : 0.037 0.323 11544 Planarity : 0.004 0.061 9033 Dihedral : 13.459 177.819 17672 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.00 % Favored : 93.93 % Rotamer Outliers : 0.50 % 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: -0.41 (0.12), residues: 5437 helix: 1.14 (0.11), residues: 2384 sheet: -1.06 (0.23), residues: 488 loop : -1.50 (0.12), residues: 2565 ********************** 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 607 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 583 time to evaluate : 4.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 597 average time/residue: 0.6499 time to fit residues: 669.1484 Evaluate side-chains 575 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 565 time to evaluate : 4.632 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.5176 time to fit residues: 15.6769 ------------------------------------------------------------------------------- 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: 0.9980 chunk 504 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 436 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 131 optimal weight: 0.9980 chunk 474 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 487 optimal weight: 0.9990 chunk 60 optimal weight: 40.0000 chunk 87 optimal weight: 30.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 273 ASN ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 213 ASN ** a 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 276 ASN ** e 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 238 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** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 501 GLN B 190 ASN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.097644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.067706 restraints weight = 220500.271| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.74 r_work: 0.3120 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 1.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 69161 Z= 0.223 Angle : 0.617 13.462 97963 Z= 0.307 Chirality : 0.036 0.319 11544 Planarity : 0.004 0.060 9033 Dihedral : 13.444 177.527 17672 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.41 % Favored : 94.52 % Rotamer Outliers : 0.35 % 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: -0.36 (0.12), residues: 5437 helix: 1.15 (0.11), residues: 2388 sheet: -0.94 (0.24), residues: 486 loop : -1.47 (0.12), residues: 2563 =============================================================================== Job complete usr+sys time: 16125.94 seconds wall clock time: 283 minutes 39.93 seconds (17019.93 seconds total)