Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 15:21:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2e_21526/04_2023/6w2e_21526.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2e_21526/04_2023/6w2e_21526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2e_21526/04_2023/6w2e_21526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2e_21526/04_2023/6w2e_21526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2e_21526/04_2023/6w2e_21526.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2e_21526/04_2023/6w2e_21526.pdb" } resolution = 4.4 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= 0.004 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: 4 Type Number sf(0) Gaussians S 353 5.16 5 C 39758 2.51 5 N 10845 2.21 5 O 11569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J ARG 10": "NH1" <-> "NH2" Residue "J ARG 26": "NH1" <-> "NH2" Residue "J PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 87": "NH1" <-> "NH2" Residue "J PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 114": "NH1" <-> "NH2" Residue "J ARG 186": "NH1" <-> "NH2" Residue "J ARG 232": "NH1" <-> "NH2" Residue "J ARG 245": "NH1" <-> "NH2" Residue "J ARG 247": "NH1" <-> "NH2" Residue "J ARG 364": "NH1" <-> "NH2" Residue "J ARG 481": "NH1" <-> "NH2" Residue "J TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 650": "NH1" <-> "NH2" Residue "J ARG 668": "NH1" <-> "NH2" Residue "J ARG 699": "NH1" <-> "NH2" Residue "J ARG 793": "NH1" <-> "NH2" Residue "J ARG 866": "NH1" <-> "NH2" Residue "J ARG 896": "NH1" <-> "NH2" Residue "J ARG 918": "NH1" <-> "NH2" Residue "J ARG 958": "NH1" <-> "NH2" Residue "J ARG 973": "NH1" <-> "NH2" Residue "J ARG 985": "NH1" <-> "NH2" Residue "J ARG 994": "NH1" <-> "NH2" Residue "J ARG 998": "NH1" <-> "NH2" Residue "J ARG 1062": "NH1" <-> "NH2" Residue "J ARG 1076": "NH1" <-> "NH2" Residue "J ARG 1229": "NH1" <-> "NH2" Residue "J TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 1272": "NH1" <-> "NH2" Residue "J ARG 1285": "NH1" <-> "NH2" Residue "J ARG 1297": "NH1" <-> "NH2" Residue "J ARG 1370": "NH1" <-> "NH2" Residue "K ARG 26": "NH1" <-> "NH2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K ARG 108": "NH1" <-> "NH2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K ARG 114": "NH1" <-> "NH2" Residue "K ARG 205": "NH1" <-> "NH2" Residue "K ARG 232": "NH1" <-> "NH2" Residue "K PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 247": "NH1" <-> "NH2" Residue "K ARG 314": "NH1" <-> "NH2" Residue "K ARG 400": "NH1" <-> "NH2" Residue "K ARG 483": "NH1" <-> "NH2" Residue "K ARG 492": "NH1" <-> "NH2" Residue "K ARG 493": "NH1" <-> "NH2" Residue "K ARG 557": "NH1" <-> "NH2" Residue "K ARG 559": "NH1" <-> "NH2" Residue "K ARG 650": "NH1" <-> "NH2" Residue "K ARG 653": "NH1" <-> "NH2" Residue "K ARG 668": "NH1" <-> "NH2" Residue "K ARG 699": "NH1" <-> "NH2" Residue "K ARG 793": "NH1" <-> "NH2" Residue "K ARG 852": "NH1" <-> "NH2" Residue "K ARG 866": "NH1" <-> "NH2" Residue "K ARG 896": "NH1" <-> "NH2" Residue "K ARG 918": "NH1" <-> "NH2" Residue "K ARG 938": "NH1" <-> "NH2" Residue "K ARG 973": "NH1" <-> "NH2" Residue "K ARG 978": "NH1" <-> "NH2" Residue "K ARG 994": "NH1" <-> "NH2" Residue "K ARG 998": "NH1" <-> "NH2" Residue "K ARG 1080": "NH1" <-> "NH2" Residue "K ARG 1109": "NH1" <-> "NH2" Residue "K ARG 1297": "NH1" <-> "NH2" Residue "K TYR 1361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 1370": "NH1" <-> "NH2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 108": "NH1" <-> "NH2" Residue "N ARG 109": "NH1" <-> "NH2" Residue "N PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 232": "NH1" <-> "NH2" Residue "N ARG 247": "NH1" <-> "NH2" Residue "N ARG 329": "NH1" <-> "NH2" Residue "N ARG 400": "NH1" <-> "NH2" Residue "N ARG 483": "NH1" <-> "NH2" Residue "N ARG 493": "NH1" <-> "NH2" Residue "N ARG 559": "NH1" <-> "NH2" Residue "N ARG 650": "NH1" <-> "NH2" Residue "N ARG 653": "NH1" <-> "NH2" Residue "N ARG 668": "NH1" <-> "NH2" Residue "N ARG 742": "NH1" <-> "NH2" Residue "N ARG 793": "NH1" <-> "NH2" Residue "N ARG 852": "NH1" <-> "NH2" Residue "N ARG 866": "NH1" <-> "NH2" Residue "N ARG 918": "NH1" <-> "NH2" Residue "N ARG 938": "NH1" <-> "NH2" Residue "N ARG 958": "NH1" <-> "NH2" Residue "N ARG 978": "NH1" <-> "NH2" Residue "N ARG 1109": "NH1" <-> "NH2" Residue "N ARG 1297": "NH1" <-> "NH2" Residue "N ARG 1370": "NH1" <-> "NH2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 108": "NH1" <-> "NH2" Residue "O ARG 109": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 221": "NH1" <-> "NH2" Residue "O ARG 232": "NH1" <-> "NH2" Residue "O ARG 247": "NH1" <-> "NH2" Residue "O ARG 288": "NH1" <-> "NH2" Residue "O ARG 314": "NH1" <-> "NH2" Residue "O ARG 329": "NH1" <-> "NH2" Residue "O ARG 463": "NH1" <-> "NH2" Residue "O ARG 481": "NH1" <-> "NH2" Residue "O ARG 492": "NH1" <-> "NH2" Residue "O ARG 552": "NH1" <-> "NH2" Residue "O ARG 559": "NH1" <-> "NH2" Residue "O ARG 650": "NH1" <-> "NH2" Residue "O ARG 653": "NH1" <-> "NH2" Residue "O ARG 668": "NH1" <-> "NH2" Residue "O ARG 684": "NH1" <-> "NH2" Residue "O ARG 699": "NH1" <-> "NH2" Residue "O ARG 742": "NH1" <-> "NH2" Residue "O ARG 765": "NH1" <-> "NH2" Residue "O ARG 793": "NH1" <-> "NH2" Residue "O ARG 896": "NH1" <-> "NH2" Residue "O ARG 918": "NH1" <-> "NH2" Residue "O ARG 936": "NH1" <-> "NH2" Residue "O ARG 938": "NH1" <-> "NH2" Residue "O ARG 958": "NH1" <-> "NH2" Residue "O ARG 985": "NH1" <-> "NH2" Residue "O ARG 994": "NH1" <-> "NH2" Residue "O ARG 998": "NH1" <-> "NH2" Residue "O ARG 1109": "NH1" <-> "NH2" Residue "O ARG 1229": "NH1" <-> "NH2" Residue "O ARG 1297": "NH1" <-> "NH2" Residue "O ARG 1370": "NH1" <-> "NH2" Residue "v ARG 35": "NH1" <-> "NH2" Residue "v ARG 51": "NH1" <-> "NH2" Residue "v ARG 59": "NH1" <-> "NH2" Residue "v ARG 70": "NH1" <-> "NH2" Residue "v ARG 74": "NH1" <-> "NH2" Residue "v ARG 125": "NH1" <-> "NH2" Residue "v ARG 286": "NH1" <-> "NH2" Residue "v ARG 340": "NH1" <-> "NH2" Residue "v ARG 348": "NH1" <-> "NH2" Residue "v ARG 354": "NH1" <-> "NH2" Residue "v ARG 378": "NH1" <-> "NH2" Residue "v ARG 387": "NH1" <-> "NH2" Residue "v PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 396": "NH1" <-> "NH2" Residue "v ARG 494": "NH1" <-> "NH2" Residue "w ARG 44": "NH1" <-> "NH2" Residue "w ARG 48": "NH1" <-> "NH2" Residue "w ARG 53": "NH1" <-> "NH2" Residue "w ARG 56": "NH1" <-> "NH2" Residue "w ARG 64": "NH1" <-> "NH2" Residue "w ARG 75": "NH1" <-> "NH2" Residue "w ARG 85": "NH1" <-> "NH2" Residue "x ARG 44": "NH1" <-> "NH2" Residue "x ARG 48": "NH1" <-> "NH2" Residue "x ARG 53": "NH1" <-> "NH2" Residue "x ARG 56": "NH1" <-> "NH2" Residue "x ARG 64": "NH1" <-> "NH2" Residue "x ARG 67": "NH1" <-> "NH2" Residue "x ARG 75": "NH1" <-> "NH2" Residue "x ARG 80": "NH1" <-> "NH2" Residue "x ARG 85": "NH1" <-> "NH2" Residue "y ARG 3117": "NH1" <-> "NH2" Residue "y ARG 3121": "NH1" <-> "NH2" Residue "y ARG 3127": "NH1" <-> "NH2" Residue "y ARG 3128": "NH1" <-> "NH2" Residue "y ARG 3132": "NH1" <-> "NH2" Residue "y ARG 3136": "NH1" <-> "NH2" Residue "z ARG 3117": "NH1" <-> "NH2" Residue "z ARG 3121": "NH1" <-> "NH2" Residue "z ARG 3127": "NH1" <-> "NH2" Residue "z ARG 3128": "NH1" <-> "NH2" Residue "z ARG 3132": "NH1" <-> "NH2" Residue "z ARG 3136": "NH1" <-> "NH2" Residue "Z ARG 4": "NH1" <-> "NH2" Residue "Z ARG 41": "NH1" <-> "NH2" Residue "Z ARG 63": "NH1" <-> "NH2" Residue "Z ARG 69": "NH1" <-> "NH2" Residue "Z ARG 70": "NH1" <-> "NH2" Residue "Z ARG 72": "NH1" <-> "NH2" Residue "a ARG 3": "NH1" <-> "NH2" Residue "a ARG 41": "NH1" <-> "NH2" Residue "a ARG 72": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 69": "NH1" <-> "NH2" Residue "e ARG 4": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 45": "NH1" <-> "NH2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 77": "NH1" <-> "NH2" Residue "f ARG 174": "NH1" <-> "NH2" Residue "f ARG 179": "NH1" <-> "NH2" Residue "f ARG 180": "NH1" <-> "NH2" Residue "f ARG 218": "NH1" <-> "NH2" Residue "f ARG 263": "NH1" <-> "NH2" Residue "f ARG 276": "NH1" <-> "NH2" Residue "f ARG 284": "NH1" <-> "NH2" Residue "f ARG 294": "NH1" <-> "NH2" Residue "f ARG 304": "NH1" <-> "NH2" Residue "f ARG 334": "NH1" <-> "NH2" Residue "f ARG 335": "NH1" <-> "NH2" Residue "f ARG 341": "NH1" <-> "NH2" Residue "h ARG 10": "NH1" <-> "NH2" Residue "h ARG 11": "NH1" <-> "NH2" Residue "h ARG 15": "NH1" <-> "NH2" Residue "h ARG 25": "NH1" <-> "NH2" Residue "h ARG 31": "NH1" <-> "NH2" Residue "h ARG 86": "NH1" <-> "NH2" Residue "h ARG 174": "NH1" <-> "NH2" Residue "h ARG 179": "NH1" <-> "NH2" Residue "h ARG 263": "NH1" <-> "NH2" Residue "h ARG 276": "NH1" <-> "NH2" Residue "h ARG 284": "NH1" <-> "NH2" Residue "h ARG 294": "NH1" <-> "NH2" Residue "h ARG 304": "NH1" <-> "NH2" Residue "h ARG 334": "NH1" <-> "NH2" Residue "h ARG 335": "NH1" <-> "NH2" Residue "h ARG 341": "NH1" <-> "NH2" Residue "k ARG 12": "NH1" <-> "NH2" Residue "k ARG 24": "NH1" <-> "NH2" Residue "k ARG 225": "NH1" <-> "NH2" Residue "k ARG 249": "NH1" <-> "NH2" Residue "m ARG 12": "NH1" <-> "NH2" Residue "m ARG 24": "NH1" <-> "NH2" Residue "m ARG 158": "NH1" <-> "NH2" Residue "m ARG 229": "NH1" <-> "NH2" Residue "m ARG 249": "NH1" <-> "NH2" Residue "p ARG 12": "NH1" <-> "NH2" Residue "p ARG 24": "NH1" <-> "NH2" Residue "p ARG 225": "NH1" <-> "NH2" Residue "r ARG 24": "NH1" <-> "NH2" Residue "r ARG 158": "NH1" <-> "NH2" Residue "r ARG 225": "NH1" <-> "NH2" Residue "r ARG 229": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 62525 Number of models: 1 Model: "" Number of chains: 19 Chain: "J" Number of atoms: 10252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10252 Classifications: {'peptide': 1305} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 68, 'TRANS': 1236} Chain breaks: 2 Chain: "K" Number of atoms: 10832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1381, 10832 Classifications: {'peptide': 1381} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 72, 'TRANS': 1308} Chain: "N" Number of atoms: 10683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1362, 10683 Classifications: {'peptide': 1362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 71, 'TRANS': 1290} Chain breaks: 1 Chain: "O" Number of atoms: 10194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1299, 10194 Classifications: {'peptide': 1299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 69, 'TRANS': 1229} Chain breaks: 1 Chain: "v" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2288 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 17, 'TRANS': 275} Chain breaks: 4 Chain: "w" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 549 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "x" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 549 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "y" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 317 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'TRANS': 36} Chain: "z" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 317 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'TRANS': 36} Chain: "Z" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 649 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 7, 'TRANS': 69} Chain: "a" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 649 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 7, 'TRANS': 69} Chain: "d" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 649 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 7, 'TRANS': 69} Chain: "e" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 649 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 7, 'TRANS': 69} Chain: "f" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1992 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 234} Chain breaks: 2 Chain: "h" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2604 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 313} Chain breaks: 2 Chain: "k" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2338 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 16, 'TRANS': 282} Chain: "m" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2338 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 16, 'TRANS': 282} Chain: "p" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2338 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 16, 'TRANS': 282} Chain: "r" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2338 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 16, 'TRANS': 282} Time building chain proxies: 23.81, per 1000 atoms: 0.38 Number of scatterers: 62525 At special positions: 0 Unit cell: (238, 240.72, 208.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 353 16.00 O 11569 8.00 N 10845 7.00 C 39758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 18.10 Conformation dependent library (CDL) restraints added in 7.3 seconds 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15018 Finding SS restraints... Secondary structure from input PDB file: 329 helices and 84 sheets defined 44.3% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'J' and resid 24 through 31 Processing helix chain 'J' and resid 71 through 75 Processing helix chain 'J' and resid 135 through 141 Processing helix chain 'J' and resid 147 through 188 removed outlier: 3.603A pdb=" N ILE J 177 " --> pdb=" O GLU J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 199 removed outlier: 5.237A pdb=" N THR J 196 " --> pdb=" O PHE J 192 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU J 197 " --> pdb=" O ILE J 193 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP J 199 " --> pdb=" O GLN J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 226 Processing helix chain 'J' and resid 228 through 237 removed outlier: 4.073A pdb=" N GLU J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASN J 235 " --> pdb=" O ASP J 231 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET J 236 " --> pdb=" O ARG J 232 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY J 237 " --> pdb=" O ALA J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 255 removed outlier: 3.778A pdb=" N TYR J 243 " --> pdb=" O GLY J 239 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL J 244 " --> pdb=" O PHE J 240 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL J 255 " --> pdb=" O MET J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 294 Processing helix chain 'J' and resid 384 through 390 removed outlier: 3.859A pdb=" N TYR J 388 " --> pdb=" O LEU J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 429 through 433 removed outlier: 3.587A pdb=" N GLN J 433 " --> pdb=" O PRO J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 460 removed outlier: 4.419A pdb=" N LYS J 457 " --> pdb=" O GLN J 453 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL J 458 " --> pdb=" O ASN J 454 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU J 459 " --> pdb=" O ALA J 455 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS J 460 " --> pdb=" O LEU J 456 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 466 removed outlier: 3.738A pdb=" N HIS J 465 " --> pdb=" O HIS J 461 " (cutoff:3.500A) Processing helix chain 'J' and resid 467 through 477 removed outlier: 3.712A pdb=" N ALA J 477 " --> pdb=" O SER J 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 498 through 508 Processing helix chain 'J' and resid 516 through 522 Processing helix chain 'J' and resid 534 through 540 removed outlier: 3.952A pdb=" N LEU J 540 " --> pdb=" O ASP J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 577 through 593 Processing helix chain 'J' and resid 599 through 611 Processing helix chain 'J' and resid 616 through 627 removed outlier: 4.046A pdb=" N TYR J 620 " --> pdb=" O PRO J 616 " (cutoff:3.500A) Processing helix chain 'J' and resid 629 through 636 Processing helix chain 'J' and resid 636 through 651 removed outlier: 3.513A pdb=" N SER J 651 " --> pdb=" O TYR J 647 " (cutoff:3.500A) Processing helix chain 'J' and resid 659 through 669 removed outlier: 3.643A pdb=" N ILE J 663 " --> pdb=" O SER J 659 " (cutoff:3.500A) Processing helix chain 'J' and resid 676 through 702 removed outlier: 4.150A pdb=" N MET J 682 " --> pdb=" O GLU J 678 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE J 686 " --> pdb=" O MET J 682 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR J 687 " --> pdb=" O TYR J 683 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY J 702 " --> pdb=" O MET J 698 " (cutoff:3.500A) Processing helix chain 'J' and resid 711 through 716 Processing helix chain 'J' and resid 731 through 738 removed outlier: 3.858A pdb=" N HIS J 735 " --> pdb=" O ASP J 731 " (cutoff:3.500A) Processing helix chain 'J' and resid 755 through 757 No H-bonds generated for 'chain 'J' and resid 755 through 757' Processing helix chain 'J' and resid 758 through 762 Processing helix chain 'J' and resid 770 through 774 removed outlier: 3.755A pdb=" N ALA J 773 " --> pdb=" O ASP J 770 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA J 774 " --> pdb=" O GLU J 771 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 770 through 774' Processing helix chain 'J' and resid 775 through 786 removed outlier: 3.796A pdb=" N ARG J 783 " --> pdb=" O LEU J 779 " (cutoff:3.500A) Processing helix chain 'J' and resid 806 through 813 Processing helix chain 'J' and resid 815 through 821 Processing helix chain 'J' and resid 831 through 841 Processing helix chain 'J' and resid 856 through 860 Processing helix chain 'J' and resid 863 through 873 Processing helix chain 'J' and resid 877 through 886 Processing helix chain 'J' and resid 887 through 891 Processing helix chain 'J' and resid 913 through 916 removed outlier: 3.638A pdb=" N ASP J 916 " --> pdb=" O ASN J 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 913 through 916' Processing helix chain 'J' and resid 936 through 942 removed outlier: 4.267A pdb=" N VAL J 940 " --> pdb=" O ARG J 936 " (cutoff:3.500A) Processing helix chain 'J' and resid 956 through 964 Processing helix chain 'J' and resid 964 through 974 Processing helix chain 'J' and resid 998 through 1007 removed outlier: 3.550A pdb=" N GLU J1007 " --> pdb=" O LYS J1003 " (cutoff:3.500A) Processing helix chain 'J' and resid 1011 through 1022 removed outlier: 3.686A pdb=" N HIS J1022 " --> pdb=" O MET J1018 " (cutoff:3.500A) Processing helix chain 'J' and resid 1026 through 1036 removed outlier: 3.839A pdb=" N LEU J1036 " --> pdb=" O ALA J1032 " (cutoff:3.500A) Processing helix chain 'J' and resid 1123 through 1128 removed outlier: 4.162A pdb=" N VAL J1127 " --> pdb=" O ASP J1123 " (cutoff:3.500A) Processing helix chain 'J' and resid 1135 through 1147 Processing helix chain 'J' and resid 1192 through 1198 removed outlier: 3.963A pdb=" N PHE J1196 " --> pdb=" O ASP J1192 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS J1198 " --> pdb=" O ALA J1194 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1241 through 1246 removed outlier: 3.710A pdb=" N GLN J1246 " --> pdb=" O PRO J1242 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1256 Processing helix chain 'J' and resid 1271 through 1276 Processing helix chain 'J' and resid 1277 through 1282 Processing helix chain 'J' and resid 1283 through 1285 No H-bonds generated for 'chain 'J' and resid 1283 through 1285' Processing helix chain 'J' and resid 1286 through 1297 removed outlier: 3.561A pdb=" N SER J1295 " --> pdb=" O VAL J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1324 through 1329 removed outlier: 3.536A pdb=" N LEU J1328 " --> pdb=" O PRO J1324 " (cutoff:3.500A) Processing helix chain 'J' and resid 1339 through 1349 removed outlier: 3.689A pdb=" N ILE J1343 " --> pdb=" O SER J1339 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 46 removed outlier: 3.538A pdb=" N ASP K 44 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG K 46 " --> pdb=" O LYS K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 75 Processing helix chain 'K' and resid 84 through 88 Processing helix chain 'K' and resid 135 through 143 Processing helix chain 'K' and resid 147 through 187 removed outlier: 3.764A pdb=" N GLY K 175 " --> pdb=" O ALA K 171 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU K 176 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE K 177 " --> pdb=" O GLU K 173 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS K 187 " --> pdb=" O VAL K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 199 removed outlier: 4.684A pdb=" N THR K 196 " --> pdb=" O PHE K 192 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU K 197 " --> pdb=" O ILE K 193 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP K 199 " --> pdb=" O GLN K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 203 Processing helix chain 'K' and resid 208 through 227 removed outlier: 4.104A pdb=" N SER K 227 " --> pdb=" O LEU K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 236 Processing helix chain 'K' and resid 239 through 255 removed outlier: 3.725A pdb=" N VAL K 255 " --> pdb=" O MET K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 264 removed outlier: 4.112A pdb=" N GLY K 263 " --> pdb=" O VAL K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 295 removed outlier: 3.915A pdb=" N GLN K 289 " --> pdb=" O ASN K 285 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY K 295 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 324 Processing helix chain 'K' and resid 330 through 339 removed outlier: 3.659A pdb=" N ALA K 336 " --> pdb=" O GLU K 332 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG K 337 " --> pdb=" O HIS K 333 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE K 338 " --> pdb=" O PHE K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 347 through 357 Proline residue: K 353 - end of helix removed outlier: 3.911A pdb=" N ALA K 356 " --> pdb=" O LEU K 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 392 removed outlier: 4.309A pdb=" N TYR K 388 " --> pdb=" O LEU K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 460 removed outlier: 3.732A pdb=" N ALA K 455 " --> pdb=" O ASN K 451 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS K 457 " --> pdb=" O GLN K 453 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL K 458 " --> pdb=" O ASN K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 466 removed outlier: 4.000A pdb=" N HIS K 465 " --> pdb=" O HIS K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 477 Processing helix chain 'K' and resid 499 through 508 Processing helix chain 'K' and resid 516 through 524 removed outlier: 3.537A pdb=" N GLY K 523 " --> pdb=" O ALA K 519 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU K 524 " --> pdb=" O LEU K 520 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 531 Processing helix chain 'K' and resid 534 through 540 removed outlier: 3.519A pdb=" N LEU K 538 " --> pdb=" O ASN K 534 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU K 540 " --> pdb=" O ASP K 536 " (cutoff:3.500A) Processing helix chain 'K' and resid 567 through 571 Processing helix chain 'K' and resid 577 through 592 Processing helix chain 'K' and resid 599 through 611 removed outlier: 3.597A pdb=" N ILE K 603 " --> pdb=" O ASP K 599 " (cutoff:3.500A) Processing helix chain 'K' and resid 616 through 627 removed outlier: 4.299A pdb=" N TYR K 620 " --> pdb=" O PRO K 616 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL K 621 " --> pdb=" O ALA K 617 " (cutoff:3.500A) Processing helix chain 'K' and resid 629 through 636 removed outlier: 3.874A pdb=" N ASN K 636 " --> pdb=" O LYS K 632 " (cutoff:3.500A) Processing helix chain 'K' and resid 636 through 651 removed outlier: 3.576A pdb=" N SER K 651 " --> pdb=" O TYR K 647 " (cutoff:3.500A) Processing helix chain 'K' and resid 659 through 669 Processing helix chain 'K' and resid 676 through 701 removed outlier: 4.022A pdb=" N MET K 682 " --> pdb=" O GLU K 678 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR K 683 " --> pdb=" O ALA K 679 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA K 701 " --> pdb=" O LEU K 697 " (cutoff:3.500A) Processing helix chain 'K' and resid 711 through 716 Processing helix chain 'K' and resid 731 through 740 removed outlier: 4.180A pdb=" N HIS K 735 " --> pdb=" O ASP K 731 " (cutoff:3.500A) Processing helix chain 'K' and resid 758 through 762 Processing helix chain 'K' and resid 775 through 786 removed outlier: 3.829A pdb=" N TYR K 780 " --> pdb=" O PHE K 776 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL K 784 " --> pdb=" O TYR K 780 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN K 785 " --> pdb=" O GLY K 781 " (cutoff:3.500A) Processing helix chain 'K' and resid 806 through 815 Processing helix chain 'K' and resid 815 through 821 Processing helix chain 'K' and resid 831 through 840 Processing helix chain 'K' and resid 842 through 847 Processing helix chain 'K' and resid 855 through 860 removed outlier: 4.355A pdb=" N ASN K 859 " --> pdb=" O ASP K 855 " (cutoff:3.500A) Processing helix chain 'K' and resid 863 through 873 removed outlier: 3.738A pdb=" N ASP K 867 " --> pdb=" O GLY K 863 " (cutoff:3.500A) Processing helix chain 'K' and resid 877 through 887 removed outlier: 3.884A pdb=" N ILE K 881 " --> pdb=" O THR K 877 " (cutoff:3.500A) Processing helix chain 'K' and resid 940 through 943 Processing helix chain 'K' and resid 956 through 964 Processing helix chain 'K' and resid 965 through 974 Processing helix chain 'K' and resid 975 through 979 removed outlier: 3.738A pdb=" N ALA K 979 " --> pdb=" O GLN K 976 " (cutoff:3.500A) Processing helix chain 'K' and resid 998 through 1008 removed outlier: 3.893A pdb=" N GLY K1002 " --> pdb=" O ARG K 998 " (cutoff:3.500A) Processing helix chain 'K' and resid 1011 through 1021 Processing helix chain 'K' and resid 1026 through 1036 Processing helix chain 'K' and resid 1123 through 1128 removed outlier: 3.515A pdb=" N VAL K1127 " --> pdb=" O ASP K1123 " (cutoff:3.500A) Processing helix chain 'K' and resid 1135 through 1147 Processing helix chain 'K' and resid 1192 through 1198 removed outlier: 3.877A pdb=" N PHE K1196 " --> pdb=" O ASP K1192 " (cutoff:3.500A) Processing helix chain 'K' and resid 1216 through 1226 removed outlier: 3.524A pdb=" N ALA K1220 " --> pdb=" O ASN K1216 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE K1224 " --> pdb=" O ALA K1220 " (cutoff:3.500A) Processing helix chain 'K' and resid 1241 through 1246 removed outlier: 3.731A pdb=" N SER K1245 " --> pdb=" O ASN K1241 " (cutoff:3.500A) Processing helix chain 'K' and resid 1249 through 1255 Processing helix chain 'K' and resid 1269 through 1276 removed outlier: 4.093A pdb=" N ALA K1273 " --> pdb=" O SER K1269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE K1274 " --> pdb=" O PRO K1270 " (cutoff:3.500A) Processing helix chain 'K' and resid 1276 through 1283 removed outlier: 4.205A pdb=" N ASN K1283 " --> pdb=" O GLU K1279 " (cutoff:3.500A) Processing helix chain 'K' and resid 1286 through 1297 removed outlier: 3.786A pdb=" N ASN K1292 " --> pdb=" O TYR K1288 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG K1297 " --> pdb=" O GLU K1293 " (cutoff:3.500A) Processing helix chain 'K' and resid 1324 through 1329 Processing helix chain 'K' and resid 1339 through 1349 removed outlier: 3.659A pdb=" N ILE K1343 " --> pdb=" O SER K1339 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 32 Processing helix chain 'N' and resid 41 through 45 Processing helix chain 'N' and resid 71 through 75 Processing helix chain 'N' and resid 135 through 141 Processing helix chain 'N' and resid 147 through 187 removed outlier: 4.088A pdb=" N GLY N 168 " --> pdb=" O ALA N 164 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS N 187 " --> pdb=" O VAL N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 199 removed outlier: 4.486A pdb=" N THR N 196 " --> pdb=" O PHE N 192 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU N 197 " --> pdb=" O ILE N 193 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP N 199 " --> pdb=" O GLN N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 208 through 226 removed outlier: 3.743A pdb=" N ALA N 217 " --> pdb=" O SER N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 228 through 237 removed outlier: 4.288A pdb=" N GLU N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN N 235 " --> pdb=" O ASP N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 255 removed outlier: 3.785A pdb=" N VAL N 255 " --> pdb=" O MET N 251 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 295 Processing helix chain 'N' and resid 315 through 324 removed outlier: 3.920A pdb=" N VAL N 319 " --> pdb=" O GLY N 315 " (cutoff:3.500A) Processing helix chain 'N' and resid 330 through 339 removed outlier: 3.586A pdb=" N ILE N 338 " --> pdb=" O PHE N 334 " (cutoff:3.500A) Processing helix chain 'N' and resid 347 through 356 Proline residue: N 353 - end of helix removed outlier: 3.600A pdb=" N ALA N 356 " --> pdb=" O LEU N 352 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 390 Processing helix chain 'N' and resid 453 through 459 removed outlier: 3.713A pdb=" N LYS N 457 " --> pdb=" O ASN N 454 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL N 458 " --> pdb=" O ALA N 455 " (cutoff:3.500A) Processing helix chain 'N' and resid 467 through 477 removed outlier: 3.833A pdb=" N ALA N 477 " --> pdb=" O SER N 473 " (cutoff:3.500A) Processing helix chain 'N' and resid 498 through 508 removed outlier: 3.724A pdb=" N ILE N 502 " --> pdb=" O ASN N 498 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE N 506 " --> pdb=" O ILE N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 516 through 522 removed outlier: 3.833A pdb=" N LEU N 520 " --> pdb=" O THR N 516 " (cutoff:3.500A) Processing helix chain 'N' and resid 525 through 531 Processing helix chain 'N' and resid 534 through 540 removed outlier: 3.566A pdb=" N LEU N 538 " --> pdb=" O ASN N 534 " (cutoff:3.500A) Processing helix chain 'N' and resid 567 through 571 Processing helix chain 'N' and resid 572 through 576 Processing helix chain 'N' and resid 577 through 593 removed outlier: 3.581A pdb=" N GLN N 581 " --> pdb=" O PRO N 577 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER N 593 " --> pdb=" O GLU N 589 " (cutoff:3.500A) Processing helix chain 'N' and resid 599 through 611 Processing helix chain 'N' and resid 616 through 627 removed outlier: 3.502A pdb=" N TYR N 620 " --> pdb=" O PRO N 616 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS N 627 " --> pdb=" O GLU N 623 " (cutoff:3.500A) Processing helix chain 'N' and resid 629 through 635 Processing helix chain 'N' and resid 636 through 651 removed outlier: 3.522A pdb=" N SER N 651 " --> pdb=" O TYR N 647 " (cutoff:3.500A) Processing helix chain 'N' and resid 659 through 669 Processing helix chain 'N' and resid 676 through 701 removed outlier: 3.748A pdb=" N SER N 681 " --> pdb=" O LYS N 677 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET N 682 " --> pdb=" O GLU N 678 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR N 683 " --> pdb=" O ALA N 679 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU N 694 " --> pdb=" O LEU N 690 " (cutoff:3.500A) Processing helix chain 'N' and resid 711 through 716 Processing helix chain 'N' and resid 731 through 740 removed outlier: 4.208A pdb=" N HIS N 735 " --> pdb=" O ASP N 731 " (cutoff:3.500A) Processing helix chain 'N' and resid 755 through 757 No H-bonds generated for 'chain 'N' and resid 755 through 757' Processing helix chain 'N' and resid 758 through 762 Processing helix chain 'N' and resid 770 through 774 removed outlier: 3.582A pdb=" N ALA N 773 " --> pdb=" O ASP N 770 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA N 774 " --> pdb=" O GLU N 771 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 770 through 774' Processing helix chain 'N' and resid 775 through 786 removed outlier: 3.748A pdb=" N TYR N 782 " --> pdb=" O ALA N 778 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG N 783 " --> pdb=" O LEU N 779 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL N 784 " --> pdb=" O TYR N 780 " (cutoff:3.500A) Processing helix chain 'N' and resid 806 through 815 removed outlier: 3.508A pdb=" N LYS N 810 " --> pdb=" O ASP N 806 " (cutoff:3.500A) Processing helix chain 'N' and resid 815 through 821 Processing helix chain 'N' and resid 831 through 841 removed outlier: 3.630A pdb=" N TYR N 841 " --> pdb=" O GLN N 837 " (cutoff:3.500A) Processing helix chain 'N' and resid 842 through 847 removed outlier: 3.501A pdb=" N PHE N 846 " --> pdb=" O ASN N 842 " (cutoff:3.500A) Processing helix chain 'N' and resid 855 through 860 removed outlier: 4.050A pdb=" N ASN N 859 " --> pdb=" O ASP N 855 " (cutoff:3.500A) Processing helix chain 'N' and resid 863 through 872 Processing helix chain 'N' and resid 877 through 887 removed outlier: 3.542A pdb=" N ILE N 881 " --> pdb=" O THR N 877 " (cutoff:3.500A) Processing helix chain 'N' and resid 914 through 916 No H-bonds generated for 'chain 'N' and resid 914 through 916' Processing helix chain 'N' and resid 940 through 943 Processing helix chain 'N' and resid 956 through 964 Processing helix chain 'N' and resid 964 through 974 Processing helix chain 'N' and resid 975 through 979 removed outlier: 3.921A pdb=" N ALA N 979 " --> pdb=" O GLN N 976 " (cutoff:3.500A) Processing helix chain 'N' and resid 998 through 1007 removed outlier: 3.694A pdb=" N GLY N1002 " --> pdb=" O ARG N 998 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU N1007 " --> pdb=" O LYS N1003 " (cutoff:3.500A) Processing helix chain 'N' and resid 1011 through 1021 Processing helix chain 'N' and resid 1026 through 1037 removed outlier: 3.702A pdb=" N LEU N1036 " --> pdb=" O ALA N1032 " (cutoff:3.500A) Processing helix chain 'N' and resid 1123 through 1128 Processing helix chain 'N' and resid 1135 through 1147 removed outlier: 3.610A pdb=" N GLY N1147 " --> pdb=" O LYS N1143 " (cutoff:3.500A) Processing helix chain 'N' and resid 1192 through 1196 Processing helix chain 'N' and resid 1216 through 1226 Processing helix chain 'N' and resid 1249 through 1256 Processing helix chain 'N' and resid 1269 through 1276 removed outlier: 4.069A pdb=" N ALA N1273 " --> pdb=" O SER N1269 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE N1274 " --> pdb=" O PRO N1270 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN N1276 " --> pdb=" O ARG N1272 " (cutoff:3.500A) Processing helix chain 'N' and resid 1276 through 1283 removed outlier: 3.750A pdb=" N ASN N1283 " --> pdb=" O GLU N1279 " (cutoff:3.500A) Processing helix chain 'N' and resid 1286 through 1297 Processing helix chain 'N' and resid 1324 through 1329 removed outlier: 3.572A pdb=" N LEU N1328 " --> pdb=" O PRO N1324 " (cutoff:3.500A) Processing helix chain 'N' and resid 1339 through 1349 removed outlier: 3.885A pdb=" N ILE N1343 " --> pdb=" O SER N1339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP N1344 " --> pdb=" O ARG N1340 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU N1345 " --> pdb=" O ALA N1341 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET N1347 " --> pdb=" O ILE N1343 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 75 Processing helix chain 'O' and resid 135 through 143 removed outlier: 3.775A pdb=" N ILE O 140 " --> pdb=" O LEU O 136 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU O 141 " --> pdb=" O ASP O 137 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N HIS O 142 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER O 143 " --> pdb=" O GLU O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 187 removed outlier: 3.713A pdb=" N LYS O 159 " --> pdb=" O VAL O 155 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS O 187 " --> pdb=" O VAL O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 190 through 199 removed outlier: 5.104A pdb=" N THR O 196 " --> pdb=" O PHE O 192 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU O 197 " --> pdb=" O ILE O 193 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP O 199 " --> pdb=" O GLN O 195 " (cutoff:3.500A) Processing helix chain 'O' and resid 208 through 226 Processing helix chain 'O' and resid 228 through 237 removed outlier: 3.582A pdb=" N ARG O 232 " --> pdb=" O PHE O 228 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU O 234 " --> pdb=" O LEU O 230 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN O 235 " --> pdb=" O ASP O 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY O 237 " --> pdb=" O ALA O 233 " (cutoff:3.500A) Processing helix chain 'O' and resid 239 through 255 Processing helix chain 'O' and resid 259 through 263 removed outlier: 4.564A pdb=" N GLY O 263 " --> pdb=" O VAL O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 283 through 294 Processing helix chain 'O' and resid 314 through 325 removed outlier: 3.886A pdb=" N THR O 320 " --> pdb=" O GLU O 316 " (cutoff:3.500A) Processing helix chain 'O' and resid 330 through 339 removed outlier: 3.811A pdb=" N PHE O 334 " --> pdb=" O THR O 330 " (cutoff:3.500A) Processing helix chain 'O' and resid 347 through 356 Proline residue: O 353 - end of helix removed outlier: 3.879A pdb=" N ALA O 356 " --> pdb=" O LEU O 352 " (cutoff:3.500A) Processing helix chain 'O' and resid 385 through 390 Processing helix chain 'O' and resid 455 through 460 removed outlier: 3.596A pdb=" N LEU O 459 " --> pdb=" O ALA O 455 " (cutoff:3.500A) Processing helix chain 'O' and resid 461 through 466 removed outlier: 4.206A pdb=" N HIS O 465 " --> pdb=" O HIS O 461 " (cutoff:3.500A) Processing helix chain 'O' and resid 467 through 476 Processing helix chain 'O' and resid 498 through 508 removed outlier: 3.944A pdb=" N ILE O 502 " --> pdb=" O ASN O 498 " (cutoff:3.500A) Processing helix chain 'O' and resid 516 through 522 Processing helix chain 'O' and resid 525 through 531 Processing helix chain 'O' and resid 537 through 541 Processing helix chain 'O' and resid 567 through 571 Processing helix chain 'O' and resid 577 through 593 Processing helix chain 'O' and resid 599 through 611 removed outlier: 3.621A pdb=" N ILE O 603 " --> pdb=" O ASP O 599 " (cutoff:3.500A) Processing helix chain 'O' and resid 617 through 627 removed outlier: 3.735A pdb=" N VAL O 621 " --> pdb=" O ALA O 617 " (cutoff:3.500A) Processing helix chain 'O' and resid 629 through 651 Proline residue: O 638 - end of helix removed outlier: 4.061A pdb=" N LEU O 642 " --> pdb=" O PRO O 638 " (cutoff:3.500A) Processing helix chain 'O' and resid 659 through 670 removed outlier: 3.548A pdb=" N ILE O 663 " --> pdb=" O SER O 659 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU O 670 " --> pdb=" O ILE O 666 " (cutoff:3.500A) Processing helix chain 'O' and resid 676 through 702 removed outlier: 3.752A pdb=" N MET O 682 " --> pdb=" O GLU O 678 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR O 683 " --> pdb=" O ALA O 679 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY O 702 " --> pdb=" O MET O 698 " (cutoff:3.500A) Processing helix chain 'O' and resid 711 through 716 Processing helix chain 'O' and resid 731 through 740 removed outlier: 4.078A pdb=" N HIS O 735 " --> pdb=" O ASP O 731 " (cutoff:3.500A) Processing helix chain 'O' and resid 758 through 762 removed outlier: 4.111A pdb=" N PHE O 762 " --> pdb=" O ALA O 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 758 through 762' Processing helix chain 'O' and resid 768 through 773 Processing helix chain 'O' and resid 775 through 785 removed outlier: 3.891A pdb=" N ARG O 783 " --> pdb=" O LEU O 779 " (cutoff:3.500A) Processing helix chain 'O' and resid 807 through 815 Processing helix chain 'O' and resid 815 through 822 Processing helix chain 'O' and resid 831 through 840 Processing helix chain 'O' and resid 841 through 843 No H-bonds generated for 'chain 'O' and resid 841 through 843' Processing helix chain 'O' and resid 863 through 873 removed outlier: 3.741A pdb=" N SER O 872 " --> pdb=" O LEU O 868 " (cutoff:3.500A) Processing helix chain 'O' and resid 877 through 886 Processing helix chain 'O' and resid 887 through 889 No H-bonds generated for 'chain 'O' and resid 887 through 889' Processing helix chain 'O' and resid 937 through 942 Processing helix chain 'O' and resid 956 through 964 removed outlier: 4.084A pdb=" N THR O 962 " --> pdb=" O ARG O 958 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET O 963 " --> pdb=" O VAL O 959 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS O 964 " --> pdb=" O ALA O 960 " (cutoff:3.500A) Processing helix chain 'O' and resid 964 through 974 removed outlier: 3.532A pdb=" N ASN O 974 " --> pdb=" O PHE O 970 " (cutoff:3.500A) Processing helix chain 'O' and resid 975 through 979 removed outlier: 4.013A pdb=" N ALA O 979 " --> pdb=" O GLN O 976 " (cutoff:3.500A) Processing helix chain 'O' and resid 998 through 1007 removed outlier: 3.633A pdb=" N GLY O1002 " --> pdb=" O ARG O 998 " (cutoff:3.500A) Processing helix chain 'O' and resid 1012 through 1022 removed outlier: 3.668A pdb=" N SER O1016 " --> pdb=" O LEU O1012 " (cutoff:3.500A) Processing helix chain 'O' and resid 1026 through 1037 removed outlier: 3.744A pdb=" N LEU O1036 " --> pdb=" O ALA O1032 " (cutoff:3.500A) Processing helix chain 'O' and resid 1123 through 1128 removed outlier: 3.687A pdb=" N VAL O1127 " --> pdb=" O ASP O1123 " (cutoff:3.500A) Processing helix chain 'O' and resid 1135 through 1146 Processing helix chain 'O' and resid 1193 through 1198 removed outlier: 4.041A pdb=" N LYS O1198 " --> pdb=" O ALA O1194 " (cutoff:3.500A) Processing helix chain 'O' and resid 1216 through 1226 Processing helix chain 'O' and resid 1241 through 1246 removed outlier: 3.869A pdb=" N GLN O1246 " --> pdb=" O PRO O1242 " (cutoff:3.500A) Processing helix chain 'O' and resid 1249 through 1256 Processing helix chain 'O' and resid 1271 through 1276 Processing helix chain 'O' and resid 1276 through 1282 Processing helix chain 'O' and resid 1283 through 1285 No H-bonds generated for 'chain 'O' and resid 1283 through 1285' Processing helix chain 'O' and resid 1286 through 1297 removed outlier: 3.780A pdb=" N SER O1295 " --> pdb=" O VAL O1291 " (cutoff:3.500A) Processing helix chain 'O' and resid 1324 through 1329 Processing helix chain 'O' and resid 1339 through 1349 removed outlier: 3.629A pdb=" N ILE O1343 " --> pdb=" O SER O1339 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 11 Processing helix chain 'v' and resid 24 through 32 removed outlier: 3.953A pdb=" N GLU v 30 " --> pdb=" O THR v 26 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU v 31 " --> pdb=" O VAL v 27 " (cutoff:3.500A) Processing helix chain 'v' and resid 70 through 74 removed outlier: 3.727A pdb=" N HIS v 73 " --> pdb=" O ARG v 70 " (cutoff:3.500A) Processing helix chain 'v' and resid 118 through 123 Processing helix chain 'v' and resid 332 through 360 removed outlier: 4.276A pdb=" N GLU v 336 " --> pdb=" O LEU v 332 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG v 337 " --> pdb=" O GLY v 333 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU v 338 " --> pdb=" O ALA v 334 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE v 339 " --> pdb=" O PRO v 335 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU v 342 " --> pdb=" O GLU v 338 " (cutoff:3.500A) Processing helix chain 'v' and resid 382 through 396 removed outlier: 3.714A pdb=" N GLU v 388 " --> pdb=" O ASP v 384 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN v 394 " --> pdb=" O PHE v 390 " (cutoff:3.500A) Processing helix chain 'v' and resid 401 through 408 removed outlier: 3.510A pdb=" N LYS v 405 " --> pdb=" O SER v 401 " (cutoff:3.500A) Processing helix chain 'v' and resid 412 through 418 Processing helix chain 'v' and resid 425 through 429 removed outlier: 4.259A pdb=" N GLU v 428 " --> pdb=" O PRO v 425 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU v 429 " --> pdb=" O LEU v 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 425 through 429' Processing helix chain 'v' and resid 455 through 459 Processing helix chain 'v' and resid 490 through 502 Processing helix chain 'w' and resid 36 through 53 Processing helix chain 'w' and resid 60 through 98 removed outlier: 3.886A pdb=" N ARG w 64 " --> pdb=" O VAL w 60 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU w 70 " --> pdb=" O LEU w 66 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP w 71 " --> pdb=" O ARG w 67 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL w 92 " --> pdb=" O LEU w 88 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA w 93 " --> pdb=" O ASP w 89 " (cutoff:3.500A) Processing helix chain 'w' and resid 99 through 101 No H-bonds generated for 'chain 'w' and resid 99 through 101' Processing helix chain 'x' and resid 36 through 96 removed outlier: 4.399A pdb=" N GLU x 40 " --> pdb=" O PRO x 36 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU x 41 " --> pdb=" O GLU x 37 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU x 83 " --> pdb=" O ALA x 79 " (cutoff:3.500A) Processing helix chain 'y' and resid 3114 through 3148 removed outlier: 3.795A pdb=" N SER y3120 " --> pdb=" O SER y3116 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG y3121 " --> pdb=" O ARG y3117 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL y3123 " --> pdb=" O LEU y3119 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS y3129 " --> pdb=" O GLN y3125 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG y3132 " --> pdb=" O ARG y3128 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER y3133 " --> pdb=" O LYS y3129 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR y3134 " --> pdb=" O LEU y3130 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU y3142 " --> pdb=" O ILE y3138 " (cutoff:3.500A) Processing helix chain 'z' and resid 3114 through 3119 Processing helix chain 'z' and resid 3120 through 3148 removed outlier: 4.230A pdb=" N ARG z3132 " --> pdb=" O ARG z3128 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER z3133 " --> pdb=" O LYS z3129 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR z3134 " --> pdb=" O LEU z3130 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR z3148 " --> pdb=" O LEU z3144 " (cutoff:3.500A) Processing helix chain 'Z' and resid 13 through 18 Processing helix chain 'Z' and resid 22 through 29 removed outlier: 4.799A pdb=" N LYS Z 26 " --> pdb=" O PRO Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 66 removed outlier: 4.112A pdb=" N PHE Z 65 " --> pdb=" O VAL Z 61 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY Z 66 " --> pdb=" O GLN Z 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 77 removed outlier: 4.020A pdb=" N ARG Z 77 " --> pdb=" O ALA Z 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 13 through 18 removed outlier: 3.531A pdb=" N ASP a 17 " --> pdb=" O ARG a 13 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 29 removed outlier: 4.636A pdb=" N LYS a 26 " --> pdb=" O PRO a 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 36 through 65 removed outlier: 4.219A pdb=" N PHE a 65 " --> pdb=" O VAL a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 77 removed outlier: 3.789A pdb=" N ARG a 77 " --> pdb=" O ALA a 73 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 18 removed outlier: 3.528A pdb=" N ASP d 17 " --> pdb=" O ARG d 13 " (cutoff:3.500A) Processing helix chain 'd' and resid 22 through 28 removed outlier: 4.074A pdb=" N LYS d 26 " --> pdb=" O PRO d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 36 through 65 removed outlier: 3.776A pdb=" N PHE d 65 " --> pdb=" O VAL d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 76 removed outlier: 3.953A pdb=" N ARG d 72 " --> pdb=" O PRO d 68 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 28 Processing helix chain 'e' and resid 36 through 65 removed outlier: 3.867A pdb=" N PHE e 65 " --> pdb=" O VAL e 61 " (cutoff:3.500A) Processing helix chain 'e' and resid 68 through 75 removed outlier: 3.592A pdb=" N ARG e 72 " --> pdb=" O PRO e 68 " (cutoff:3.500A) Processing helix chain 'f' and resid 98 through 100 No H-bonds generated for 'chain 'f' and resid 98 through 100' Processing helix chain 'f' and resid 127 through 136 removed outlier: 3.560A pdb=" N ILE f 133 " --> pdb=" O LEU f 129 " (cutoff:3.500A) Processing helix chain 'f' and resid 151 through 159 removed outlier: 3.501A pdb=" N TYR f 159 " --> pdb=" O ALA f 155 " (cutoff:3.500A) Processing helix chain 'f' and resid 162 through 169 Processing helix chain 'f' and resid 171 through 179 removed outlier: 3.707A pdb=" N ALA f 177 " --> pdb=" O GLY f 173 " (cutoff:3.500A) Processing helix chain 'f' and resid 180 through 184 Processing helix chain 'f' and resid 285 through 297 removed outlier: 3.943A pdb=" N MET f 290 " --> pdb=" O HIS f 286 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN f 291 " --> pdb=" O CYS f 287 " (cutoff:3.500A) Processing helix chain 'f' and resid 297 through 303 Processing helix chain 'f' and resid 312 through 317 removed outlier: 3.514A pdb=" N GLU f 315 " --> pdb=" O HIS f 312 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR f 317 " --> pdb=" O GLU f 314 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 20 removed outlier: 3.845A pdb=" N ARG h 15 " --> pdb=" O ARG h 11 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY h 18 " --> pdb=" O ARG h 14 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 44 removed outlier: 3.963A pdb=" N LEU h 42 " --> pdb=" O ASP h 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 53 through 61 Processing helix chain 'h' and resid 127 through 136 Processing helix chain 'h' and resid 150 through 159 Processing helix chain 'h' and resid 162 through 167 Processing helix chain 'h' and resid 171 through 179 removed outlier: 3.931A pdb=" N ALA h 177 " --> pdb=" O GLY h 173 " (cutoff:3.500A) Processing helix chain 'h' and resid 180 through 185 removed outlier: 4.142A pdb=" N PHE h 184 " --> pdb=" O ARG h 180 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE h 185 " --> pdb=" O PHE h 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 180 through 185' Processing helix chain 'h' and resid 233 through 237 removed outlier: 3.846A pdb=" N LEU h 237 " --> pdb=" O LEU h 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 233 through 237' Processing helix chain 'h' and resid 285 through 306 removed outlier: 3.530A pdb=" N ASN h 291 " --> pdb=" O CYS h 287 " (cutoff:3.500A) Proline residue: h 299 - end of helix Processing helix chain 'h' and resid 312 through 317 removed outlier: 3.772A pdb=" N LEU h 316 " --> pdb=" O ILE h 313 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR h 317 " --> pdb=" O GLU h 314 " (cutoff:3.500A) Processing helix chain 'k' and resid 14 through 24 removed outlier: 3.605A pdb=" N LYS k 20 " --> pdb=" O ASP k 16 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 44 Processing helix chain 'k' and resid 45 through 48 Processing helix chain 'k' and resid 56 through 67 Processing helix chain 'k' and resid 117 through 121 removed outlier: 3.721A pdb=" N ALA k 121 " --> pdb=" O GLY k 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 117 through 121' Processing helix chain 'k' and resid 140 through 161 removed outlier: 4.209A pdb=" N ARG k 158 " --> pdb=" O ASN k 154 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET k 161 " --> pdb=" O SER k 157 " (cutoff:3.500A) Processing helix chain 'k' and resid 164 through 172 removed outlier: 3.540A pdb=" N ASP k 168 " --> pdb=" O PRO k 164 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU k 170 " --> pdb=" O ASN k 166 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL k 172 " --> pdb=" O ASP k 168 " (cutoff:3.500A) Processing helix chain 'k' and resid 197 through 215 removed outlier: 3.687A pdb=" N LEU k 201 " --> pdb=" O LEU k 197 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU k 215 " --> pdb=" O ILE k 211 " (cutoff:3.500A) Processing helix chain 'k' and resid 218 through 231 removed outlier: 4.110A pdb=" N ARG k 229 " --> pdb=" O ARG k 225 " (cutoff:3.500A) Processing helix chain 'k' and resid 234 through 239 removed outlier: 4.290A pdb=" N LEU k 238 " --> pdb=" O LEU k 235 " (cutoff:3.500A) Processing helix chain 'k' and resid 244 through 251 removed outlier: 3.890A pdb=" N ALA k 248 " --> pdb=" O PRO k 244 " (cutoff:3.500A) Processing helix chain 'k' and resid 256 through 272 removed outlier: 3.560A pdb=" N ASP k 260 " --> pdb=" O SER k 256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER k 262 " --> pdb=" O ALA k 258 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN k 272 " --> pdb=" O MET k 268 " (cutoff:3.500A) Processing helix chain 'k' and resid 273 through 279 removed outlier: 3.525A pdb=" N LEU k 277 " --> pdb=" O SER k 273 " (cutoff:3.500A) Processing helix chain 'm' and resid 16 through 24 Processing helix chain 'm' and resid 56 through 67 removed outlier: 3.989A pdb=" N SER m 65 " --> pdb=" O TYR m 61 " (cutoff:3.500A) Processing helix chain 'm' and resid 139 through 161 Processing helix chain 'm' and resid 165 through 173 Processing helix chain 'm' and resid 197 through 213 removed outlier: 3.570A pdb=" N TYR m 208 " --> pdb=" O ASN m 204 " (cutoff:3.500A) Processing helix chain 'm' and resid 217 through 231 removed outlier: 4.053A pdb=" N MET m 221 " --> pdb=" O PRO m 217 " (cutoff:3.500A) Processing helix chain 'm' and resid 244 through 252 removed outlier: 4.430A pdb=" N ALA m 248 " --> pdb=" O PRO m 244 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG m 249 " --> pdb=" O ASP m 245 " (cutoff:3.500A) Processing helix chain 'm' and resid 256 through 279 removed outlier: 3.956A pdb=" N GLN m 272 " --> pdb=" O MET m 268 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER m 273 " --> pdb=" O THR m 269 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN m 279 " --> pdb=" O ALA m 275 " (cutoff:3.500A) Processing helix chain 'p' and resid 14 through 24 removed outlier: 3.517A pdb=" N ARG p 24 " --> pdb=" O LYS p 20 " (cutoff:3.500A) Processing helix chain 'p' and resid 56 through 67 removed outlier: 3.762A pdb=" N MET p 60 " --> pdb=" O ASP p 56 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP p 66 " --> pdb=" O ASN p 62 " (cutoff:3.500A) Processing helix chain 'p' and resid 117 through 121 Processing helix chain 'p' and resid 140 through 163 Processing helix chain 'p' and resid 168 through 177 removed outlier: 3.698A pdb=" N HIS p 175 " --> pdb=" O ASP p 171 " (cutoff:3.500A) Processing helix chain 'p' and resid 203 through 228 removed outlier: 3.673A pdb=" N LEU p 207 " --> pdb=" O ASP p 203 " (cutoff:3.500A) Proline residue: p 217 - end of helix removed outlier: 3.649A pdb=" N ARG p 222 " --> pdb=" O ARG p 218 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE p 228 " --> pdb=" O VAL p 224 " (cutoff:3.500A) Processing helix chain 'p' and resid 234 through 241 removed outlier: 3.592A pdb=" N LEU p 238 " --> pdb=" O ASP p 234 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU p 241 " --> pdb=" O ASN p 237 " (cutoff:3.500A) Processing helix chain 'p' and resid 244 through 249 Processing helix chain 'p' and resid 256 through 279 removed outlier: 3.894A pdb=" N LEU p 261 " --> pdb=" O VAL p 257 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER p 276 " --> pdb=" O GLN p 272 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU p 277 " --> pdb=" O SER p 273 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE p 278 " --> pdb=" O LEU p 274 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN p 279 " --> pdb=" O ALA p 275 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 23 removed outlier: 3.666A pdb=" N ALA r 19 " --> pdb=" O THR r 15 " (cutoff:3.500A) Processing helix chain 'r' and resid 39 through 43 removed outlier: 3.555A pdb=" N GLY r 42 " --> pdb=" O ASN r 39 " (cutoff:3.500A) Processing helix chain 'r' and resid 57 through 67 Processing helix chain 'r' and resid 117 through 121 Processing helix chain 'r' and resid 140 through 163 removed outlier: 3.731A pdb=" N LEU r 147 " --> pdb=" O ALA r 143 " (cutoff:3.500A) Processing helix chain 'r' and resid 164 through 167 removed outlier: 3.937A pdb=" N ALA r 167 " --> pdb=" O PRO r 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 164 through 167' Processing helix chain 'r' and resid 168 through 177 Processing helix chain 'r' and resid 204 through 228 Proline residue: r 217 - end of helix removed outlier: 3.754A pdb=" N MET r 221 " --> pdb=" O PRO r 217 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG r 222 " --> pdb=" O ARG r 218 " (cutoff:3.500A) Processing helix chain 'r' and resid 233 through 240 removed outlier: 4.184A pdb=" N ASN r 237 " --> pdb=" O HIS r 233 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU r 238 " --> pdb=" O ASP r 234 " (cutoff:3.500A) Processing helix chain 'r' and resid 241 through 243 No H-bonds generated for 'chain 'r' and resid 241 through 243' Processing helix chain 'r' and resid 244 through 249 removed outlier: 3.657A pdb=" N ALA r 248 " --> pdb=" O PRO r 244 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG r 249 " --> pdb=" O ASP r 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 244 through 249' Processing helix chain 'r' and resid 256 through 278 Processing sheet with id=AA1, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AA2, first strand: chain 'J' and resid 57 through 60 removed outlier: 6.699A pdb=" N GLY J 57 " --> pdb=" O GLN K 94 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ARG K 96 " --> pdb=" O GLY J 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TYR J 59 " --> pdb=" O ARG K 96 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N SER K 98 " --> pdb=" O TYR J 59 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG K 114 " --> pdb=" O VAL K 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 77 through 78 removed outlier: 6.843A pdb=" N VAL J 78 " --> pdb=" O MET J1067 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE J1069 " --> pdb=" O VAL J 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 77 through 78 removed outlier: 6.843A pdb=" N VAL J 78 " --> pdb=" O MET J1067 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE J1069 " --> pdb=" O VAL J 78 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA J1083 " --> pdb=" O ALA J1079 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA J1079 " --> pdb=" O ALA J1083 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR J1085 " --> pdb=" O ARG J1077 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG J1077 " --> pdb=" O THR J1085 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 94 through 99 removed outlier: 4.520A pdb=" N ARG J 114 " --> pdb=" O VAL J 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 371 through 374 removed outlier: 4.757A pdb=" N VAL J 276 " --> pdb=" O ALA J 378 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA J 380 " --> pdb=" O VAL J 276 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY J 278 " --> pdb=" O ALA J 380 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLU J 382 " --> pdb=" O GLY J 278 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE J 280 " --> pdb=" O GLU J 382 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 1183 through 1187 removed outlier: 7.366A pdb=" N GLU J1051 " --> pdb=" O ALA J1112 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA J1112 " --> pdb=" O GLU J1051 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU J1053 " --> pdb=" O VAL J1110 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL J1110 " --> pdb=" O LEU J1053 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU J1055 " --> pdb=" O ALA J1108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 1103 through 1112 removed outlier: 6.663A pdb=" N GLU J1055 " --> pdb=" O ALA J1108 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL J1110 " --> pdb=" O LEU J1053 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU J1053 " --> pdb=" O VAL J1110 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA J1112 " --> pdb=" O GLU J1051 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLU J1051 " --> pdb=" O ALA J1112 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N PHE J1332 " --> pdb=" O GLN J 402 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER J 404 " --> pdb=" O PHE J1332 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 1332 through 1333 removed outlier: 9.540A pdb=" N PHE J1332 " --> pdb=" O GLN J 402 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER J 404 " --> pdb=" O PHE J1332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 371 through 374 removed outlier: 4.757A pdb=" N VAL J 276 " --> pdb=" O ALA J 378 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA J 380 " --> pdb=" O VAL J 276 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY J 278 " --> pdb=" O ALA J 380 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLU J 382 " --> pdb=" O GLY J 278 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE J 280 " --> pdb=" O GLU J 382 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 438 through 441 Processing sheet with id=AB3, first strand: chain 'J' and resid 546 through 549 Processing sheet with id=AB4, first strand: chain 'J' and resid 727 through 728 Processing sheet with id=AB5, first strand: chain 'J' and resid 763 through 765 Processing sheet with id=AB6, first strand: chain 'J' and resid 928 through 930 Processing sheet with id=AB7, first strand: chain 'J' and resid 1336 through 1337 removed outlier: 3.743A pdb=" N SER J1336 " --> pdb=" O ILE J1363 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 1373 through 1375 Processing sheet with id=AB9, first strand: chain 'K' and resid 123 through 134 removed outlier: 3.770A pdb=" N LEU K 133 " --> pdb=" O VAL K1084 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL K1084 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR K 80 " --> pdb=" O MET K1067 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE K1069 " --> pdb=" O THR K 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 123 through 134 removed outlier: 3.770A pdb=" N LEU K 133 " --> pdb=" O VAL K1084 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL K1084 " --> pdb=" O LEU K 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 268 through 269 Processing sheet with id=AC3, first strand: chain 'K' and resid 371 through 374 removed outlier: 6.839A pdb=" N ALA K 378 " --> pdb=" O VAL K 276 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY K 278 " --> pdb=" O ALA K 378 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 1103 through 1113 removed outlier: 6.873A pdb=" N GLU K1055 " --> pdb=" O ALA K1108 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL K1110 " --> pdb=" O LEU K1053 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU K1053 " --> pdb=" O VAL K1110 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA K1112 " --> pdb=" O GLU K1051 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLU K1051 " --> pdb=" O ALA K1112 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 438 through 441 Processing sheet with id=AC6, first strand: chain 'K' and resid 546 through 550 Processing sheet with id=AC7, first strand: chain 'K' and resid 727 through 728 Processing sheet with id=AC8, first strand: chain 'K' and resid 763 through 765 removed outlier: 3.521A pdb=" N LEU K 796 " --> pdb=" O GLU K 764 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 928 through 930 Processing sheet with id=AD1, first strand: chain 'K' and resid 1336 through 1337 Processing sheet with id=AD2, first strand: chain 'O' and resid 114 through 121 removed outlier: 4.428A pdb=" N ARG O 114 " --> pdb=" O VAL O 99 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N PHE N 52 " --> pdb=" O THR O 89 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY O 91 " --> pdb=" O PHE N 52 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL N 54 " --> pdb=" O GLY O 91 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE O 93 " --> pdb=" O VAL N 54 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU N 56 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 10.180A pdb=" N PHE O 95 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N VAL N 58 " --> pdb=" O PHE O 95 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N ILE O 97 " --> pdb=" O VAL N 58 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N THR N 60 " --> pdb=" O ILE O 97 " (cutoff:3.500A) removed outlier: 10.573A pdb=" N VAL O 99 " --> pdb=" O THR N 60 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLU N 53 " --> pdb=" O VAL O 327 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 123 through 134 removed outlier: 9.653A pdb=" N ALA N 309 " --> pdb=" O CYS N 77 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASN N 79 " --> pdb=" O ALA N 309 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N PHE N 311 " --> pdb=" O ASN N 79 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU N 81 " --> pdb=" O PHE N 311 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 123 through 134 Processing sheet with id=AD5, first strand: chain 'N' and resid 92 through 99 removed outlier: 3.861A pdb=" N ARG N 114 " --> pdb=" O VAL N 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 268 through 269 Processing sheet with id=AD7, first strand: chain 'N' and resid 371 through 374 removed outlier: 7.057A pdb=" N ALA N 380 " --> pdb=" O GLY N 277 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL N 279 " --> pdb=" O ALA N 380 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU N 382 " --> pdb=" O VAL N 279 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE N 281 " --> pdb=" O GLU N 382 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 1103 through 1113 removed outlier: 7.144A pdb=" N SER N1103 " --> pdb=" O SER N1061 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N SER N1061 " --> pdb=" O SER N1103 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N MET N1105 " --> pdb=" O PHE N1059 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE N1059 " --> pdb=" O MET N1105 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE N1057 " --> pdb=" O PRO N1107 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG N1109 " --> pdb=" O GLU N1055 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU N1055 " --> pdb=" O ARG N1109 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU N1053 " --> pdb=" O ALA N1111 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE N1113 " --> pdb=" O GLU N1051 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLU N1051 " --> pdb=" O ILE N1113 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N PHE N1332 " --> pdb=" O GLN N 402 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER N 404 " --> pdb=" O PHE N1332 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 425 through 426 removed outlier: 3.618A pdb=" N LYS N 425 " --> pdb=" O THR O 419 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 438 through 441 Processing sheet with id=AE2, first strand: chain 'N' and resid 546 through 550 Processing sheet with id=AE3, first strand: chain 'N' and resid 727 through 728 Processing sheet with id=AE4, first strand: chain 'N' and resid 763 through 765 Processing sheet with id=AE5, first strand: chain 'N' and resid 928 through 930 removed outlier: 3.657A pdb=" N LEU N 928 " --> pdb=" O LEU N 828 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 123 through 134 removed outlier: 9.481A pdb=" N ALA O 309 " --> pdb=" O CYS O 77 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN O 79 " --> pdb=" O ALA O 309 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE O 311 " --> pdb=" O ASN O 79 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU O 81 " --> pdb=" O PHE O 311 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 123 through 134 removed outlier: 3.730A pdb=" N GLU O1078 " --> pdb=" O THR O1085 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU O1087 " --> pdb=" O ARG O1076 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ARG O1076 " --> pdb=" O GLU O1087 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N HIS O1089 " --> pdb=" O VAL O1074 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL O1074 " --> pdb=" O HIS O1089 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 268 through 269 Processing sheet with id=AE9, first strand: chain 'O' and resid 370 through 374 removed outlier: 4.051A pdb=" N ALA O 370 " --> pdb=" O VAL O 381 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY O 278 " --> pdb=" O ALA O 380 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLU O 382 " --> pdb=" O GLY O 278 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N PHE O 280 " --> pdb=" O GLU O 382 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 1183 through 1187 removed outlier: 7.834A pdb=" N GLU O1051 " --> pdb=" O ALA O1112 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA O1112 " --> pdb=" O GLU O1051 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU O1053 " --> pdb=" O VAL O1110 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL O1110 " --> pdb=" O LEU O1053 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU O1055 " --> pdb=" O ALA O1108 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 1103 through 1113 removed outlier: 7.092A pdb=" N GLU O1055 " --> pdb=" O ALA O1108 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL O1110 " --> pdb=" O LEU O1053 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU O1053 " --> pdb=" O VAL O1110 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA O1112 " --> pdb=" O GLU O1051 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLU O1051 " --> pdb=" O ALA O1112 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N PHE O1332 " --> pdb=" O GLN O 402 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER O 404 " --> pdb=" O PHE O1332 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 1332 through 1333 removed outlier: 9.267A pdb=" N PHE O1332 " --> pdb=" O GLN O 402 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER O 404 " --> pdb=" O PHE O1332 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 370 through 374 removed outlier: 4.051A pdb=" N ALA O 370 " --> pdb=" O VAL O 381 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY O 278 " --> pdb=" O ALA O 380 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLU O 382 " --> pdb=" O GLY O 278 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N PHE O 280 " --> pdb=" O GLU O 382 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 438 through 441 Processing sheet with id=AF6, first strand: chain 'O' and resid 546 through 550 Processing sheet with id=AF7, first strand: chain 'O' and resid 727 through 728 removed outlier: 3.519A pdb=" N ALA O 728 " --> pdb=" O LEU O 924 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 763 through 765 Processing sheet with id=AF9, first strand: chain 'O' and resid 928 through 930 Processing sheet with id=AG1, first strand: chain 'O' and resid 1336 through 1337 Processing sheet with id=AG2, first strand: chain 'O' and resid 1373 through 1375 Processing sheet with id=AG3, first strand: chain 'v' and resid 21 through 22 Processing sheet with id=AG4, first strand: chain 'v' and resid 58 through 59 Processing sheet with id=AG5, first strand: chain 'v' and resid 63 through 65 Processing sheet with id=AG6, first strand: chain 'v' and resid 433 through 438 removed outlier: 5.577A pdb=" N TRP v 434 " --> pdb=" O SER v 423 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER v 423 " --> pdb=" O TRP v 434 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU v 419 " --> pdb=" O ILE v 438 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N HIS v 424 " --> pdb=" O VAL v 463 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL v 463 " --> pdb=" O HIS v 424 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'f' and resid 89 through 96 removed outlier: 7.002A pdb=" N VAL f 89 " --> pdb=" O VAL f 207 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY f 91 " --> pdb=" O THR f 205 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY f 209 " --> pdb=" O SER f 355 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER f 355 " --> pdb=" O GLY f 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR f 354 " --> pdb=" O THR f 326 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU f 324 " --> pdb=" O ASN f 356 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY f 319 " --> pdb=" O TYR f 270 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR f 270 " --> pdb=" O GLY f 319 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL f 321 " --> pdb=" O LEU f 268 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU f 268 " --> pdb=" O VAL f 321 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N CYS f 323 " --> pdb=" O VAL f 266 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL f 266 " --> pdb=" O CYS f 323 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY f 325 " --> pdb=" O LEU f 264 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN f 281 " --> pdb=" O VAL f 231 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'f' and resid 125 through 126 removed outlier: 3.614A pdb=" N GLY f 189 " --> pdb=" O LEU f 110 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLN f 112 " --> pdb=" O PRO f 187 " (cutoff:3.500A) removed outlier: 9.724A pdb=" N GLY f 189 " --> pdb=" O HIS f 208 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N HIS f 208 " --> pdb=" O GLY f 189 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU f 191 " --> pdb=" O VAL f 206 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL f 206 " --> pdb=" O LEU f 191 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY f 209 " --> pdb=" O SER f 355 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER f 355 " --> pdb=" O GLY f 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR f 354 " --> pdb=" O THR f 326 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU f 324 " --> pdb=" O ASN f 356 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY f 319 " --> pdb=" O ILE f 363 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'f' and resid 223 through 226 removed outlier: 4.375A pdb=" N LEU f 345 " --> pdb=" O PHE f 338 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU f 349 " --> pdb=" O ARG f 334 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'h' and resid 89 through 96 removed outlier: 5.375A pdb=" N VAL h 206 " --> pdb=" O LEU h 191 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU h 191 " --> pdb=" O VAL h 206 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'h' and resid 110 through 112 removed outlier: 6.390A pdb=" N LEU h 110 " --> pdb=" O VAL h 188 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'h' and resid 209 through 210 Processing sheet with id=AH4, first strand: chain 'h' and resid 223 through 226 Processing sheet with id=AH5, first strand: chain 'h' and resid 230 through 232 removed outlier: 3.979A pdb=" N GLN h 281 " --> pdb=" O VAL h 231 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY h 325 " --> pdb=" O LEU h 264 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL h 266 " --> pdb=" O CYS h 323 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N CYS h 323 " --> pdb=" O VAL h 266 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU h 268 " --> pdb=" O VAL h 321 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL h 321 " --> pdb=" O LEU h 268 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N TYR h 270 " --> pdb=" O GLY h 319 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY h 319 " --> pdb=" O TYR h 270 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'k' and resid 28 through 30 removed outlier: 6.598A pdb=" N ILE k 81 " --> pdb=" O ASP k 73 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL k 75 " --> pdb=" O SER k 79 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER k 79 " --> pdb=" O VAL k 75 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL k 6 " --> pdb=" O GLN k 38 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'k' and resid 91 through 94 removed outlier: 4.254A pdb=" N TYR k 91 " --> pdb=" O CYS k 298 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS k 298 " --> pdb=" O TYR k 91 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR k 297 " --> pdb=" O ALA k 287 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'k' and resid 122 through 125 Processing sheet with id=AH9, first strand: chain 'k' and resid 178 through 181 Processing sheet with id=AI1, first strand: chain 'm' and resid 28 through 31 removed outlier: 3.665A pdb=" N THR m 68 " --> pdb=" O LEU m 31 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE m 81 " --> pdb=" O ASP m 73 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL m 75 " --> pdb=" O SER m 79 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N SER m 79 " --> pdb=" O VAL m 75 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'm' and resid 91 through 94 removed outlier: 3.919A pdb=" N ALA m 288 " --> pdb=" O THR m 297 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP m 299 " --> pdb=" O THR m 286 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N THR m 286 " --> pdb=" O TRP m 299 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'm' and resid 122 through 125 Processing sheet with id=AI4, first strand: chain 'm' and resid 178 through 181 Processing sheet with id=AI5, first strand: chain 'p' and resid 4 through 8 removed outlier: 6.863A pdb=" N SER p 79 " --> pdb=" O VAL p 75 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL p 75 " --> pdb=" O SER p 79 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE p 81 " --> pdb=" O ASP p 73 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR p 68 " --> pdb=" O LEU p 31 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'p' and resid 91 through 93 removed outlier: 6.413A pdb=" N THR p 295 " --> pdb=" O TYR p 289 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR p 289 " --> pdb=" O THR p 295 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR p 297 " --> pdb=" O ALA p 287 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'p' and resid 122 through 125 Processing sheet with id=AI8, first strand: chain 'p' and resid 178 through 181 Processing sheet with id=AI9, first strand: chain 'r' and resid 28 through 31 removed outlier: 3.864A pdb=" N THR r 68 " --> pdb=" O LEU r 31 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE r 81 " --> pdb=" O ASP r 73 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL r 6 " --> pdb=" O GLN r 38 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'r' and resid 91 through 94 removed outlier: 3.740A pdb=" N ALA r 288 " --> pdb=" O THR r 297 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'r' and resid 122 through 125 Processing sheet with id=AJ3, first strand: chain 'r' and resid 178 through 181 2688 hydrogen bonds defined for protein. 7596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 26.23 Time building geometry restraints manager: 19.94 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: 18795 1.34 - 1.46: 12205 1.46 - 1.58: 32365 1.58 - 1.70: 2 1.70 - 1.82: 599 Bond restraints: 63966 Sorted by residual: bond pdb=" CA TYR N 841 " pdb=" C TYR N 841 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.80e-02 3.09e+03 2.05e+01 bond pdb=" C PHE d 18 " pdb=" N PRO d 19 " ideal model delta sigma weight residual 1.329 1.372 -0.043 1.22e-02 6.72e+03 1.24e+01 bond pdb=" CA ARG K1150 " pdb=" CB ARG K1150 " ideal model delta sigma weight residual 1.527 1.613 -0.086 2.48e-02 1.63e+03 1.21e+01 bond pdb=" N PRO K 726 " pdb=" CA PRO K 726 " ideal model delta sigma weight residual 1.471 1.431 0.040 1.29e-02 6.01e+03 9.81e+00 bond pdb=" C ALA m 163 " pdb=" N PRO m 164 " ideal model delta sigma weight residual 1.332 1.371 -0.039 1.26e-02 6.30e+03 9.64e+00 ... (remaining 63961 not shown) Histogram of bond angle deviations from ideal: 90.86 - 100.38: 103 100.38 - 109.89: 11595 109.89 - 119.41: 41721 119.41 - 128.93: 33080 128.93 - 138.45: 433 Bond angle restraints: 86932 Sorted by residual: angle pdb=" C SER f 161 " pdb=" N PRO f 162 " pdb=" CA PRO f 162 " ideal model delta sigma weight residual 119.84 90.86 28.98 1.25e+00 6.40e-01 5.38e+02 angle pdb=" C PHE a 18 " pdb=" N PRO a 19 " pdb=" CA PRO a 19 " ideal model delta sigma weight residual 119.84 99.25 20.59 1.25e+00 6.40e-01 2.71e+02 angle pdb=" N ARG N 483 " pdb=" CA ARG N 483 " pdb=" C ARG N 483 " ideal model delta sigma weight residual 111.07 120.82 -9.75 1.07e+00 8.73e-01 8.31e+01 angle pdb=" C VAL K1264 " pdb=" N PRO K1265 " pdb=" CA PRO K1265 " ideal model delta sigma weight residual 119.84 130.68 -10.84 1.25e+00 6.40e-01 7.52e+01 angle pdb=" C ALA K 911 " pdb=" N PRO K 912 " pdb=" CA PRO K 912 " ideal model delta sigma weight residual 119.84 129.78 -9.94 1.25e+00 6.40e-01 6.32e+01 ... (remaining 86927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 36749 17.34 - 34.69: 1428 34.69 - 52.03: 230 52.03 - 69.38: 29 69.38 - 86.72: 28 Dihedral angle restraints: 38464 sinusoidal: 15224 harmonic: 23240 Sorted by residual: dihedral pdb=" CA TYR K1161 " pdb=" C TYR K1161 " pdb=" N LEU K1162 " pdb=" CA LEU K1162 " ideal model delta harmonic sigma weight residual 180.00 -150.18 -29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA SER J1245 " pdb=" C SER J1245 " pdb=" N GLN J1246 " pdb=" CA GLN J1246 " ideal model delta harmonic sigma weight residual -180.00 -150.86 -29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA GLN k 162 " pdb=" C GLN k 162 " pdb=" N ALA k 163 " pdb=" CA ALA k 163 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 38461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 8736 0.093 - 0.187: 987 0.187 - 0.280: 59 0.280 - 0.374: 11 0.374 - 0.467: 2 Chirality restraints: 9795 Sorted by residual: chirality pdb=" CA ARG N 484 " pdb=" N ARG N 484 " pdb=" C ARG N 484 " pdb=" CB ARG N 484 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CB THR N 922 " pdb=" CA THR N 922 " pdb=" OG1 THR N 922 " pdb=" CG2 THR N 922 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA ASN N 672 " pdb=" N ASN N 672 " pdb=" C ASN N 672 " pdb=" CB ASN N 672 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 9792 not shown) Planarity restraints: 11336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE a 18 " 0.107 5.00e-02 4.00e+02 1.63e-01 4.26e+01 pdb=" N PRO a 19 " -0.281 5.00e-02 4.00e+02 pdb=" CA PRO a 19 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO a 19 " 0.104 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER f 161 " 0.099 5.00e-02 4.00e+02 1.45e-01 3.37e+01 pdb=" N PRO f 162 " -0.249 5.00e-02 4.00e+02 pdb=" CA PRO f 162 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO f 162 " 0.100 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE f 216 " -0.055 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO f 217 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO f 217 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO f 217 " -0.048 5.00e-02 4.00e+02 ... (remaining 11333 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 34 2.27 - 2.93: 24927 2.93 - 3.59: 88616 3.59 - 4.24: 135793 4.24 - 4.90: 228245 Nonbonded interactions: 477615 Sorted by model distance: nonbonded pdb=" NH2 ARG O 483 " pdb=" OD2 ASP O 553 " model vdw 1.618 2.520 nonbonded pdb=" O VAL r 77 " pdb=" OD1 ASP r 78 " model vdw 1.729 3.040 nonbonded pdb=" O GLY K 803 " pdb=" CD2 HIS K 804 " model vdw 1.862 3.260 nonbonded pdb=" O PRO O1010 " pdb=" O SER O1011 " model vdw 1.922 3.040 nonbonded pdb=" OD1 ASP K1252 " pdb=" ND2 ASN K1256 " model vdw 1.923 2.520 ... (remaining 477610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'J' and (resid 62 through 1148 or resid 1170 through 1381)) selection = (chain 'K' and (resid 62 through 307 or resid 364 through 1148 or resid 1170 thr \ ough 1381)) selection = (chain 'N' and (resid 62 through 307 or resid 364 through 1148 or resid 1170 thr \ ough 1381)) selection = (chain 'O' and (resid 62 through 307 or resid 364 through 1381)) } ncs_group { reference = chain 'Z' selection = chain 'a' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'k' selection = chain 'm' selection = chain 'p' selection = chain 'r' } ncs_group { reference = chain 'w' selection = chain 'x' } ncs_group { reference = chain 'y' selection = chain 'z' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.040 Extract box with map and model: 11.010 Check model and map are aligned: 0.670 Set scattering table: 0.400 Process input model: 123.710 Find NCS groups from input model: 3.730 Set up NCS constraints: 0.360 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:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5352 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 : 0.006 0.093 63966 Z= 0.397 Angle : 1.038 28.981 86932 Z= 0.582 Chirality : 0.059 0.467 9795 Planarity : 0.008 0.163 11336 Dihedral : 10.302 86.722 23446 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.50 % Favored : 95.06 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.37 (0.08), residues: 7881 helix: -1.68 (0.08), residues: 2878 sheet: -0.09 (0.15), residues: 1117 loop : -1.90 (0.09), residues: 3886 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2693 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 2647 time to evaluate : 5.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 13 residues processed: 2675 average time/residue: 0.6167 time to fit residues: 2722.8678 Evaluate side-chains 1460 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1447 time to evaluate : 5.383 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4379 time to fit residues: 18.4591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 660 optimal weight: 20.0000 chunk 592 optimal weight: 10.0000 chunk 328 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 399 optimal weight: 9.9990 chunk 316 optimal weight: 9.9990 chunk 612 optimal weight: 40.0000 chunk 237 optimal weight: 7.9990 chunk 372 optimal weight: 10.0000 chunk 456 optimal weight: 10.0000 chunk 710 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 126 HIS J 289 GLN ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 HIS J 531 HIS J 596 HIS J 636 ASN J 669 HIS J 750 ASN J 804 HIS J 824 HIS ** J 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 859 ASN J 926 ASN J1022 HIS ** J1122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1178 GLN J1261 GLN J1289 ASN J1360 HIS ** K 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 362 GLN K 377 HIS K 402 GLN ** K 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 570 ASN ** K 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 822 ASN ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1022 HIS K1357 HIS N 79 ASN N 123 HIS N 126 HIS ** N 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 362 GLN N 531 HIS ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 570 ASN N 587 GLN ** N 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 669 HIS N 672 ASN N 761 GLN ** N 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 913 ASN N 926 ASN ** N 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 964 HIS ** N 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 997 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N1033 GLN ** N1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1227 HIS ** N1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1246 GLN N1283 ASN ** N1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1323 GLN N1353 HIS O 79 ASN O 178 ASN O 222 HIS ** O 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 333 HIS O 385 GLN O 415 ASN O 445 ASN ** O 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 607 GLN O 658 ASN ** O 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 997 HIS ** O1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1090 HIS O1135 ASN ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1216 ASN ** O1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 7 ASN v 73 HIS v 93 ASN ** v 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 11 GLN d 32 GLN ** e 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 115 GLN f 156 ASN ** f 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 208 HIS ** k 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 128 ASN ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 230 HIS ** m 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 89 GLN ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 162 GLN p 230 HIS r 62 ASN r 154 ASN r 233 HIS Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.135 63966 Z= 0.423 Angle : 0.912 14.229 86932 Z= 0.475 Chirality : 0.051 0.313 9795 Planarity : 0.008 0.104 11336 Dihedral : 6.297 64.207 8722 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.39 % Favored : 94.38 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.09), residues: 7881 helix: -0.76 (0.09), residues: 2957 sheet: -0.32 (0.15), residues: 1098 loop : -1.72 (0.09), residues: 3826 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1913 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1881 time to evaluate : 5.418 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 outliers start: 32 outliers final: 9 residues processed: 1901 average time/residue: 0.5920 time to fit residues: 1898.4864 Evaluate side-chains 1333 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1324 time to evaluate : 5.531 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4510 time to fit residues: 15.2029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 394 optimal weight: 20.0000 chunk 220 optimal weight: 8.9990 chunk 591 optimal weight: 7.9990 chunk 483 optimal weight: 0.0870 chunk 195 optimal weight: 0.4980 chunk 711 optimal weight: 0.7980 chunk 768 optimal weight: 4.9990 chunk 633 optimal weight: 7.9990 chunk 705 optimal weight: 20.0000 chunk 242 optimal weight: 5.9990 chunk 570 optimal weight: 20.0000 overall best weight: 2.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 187 HIS ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 587 GLN ** J 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1022 HIS J1176 HIS J1216 ASN J1289 ASN K 195 GLN K 289 GLN ** K 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 824 HIS ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 178 ASN N 222 HIS N 300 ASN ** N 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 496 HIS ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 669 HIS N 804 HIS N 913 ASN N 997 HIS N1022 HIS N1033 GLN ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 ASN O 222 HIS O 226 HIS ** O 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 445 ASN ** O 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 472 ASN O 531 HIS ** O 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 587 GLN O 607 GLN O 722 ASN O 824 HIS O 909 GLN ** O 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1022 HIS ** O1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1217 GLN O1284 ASN ** O1329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 GLN v 73 HIS v 424 HIS ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 288 GLN h 13 GLN k 62 ASN k 120 HIS ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 233 HIS m 291 GLN ** p 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 154 ASN p 162 GLN p 173 HIS r 154 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 63966 Z= 0.203 Angle : 0.677 13.623 86932 Z= 0.346 Chirality : 0.044 0.222 9795 Planarity : 0.006 0.111 11336 Dihedral : 5.614 59.453 8722 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.86 % Favored : 94.98 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.25 (0.09), residues: 7881 helix: -0.16 (0.09), residues: 2982 sheet: -0.06 (0.15), residues: 1074 loop : -1.59 (0.09), residues: 3825 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1769 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1763 time to evaluate : 5.432 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 outliers start: 6 outliers final: 1 residues processed: 1767 average time/residue: 0.5983 time to fit residues: 1778.7484 Evaluate side-chains 1273 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1272 time to evaluate : 5.441 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4290 time to fit residues: 8.4539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 702 optimal weight: 40.0000 chunk 534 optimal weight: 0.0870 chunk 369 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 339 optimal weight: 9.9990 chunk 477 optimal weight: 20.0000 chunk 713 optimal weight: 0.0670 chunk 755 optimal weight: 8.9990 chunk 373 optimal weight: 5.9990 chunk 676 optimal weight: 10.0000 chunk 203 optimal weight: 0.7980 overall best weight: 2.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 389 ASN J 587 GLN ** J 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 859 ASN K 195 GLN K 317 ASN ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 822 ASN ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1179 GLN N 79 ASN N 178 ASN N 222 HIS ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 669 HIS ** N 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 913 ASN ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 178 ASN O 222 HIS ** O 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 607 GLN O 722 ASN ** O 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1284 ASN ** O1329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 GLN d 28 GLN e 62 GLN ** f 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 39 ASN m 148 GLN p 154 ASN ** p 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 148 GLN r 154 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.6506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 63966 Z= 0.206 Angle : 0.668 15.051 86932 Z= 0.336 Chirality : 0.044 0.267 9795 Planarity : 0.005 0.088 11336 Dihedral : 5.333 55.291 8722 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.24 % Favored : 94.65 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.02 (0.09), residues: 7881 helix: 0.13 (0.09), residues: 2972 sheet: -0.07 (0.15), residues: 1091 loop : -1.50 (0.09), residues: 3818 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1675 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1667 time to evaluate : 6.429 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 outliers start: 8 outliers final: 2 residues processed: 1672 average time/residue: 0.6211 time to fit residues: 1777.1066 Evaluate side-chains 1262 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1260 time to evaluate : 5.485 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4564 time to fit residues: 9.4010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 629 optimal weight: 5.9990 chunk 429 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 562 optimal weight: 9.9990 chunk 311 optimal weight: 20.0000 chunk 645 optimal weight: 0.8980 chunk 522 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 385 optimal weight: 20.0000 chunk 678 optimal weight: 30.0000 chunk 190 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 9 ASN J 285 ASN J 587 GLN J 988 GLN J1022 HIS J1216 ASN K 195 GLN ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 822 ASN ** K 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 997 HIS ** K1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1179 GLN ** N 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 385 GLN ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 596 HIS N 695 GLN N 722 ASN N 913 ASN N1089 HIS ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N1178 GLN ** N1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 333 HIS O 445 ASN ** O 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 587 GLN O 607 GLN O 761 GLN ** O 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1090 HIS ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1178 GLN O1284 ASN ** O1329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1377 ASN v 45 GLN ** f 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 312 HIS k 23 GLN ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 240 GLN r 154 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.7090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 63966 Z= 0.212 Angle : 0.662 12.730 86932 Z= 0.335 Chirality : 0.044 0.224 9795 Planarity : 0.005 0.101 11336 Dihedral : 5.210 50.672 8722 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.63 % Favored : 94.25 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.93 (0.09), residues: 7881 helix: 0.21 (0.09), residues: 2963 sheet: -0.07 (0.15), residues: 1122 loop : -1.45 (0.10), residues: 3796 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1660 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1656 time to evaluate : 5.580 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 outliers start: 4 outliers final: 0 residues processed: 1658 average time/residue: 0.6064 time to fit residues: 1709.1752 Evaluate side-chains 1260 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1260 time to evaluate : 5.537 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 254 optimal weight: 20.0000 chunk 680 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 443 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 756 optimal weight: 0.9980 chunk 628 optimal weight: 20.0000 chunk 350 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 397 optimal weight: 30.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 433 GLN ** J 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 587 GLN ** J 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1022 HIS K 195 GLN ** K 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 722 ASN ** K 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 750 ASN ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 822 ASN ** K1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1283 ASN N 104 HIS N 491 HIS ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 636 ASN N 695 GLN N 722 ASN N 904 ASN N 913 ASN N1033 GLN N1137 GLN ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1176 HIS ** N1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 ASN ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 289 GLN O 333 HIS O 472 ASN ** O 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 596 HIS O 607 GLN ** O 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 913 ASN ** O 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1090 HIS O1122 GLN ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1329 GLN ** v 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 288 GLN ** h 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 154 ASN r 291 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.8051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.138 63966 Z= 0.260 Angle : 0.718 15.026 86932 Z= 0.364 Chirality : 0.045 0.242 9795 Planarity : 0.006 0.090 11336 Dihedral : 5.400 45.790 8722 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.14 % Favored : 93.74 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.00 (0.09), residues: 7881 helix: 0.14 (0.09), residues: 2972 sheet: -0.17 (0.15), residues: 1120 loop : -1.46 (0.10), residues: 3789 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1685 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1683 time to evaluate : 5.534 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 outliers start: 2 outliers final: 0 residues processed: 1685 average time/residue: 0.6152 time to fit residues: 1764.6126 Evaluate side-chains 1258 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1258 time to evaluate : 5.509 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.9108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 729 optimal weight: 30.0000 chunk 85 optimal weight: 7.9990 chunk 431 optimal weight: 8.9990 chunk 552 optimal weight: 6.9990 chunk 428 optimal weight: 6.9990 chunk 636 optimal weight: 3.9990 chunk 422 optimal weight: 6.9990 chunk 753 optimal weight: 20.0000 chunk 471 optimal weight: 3.9990 chunk 459 optimal weight: 20.0000 chunk 347 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 289 GLN J 415 ASN J 433 GLN J 564 HIS J1022 HIS K 429 ASN K 722 ASN ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 822 ASN K 824 HIS K 909 GLN ** K1246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 695 GLN N 722 ASN N 834 HIS N 913 ASN N1089 HIS ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 ASN ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 333 HIS O 587 GLN ** O 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1090 HIS ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1284 ASN O1301 HIS ** O1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 464 HIS ** x 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 44 GLN ** f 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.8671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 63966 Z= 0.259 Angle : 0.722 14.586 86932 Z= 0.362 Chirality : 0.045 0.280 9795 Planarity : 0.006 0.101 11336 Dihedral : 5.362 43.250 8722 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.15 % Favored : 93.74 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.01 (0.09), residues: 7881 helix: 0.17 (0.10), residues: 2955 sheet: -0.24 (0.15), residues: 1087 loop : -1.46 (0.10), residues: 3839 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1673 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1670 time to evaluate : 5.518 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: 3 outliers final: 0 residues processed: 1671 average time/residue: 0.6119 time to fit residues: 1747.6830 Evaluate side-chains 1260 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1260 time to evaluate : 5.563 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 466 optimal weight: 7.9990 chunk 300 optimal weight: 7.9990 chunk 450 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 479 optimal weight: 5.9990 chunk 513 optimal weight: 30.0000 chunk 372 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 chunk 592 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 433 GLN ** J 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 795 HIS J1022 HIS J1178 GLN K 429 ASN ** K 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 587 GLN K 722 ASN ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 822 ASN ** K 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 997 HIS K1179 GLN N 123 HIS ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 636 ASN N 695 GLN N 722 ASN N 913 ASN ** N 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1377 ASN O 79 ASN ** O 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 600 GLN ** O 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1033 GLN O1090 HIS ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 464 HIS ** x 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 201 ASN ** f 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 104 HIS m 23 GLN m 128 ASN m 148 GLN ** m 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 204 ASN ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 233 HIS ** p 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 38 GLN r 62 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.9258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 63966 Z= 0.249 Angle : 0.716 12.027 86932 Z= 0.362 Chirality : 0.045 0.221 9795 Planarity : 0.006 0.100 11336 Dihedral : 5.377 40.818 8722 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.31 % Favored : 93.60 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.05 (0.09), residues: 7881 helix: 0.13 (0.09), residues: 2942 sheet: -0.27 (0.15), residues: 1080 loop : -1.47 (0.10), residues: 3859 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1649 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1645 time to evaluate : 5.819 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 outliers start: 4 outliers final: 0 residues processed: 1648 average time/residue: 0.6054 time to fit residues: 1705.0063 Evaluate side-chains 1273 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1273 time to evaluate : 5.502 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 685 optimal weight: 8.9990 chunk 722 optimal weight: 10.0000 chunk 658 optimal weight: 30.0000 chunk 702 optimal weight: 2.9990 chunk 721 optimal weight: 20.0000 chunk 422 optimal weight: 5.9990 chunk 305 optimal weight: 30.0000 chunk 551 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 634 optimal weight: 0.9990 chunk 664 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 433 GLN ** J 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1022 HIS J1283 ASN K 429 ASN ** K 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 587 GLN K 722 ASN ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 997 HIS K1179 GLN N 9 ASN N 398 ASN ** N 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 695 GLN N 822 ASN ** N 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 913 ASN ** N 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N1033 GLN ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1217 GLN ** O 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 333 HIS ** O 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 587 GLN ** O 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 96 HIS ** v 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 464 HIS ** x 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 GLN f 208 HIS ** f 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 23 GLN m 128 ASN ** m 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 291 GLN ** p 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.9731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 63966 Z= 0.258 Angle : 0.727 12.923 86932 Z= 0.369 Chirality : 0.046 0.287 9795 Planarity : 0.006 0.101 11336 Dihedral : 5.452 39.265 8722 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.70 % Favored : 93.21 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.09), residues: 7881 helix: 0.13 (0.10), residues: 2930 sheet: -0.31 (0.15), residues: 1078 loop : -1.46 (0.10), residues: 3873 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1637 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1633 time to evaluate : 6.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 1634 average time/residue: 0.5998 time to fit residues: 1684.7866 Evaluate side-chains 1270 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1269 time to evaluate : 5.706 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4713 time to fit residues: 8.6848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 699 optimal weight: 10.0000 chunk 461 optimal weight: 7.9990 chunk 742 optimal weight: 20.0000 chunk 453 optimal weight: 20.0000 chunk 352 optimal weight: 8.9990 chunk 516 optimal weight: 20.0000 chunk 779 optimal weight: 9.9990 chunk 717 optimal weight: 8.9990 chunk 620 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 chunk 479 optimal weight: 10.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 398 ASN J 433 GLN ** J 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 672 ASN ** J 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 722 ASN ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 997 HIS K1090 HIS K1179 GLN K1292 ASN ** N 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS N 166 GLN ** N 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 398 ASN ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 695 GLN N 761 GLN ** N 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1033 GLN N1056 ASN ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1149 GLN N1283 ASN O 79 ASN ** O 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 333 HIS ** O 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1089 HIS ** O1090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 102 GLN ** x 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 102 GLN d 37 ASN f 208 HIS ** f 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 128 ASN ** m 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 279 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 1.0545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.114 63966 Z= 0.358 Angle : 0.831 15.552 86932 Z= 0.425 Chirality : 0.049 0.257 9795 Planarity : 0.006 0.105 11336 Dihedral : 5.954 39.082 8722 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.78 % Favored : 92.13 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.09), residues: 7881 helix: -0.25 (0.09), residues: 2958 sheet: -0.49 (0.15), residues: 1044 loop : -1.64 (0.10), residues: 3879 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1583 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1581 time to evaluate : 7.327 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: 2 outliers final: 0 residues processed: 1583 average time/residue: 0.6129 time to fit residues: 1671.3113 Evaluate side-chains 1215 residues out of total 6806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1215 time to evaluate : 5.545 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 380 optimal weight: 5.9990 chunk 492 optimal weight: 4.9990 chunk 660 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 572 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 172 optimal weight: 7.9990 chunk 621 optimal weight: 2.9990 chunk 260 optimal weight: 10.0000 chunk 638 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 429 ASN ** K 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 722 ASN ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 997 HIS K1179 GLN ** K1246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 695 GLN N 951 HIS N 997 HIS N1033 GLN ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 333 HIS ** O 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 587 GLN O 636 ASN ** O 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1033 GLN ** O1090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 102 GLN d 44 GLN f 208 HIS ** f 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 291 ASN h 208 HIS ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 185 HIS k 204 ASN m 128 ASN ** m 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 162 GLN p 185 HIS ** p 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 128 ASN ** r 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.136026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123240 restraints weight = 166611.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.126022 restraints weight = 102312.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126993 restraints weight = 62953.543| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 1.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 63966 Z= 0.240 Angle : 0.740 19.471 86932 Z= 0.375 Chirality : 0.047 0.256 9795 Planarity : 0.006 0.100 11336 Dihedral : 5.647 35.688 8722 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.53 % Favored : 93.38 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.09), residues: 7881 helix: -0.01 (0.09), residues: 2953 sheet: -0.42 (0.15), residues: 1050 loop : -1.52 (0.10), residues: 3878 =============================================================================== Job complete usr+sys time: 22656.95 seconds wall clock time: 393 minutes 23.50 seconds (23603.50 seconds total)