Starting phenix.real_space_refine on Sat Dec 9 14:18:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcz_9800/12_2023/6jcz_9800_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcz_9800/12_2023/6jcz_9800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcz_9800/12_2023/6jcz_9800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcz_9800/12_2023/6jcz_9800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcz_9800/12_2023/6jcz_9800_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcz_9800/12_2023/6jcz_9800_trim_updated.pdb" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.395 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: 7 Type Number sf(0) Gaussians P 36 5.49 5 Mg 24 5.21 5 S 120 5.16 5 C 20444 2.51 5 N 5204 2.21 5 O 6123 1.98 5 H 31525 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 314": "OE1" <-> "OE2" Residue "B ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 314": "OE1" <-> "OE2" Residue "C ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 314": "OE1" <-> "OE2" Residue "E TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 186": "OE1" <-> "OE2" Residue "E ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 314": "OE1" <-> "OE2" Residue "F ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 186": "OE1" <-> "OE2" Residue "F ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 88": "OE1" <-> "OE2" Residue "G GLU 186": "OE1" <-> "OE2" Residue "G GLU 243": "OE1" <-> "OE2" Residue "G ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 314": "OE1" <-> "OE2" Residue "H ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 186": "OE1" <-> "OE2" Residue "H ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 314": "OE1" <-> "OE2" Residue "I ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "I GLU 186": "OE1" <-> "OE2" Residue "I ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J GLU 186": "OE1" <-> "OE2" Residue "J ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 314": "OE1" <-> "OE2" Residue "K ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K GLU 88": "OE1" <-> "OE2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "K ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 314": "OE1" <-> "OE2" Residue "L ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L GLU 186": "OE1" <-> "OE2" Residue "L ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 314": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 63476 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "B" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "C" Number of atoms: 5236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 5236 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Chain: "D" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "E" Number of atoms: 5210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5210 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 317} Chain: "F" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "G" Number of atoms: 5221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5221 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "H" Number of atoms: 5210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5210 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 317} Chain: "I" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "J" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "K" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "L" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {' MG': 3, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 2, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 2, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 2, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 2, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {' MG': 3, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 2, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 2, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 68 Unusual residues: {' MG': 2, '9TY': 2, 'NDP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {' MG': 2, 'NDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "K" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" C1B NDP A 403 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP A 403 " occ=0.59 residue: pdb=" C1B NDP B 402 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP B 402 " occ=0.59 residue: pdb=" C1B NDP C 402 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP C 402 " occ=0.59 residue: pdb=" C1B NDP D 403 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP D 403 " occ=0.59 residue: pdb=" C1B NDP E 402 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP E 402 " occ=0.59 residue: pdb=" C1B NDP F 403 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP F 403 " occ=0.59 residue: pdb=" C1B NDP G 402 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP G 402 " occ=0.59 residue: pdb=" C1B NDP H 404 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP H 404 " occ=0.59 residue: pdb=" C1B NDP I 402 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP I 402 " occ=0.59 residue: pdb=" C1B NDP J 403 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP J 403 " occ=0.59 residue: pdb=" C1B NDP K 402 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP K 402 " occ=0.59 residue: pdb=" C1B NDP L 403 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP L 403 " occ=0.59 Time building chain proxies: 20.01, per 1000 atoms: 0.32 Number of scatterers: 63476 At special positions: 0 Unit cell: (147.03, 147.03, 145.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 120 16.00 P 36 15.00 Mg 24 11.99 O 6123 8.00 N 5204 7.00 C 20444 6.00 H 31525 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 38.26 Conformation dependent library (CDL) restraints added in 4.7 seconds 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7222 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 26 sheets defined 46.2% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.83 Creating SS restraints... Processing helix chain 'A' and resid 27 through 36 Processing helix chain 'A' and resid 49 through 56 Processing helix chain 'A' and resid 64 through 70 removed outlier: 3.725A pdb=" N ARG A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.962A pdb=" N GLN A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 97' Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.765A pdb=" N ALA A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 193 removed outlier: 3.704A pdb=" N LEU A 189 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 210 removed outlier: 3.706A pdb=" N ALA A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 228 removed outlier: 3.641A pdb=" N LEU A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 228' Processing helix chain 'A' and resid 232 through 243 removed outlier: 5.017A pdb=" N ARG A 239 " --> pdb=" O GLU A 236 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 240 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.972A pdb=" N GLY A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 284 removed outlier: 4.812A pdb=" N ARG A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 298 removed outlier: 3.736A pdb=" N LEU A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.592A pdb=" N ARG A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 324 removed outlier: 3.888A pdb=" N ALA A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 36 removed outlier: 3.505A pdb=" N MET B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 55 Processing helix chain 'B' and resid 64 through 70 removed outlier: 3.723A pdb=" N ARG B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.965A pdb=" N GLN B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLY B 97 " --> pdb=" O PRO B 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 97' Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.551A pdb=" N ALA B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 193 removed outlier: 3.698A pdb=" N LEU B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 210 removed outlier: 3.698A pdb=" N ALA B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 228 removed outlier: 3.645A pdb=" N LEU B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 243 removed outlier: 4.972A pdb=" N ARG B 239 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 240 " --> pdb=" O ILE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 265 removed outlier: 3.978A pdb=" N GLY B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 removed outlier: 4.812A pdb=" N ARG B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 298 removed outlier: 3.744A pdb=" N LEU B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.634A pdb=" N ARG B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP B 307 " --> pdb=" O PHE B 303 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 324 removed outlier: 4.006A pdb=" N ALA B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 321 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 13 No H-bonds generated for 'chain 'C' and resid 11 through 13' Processing helix chain 'C' and resid 27 through 36 removed outlier: 3.730A pdb=" N THR C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.961A pdb=" N GLU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 68 No H-bonds generated for 'chain 'C' and resid 65 through 68' Processing helix chain 'C' and resid 83 through 89 Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.999A pdb=" N GLN C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 92 through 97' Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 160 through 170 removed outlier: 3.905A pdb=" N ALA C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 193 removed outlier: 3.699A pdb=" N LEU C 189 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 210 removed outlier: 3.684A pdb=" N ALA C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 228 removed outlier: 3.661A pdb=" N LEU C 225 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 Processing helix chain 'C' and resid 255 through 265 removed outlier: 4.023A pdb=" N GLY C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 removed outlier: 3.883A pdb=" N ASN C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 298 removed outlier: 3.734A pdb=" N LEU C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN C 296 " --> pdb=" O TRP C 292 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 312 removed outlier: 4.045A pdb=" N TRP C 307 " --> pdb=" O PHE C 303 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU C 308 " --> pdb=" O TYR C 304 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 326 removed outlier: 3.690A pdb=" N GLU C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 36 removed outlier: 3.512A pdb=" N MET D 34 " --> pdb=" O GLN D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 55 Processing helix chain 'D' and resid 64 through 70 removed outlier: 3.705A pdb=" N ARG D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 92 through 97 removed outlier: 3.953A pdb=" N GLN D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLY D 97 " --> pdb=" O PRO D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 92 through 97' Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 160 through 170 removed outlier: 3.556A pdb=" N ALA D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 193 removed outlier: 3.726A pdb=" N LEU D 189 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 210 removed outlier: 3.733A pdb=" N ALA D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 228 removed outlier: 3.681A pdb=" N LEU D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 221 through 228' Processing helix chain 'D' and resid 232 through 243 removed outlier: 5.224A pdb=" N ARG D 239 " --> pdb=" O GLU D 236 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 240 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.987A pdb=" N GLY D 260 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 261 " --> pdb=" O SER D 257 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 4.800A pdb=" N ARG D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 298 removed outlier: 3.737A pdb=" N LEU D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN D 296 " --> pdb=" O TRP D 292 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 310 removed outlier: 4.128A pdb=" N TRP D 307 " --> pdb=" O PHE D 303 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 308 " --> pdb=" O TYR D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 324 removed outlier: 4.018A pdb=" N ALA D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.521A pdb=" N MET E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 57 Processing helix chain 'E' and resid 64 through 70 removed outlier: 3.708A pdb=" N ARG E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 90 Processing helix chain 'E' and resid 92 through 97 removed outlier: 4.585A pdb=" N GLY E 97 " --> pdb=" O PRO E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 161 through 170 removed outlier: 3.794A pdb=" N ALA E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS E 169 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY E 170 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 193 removed outlier: 3.828A pdb=" N LEU E 189 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 210 removed outlier: 3.694A pdb=" N ALA E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 228 removed outlier: 3.663A pdb=" N LEU E 225 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU E 226 " --> pdb=" O GLU E 222 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 241 Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.924A pdb=" N GLY E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR E 261 " --> pdb=" O SER E 257 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG E 264 " --> pdb=" O GLY E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 284 removed outlier: 4.530A pdb=" N ARG E 274 " --> pdb=" O ASP E 270 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN E 278 " --> pdb=" O ARG E 274 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 298 removed outlier: 3.717A pdb=" N LEU E 294 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN E 296 " --> pdb=" O TRP E 292 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN E 297 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 312 removed outlier: 3.695A pdb=" N ARG E 305 " --> pdb=" O PRO E 301 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TRP E 307 " --> pdb=" O PHE E 303 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU E 308 " --> pdb=" O TYR E 304 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN E 312 " --> pdb=" O GLU E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 324 removed outlier: 3.953A pdb=" N ALA E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU E 321 " --> pdb=" O LYS E 317 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS E 324 " --> pdb=" O LYS E 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 36 Processing helix chain 'F' and resid 49 through 56 Processing helix chain 'F' and resid 64 through 70 removed outlier: 3.684A pdb=" N ARG F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 89 Processing helix chain 'F' and resid 92 through 97 removed outlier: 3.958A pdb=" N GLN F 96 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLY F 97 " --> pdb=" O PRO F 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 92 through 97' Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 160 through 170 removed outlier: 3.549A pdb=" N ALA F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS F 169 " --> pdb=" O LYS F 165 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY F 170 " --> pdb=" O ALA F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 193 removed outlier: 3.715A pdb=" N LEU F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 210 removed outlier: 3.654A pdb=" N ALA F 208 " --> pdb=" O GLY F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 228 removed outlier: 3.668A pdb=" N LEU F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU F 226 " --> pdb=" O GLU F 222 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 221 through 228' Processing helix chain 'F' and resid 232 through 243 removed outlier: 4.869A pdb=" N ARG F 239 " --> pdb=" O GLU F 236 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU F 240 " --> pdb=" O ILE F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 265 removed outlier: 4.022A pdb=" N GLY F 260 " --> pdb=" O THR F 256 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR F 261 " --> pdb=" O SER F 257 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG F 264 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 284 removed outlier: 4.815A pdb=" N ARG F 274 " --> pdb=" O ASP F 270 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 298 removed outlier: 3.750A pdb=" N LEU F 294 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN F 296 " --> pdb=" O TRP F 292 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN F 297 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 310 removed outlier: 3.739A pdb=" N TRP F 307 " --> pdb=" O PHE F 303 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU F 308 " --> pdb=" O TYR F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 324 removed outlier: 4.004A pdb=" N ALA F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS F 324 " --> pdb=" O LYS F 320 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 35 removed outlier: 3.830A pdb=" N THR G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 57 removed outlier: 3.945A pdb=" N GLU G 57 " --> pdb=" O LEU G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 70 removed outlier: 3.652A pdb=" N ARG G 69 " --> pdb=" O ASP G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 89 Processing helix chain 'G' and resid 92 through 97 removed outlier: 4.144A pdb=" N GLN G 96 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY G 97 " --> pdb=" O PRO G 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 92 through 97' Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 137 through 142 removed outlier: 4.270A pdb=" N LYS G 141 " --> pdb=" O MET G 137 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLN G 142 " --> pdb=" O ASP G 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 137 through 142' Processing helix chain 'G' and resid 160 through 167 removed outlier: 3.811A pdb=" N ALA G 166 " --> pdb=" O ASP G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 193 removed outlier: 3.728A pdb=" N LEU G 189 " --> pdb=" O GLU G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 210 removed outlier: 3.631A pdb=" N ALA G 208 " --> pdb=" O GLY G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 228 removed outlier: 3.658A pdb=" N LEU G 225 " --> pdb=" O PRO G 221 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE G 228 " --> pdb=" O ALA G 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 221 through 228' Processing helix chain 'G' and resid 233 through 243 removed outlier: 3.619A pdb=" N ALA G 238 " --> pdb=" O LEU G 234 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG G 239 " --> pdb=" O ALA G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 265 removed outlier: 4.014A pdb=" N GLY G 260 " --> pdb=" O THR G 256 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR G 261 " --> pdb=" O SER G 257 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG G 264 " --> pdb=" O GLY G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 284 removed outlier: 4.391A pdb=" N ARG G 274 " --> pdb=" O ASP G 270 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE G 275 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN G 278 " --> pdb=" O ARG G 274 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE G 283 " --> pdb=" O GLU G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 298 removed outlier: 3.750A pdb=" N LEU G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN G 296 " --> pdb=" O TRP G 292 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN G 297 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 310 removed outlier: 4.062A pdb=" N TRP G 307 " --> pdb=" O PHE G 303 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU G 308 " --> pdb=" O TYR G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 324 removed outlier: 3.779A pdb=" N ALA G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU G 321 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU G 322 " --> pdb=" O ALA G 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 13 No H-bonds generated for 'chain 'H' and resid 11 through 13' Processing helix chain 'H' and resid 27 through 35 removed outlier: 3.785A pdb=" N MET H 34 " --> pdb=" O GLN H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 55 removed outlier: 3.932A pdb=" N LEU H 53 " --> pdb=" O LYS H 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA H 54 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 70 Processing helix chain 'H' and resid 83 through 89 Processing helix chain 'H' and resid 92 through 97 removed outlier: 4.486A pdb=" N GLN H 96 " --> pdb=" O PRO H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 141 Processing helix chain 'H' and resid 160 through 168 removed outlier: 3.637A pdb=" N ALA H 166 " --> pdb=" O ASP H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 193 removed outlier: 3.732A pdb=" N LEU H 189 " --> pdb=" O GLU H 185 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU H 192 " --> pdb=" O ALA H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 210 removed outlier: 3.824A pdb=" N ALA H 208 " --> pdb=" O GLY H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 228 removed outlier: 3.610A pdb=" N LEU H 225 " --> pdb=" O PRO H 221 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU H 226 " --> pdb=" O GLU H 222 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE H 228 " --> pdb=" O ALA H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 243 Processing helix chain 'H' and resid 255 through 265 removed outlier: 4.001A pdb=" N GLY H 260 " --> pdb=" O THR H 256 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR H 261 " --> pdb=" O SER H 257 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG H 264 " --> pdb=" O GLY H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 284 removed outlier: 4.478A pdb=" N ARG H 274 " --> pdb=" O ASP H 270 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN H 278 " --> pdb=" O ARG H 274 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE H 283 " --> pdb=" O GLU H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 298 removed outlier: 3.730A pdb=" N LEU H 294 " --> pdb=" O LYS H 290 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU H 295 " --> pdb=" O GLU H 291 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN H 296 " --> pdb=" O TRP H 292 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN H 297 " --> pdb=" O SER H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 312 removed outlier: 3.950A pdb=" N TRP H 307 " --> pdb=" O PHE H 303 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU H 308 " --> pdb=" O TYR H 304 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN H 312 " --> pdb=" O GLU H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 320 Processing helix chain 'I' and resid 27 through 36 removed outlier: 3.510A pdb=" N MET I 34 " --> pdb=" O GLN I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 64 through 70 removed outlier: 3.646A pdb=" N ARG I 69 " --> pdb=" O ASP I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 89 Processing helix chain 'I' and resid 92 through 97 removed outlier: 3.959A pdb=" N GLN I 96 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLY I 97 " --> pdb=" O PRO I 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 92 through 97' Processing helix chain 'I' and resid 108 through 110 No H-bonds generated for 'chain 'I' and resid 108 through 110' Processing helix chain 'I' and resid 135 through 140 Processing helix chain 'I' and resid 160 through 170 removed outlier: 3.563A pdb=" N ALA I 164 " --> pdb=" O ALA I 160 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA I 166 " --> pdb=" O ASP I 162 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA I 168 " --> pdb=" O ALA I 164 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS I 169 " --> pdb=" O LYS I 165 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY I 170 " --> pdb=" O ALA I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 193 removed outlier: 3.704A pdb=" N LEU I 189 " --> pdb=" O GLU I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 210 removed outlier: 3.699A pdb=" N ALA I 208 " --> pdb=" O GLY I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 228 removed outlier: 3.659A pdb=" N LEU I 225 " --> pdb=" O PRO I 221 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU I 226 " --> pdb=" O GLU I 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE I 228 " --> pdb=" O ALA I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 243 removed outlier: 4.718A pdb=" N ARG I 239 " --> pdb=" O GLU I 236 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU I 240 " --> pdb=" O ILE I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 265 removed outlier: 3.954A pdb=" N GLY I 260 " --> pdb=" O THR I 256 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 284 removed outlier: 4.815A pdb=" N ARG I 274 " --> pdb=" O ASP I 270 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE I 283 " --> pdb=" O GLU I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 298 removed outlier: 3.788A pdb=" N LEU I 294 " --> pdb=" O LYS I 290 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU I 295 " --> pdb=" O GLU I 291 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN I 296 " --> pdb=" O TRP I 292 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN I 297 " --> pdb=" O SER I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 310 removed outlier: 3.779A pdb=" N TRP I 307 " --> pdb=" O PHE I 303 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU I 308 " --> pdb=" O TYR I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 324 removed outlier: 4.006A pdb=" N ALA I 318 " --> pdb=" O GLU I 314 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU I 321 " --> pdb=" O LYS I 317 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU I 322 " --> pdb=" O ALA I 318 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS I 324 " --> pdb=" O LYS I 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 36 removed outlier: 3.533A pdb=" N MET J 34 " --> pdb=" O GLN J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 55 Processing helix chain 'J' and resid 64 through 70 removed outlier: 3.933A pdb=" N ARG J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 89 Processing helix chain 'J' and resid 92 through 97 removed outlier: 3.961A pdb=" N GLN J 96 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLY J 97 " --> pdb=" O PRO J 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 92 through 97' Processing helix chain 'J' and resid 108 through 110 No H-bonds generated for 'chain 'J' and resid 108 through 110' Processing helix chain 'J' and resid 135 through 140 Processing helix chain 'J' and resid 160 through 171 removed outlier: 3.769A pdb=" N ALA J 166 " --> pdb=" O ASP J 162 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA J 168 " --> pdb=" O ALA J 164 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS J 169 " --> pdb=" O LYS J 165 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY J 170 " --> pdb=" O ALA J 166 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE J 171 " --> pdb=" O ILE J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 193 removed outlier: 3.713A pdb=" N LEU J 189 " --> pdb=" O GLU J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 210 removed outlier: 3.703A pdb=" N ALA J 208 " --> pdb=" O GLY J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 228 removed outlier: 3.646A pdb=" N LEU J 225 " --> pdb=" O PRO J 221 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU J 226 " --> pdb=" O GLU J 222 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE J 228 " --> pdb=" O ALA J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 243 removed outlier: 4.209A pdb=" N LEU J 240 " --> pdb=" O GLU J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 265 removed outlier: 4.038A pdb=" N GLY J 260 " --> pdb=" O THR J 256 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR J 261 " --> pdb=" O SER J 257 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG J 264 " --> pdb=" O GLY J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 284 removed outlier: 4.793A pdb=" N ARG J 274 " --> pdb=" O ASP J 270 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 295 removed outlier: 3.817A pdb=" N LEU J 294 " --> pdb=" O LYS J 290 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU J 295 " --> pdb=" O GLU J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 310 removed outlier: 3.752A pdb=" N ARG J 305 " --> pdb=" O PRO J 301 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TRP J 307 " --> pdb=" O PHE J 303 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU J 308 " --> pdb=" O TYR J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 324 removed outlier: 3.989A pdb=" N ALA J 318 " --> pdb=" O GLU J 314 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU J 321 " --> pdb=" O LYS J 317 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU J 322 " --> pdb=" O ALA J 318 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS J 324 " --> pdb=" O LYS J 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 36 removed outlier: 3.592A pdb=" N MET K 34 " --> pdb=" O GLN K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 56 Processing helix chain 'K' and resid 64 through 70 removed outlier: 3.641A pdb=" N ARG K 69 " --> pdb=" O ASP K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 89 Processing helix chain 'K' and resid 92 through 97 removed outlier: 3.964A pdb=" N GLN K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLY K 97 " --> pdb=" O PRO K 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 92 through 97' Processing helix chain 'K' and resid 108 through 110 No H-bonds generated for 'chain 'K' and resid 108 through 110' Processing helix chain 'K' and resid 135 through 140 Processing helix chain 'K' and resid 160 through 170 removed outlier: 3.523A pdb=" N ALA K 164 " --> pdb=" O ALA K 160 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA K 166 " --> pdb=" O ASP K 162 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA K 168 " --> pdb=" O ALA K 164 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS K 169 " --> pdb=" O LYS K 165 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY K 170 " --> pdb=" O ALA K 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 193 removed outlier: 3.689A pdb=" N LEU K 189 " --> pdb=" O GLU K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 210 removed outlier: 3.696A pdb=" N ALA K 208 " --> pdb=" O GLY K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 228 removed outlier: 3.652A pdb=" N LEU K 225 " --> pdb=" O PRO K 221 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU K 226 " --> pdb=" O GLU K 222 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE K 228 " --> pdb=" O ALA K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 243 removed outlier: 4.187A pdb=" N LEU K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 265 removed outlier: 4.005A pdb=" N GLY K 260 " --> pdb=" O THR K 256 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR K 261 " --> pdb=" O SER K 257 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG K 264 " --> pdb=" O GLY K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 284 removed outlier: 4.823A pdb=" N ARG K 274 " --> pdb=" O ASP K 270 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 289 through 298 removed outlier: 3.732A pdb=" N LEU K 294 " --> pdb=" O LYS K 290 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU K 295 " --> pdb=" O GLU K 291 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN K 296 " --> pdb=" O TRP K 292 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN K 297 " --> pdb=" O SER K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 303 through 310 removed outlier: 3.791A pdb=" N TRP K 307 " --> pdb=" O PHE K 303 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU K 308 " --> pdb=" O TYR K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 324 removed outlier: 3.891A pdb=" N ALA K 318 " --> pdb=" O GLU K 314 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU K 321 " --> pdb=" O LYS K 317 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU K 322 " --> pdb=" O ALA K 318 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS K 324 " --> pdb=" O LYS K 320 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 36 removed outlier: 3.544A pdb=" N MET L 34 " --> pdb=" O GLN L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 56 Processing helix chain 'L' and resid 64 through 70 removed outlier: 3.937A pdb=" N ARG L 69 " --> pdb=" O ASP L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 89 Processing helix chain 'L' and resid 92 through 97 removed outlier: 3.962A pdb=" N GLN L 96 " --> pdb=" O ALA L 92 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLY L 97 " --> pdb=" O PRO L 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 92 through 97' Processing helix chain 'L' and resid 108 through 110 No H-bonds generated for 'chain 'L' and resid 108 through 110' Processing helix chain 'L' and resid 135 through 140 Processing helix chain 'L' and resid 160 through 171 removed outlier: 3.754A pdb=" N ALA L 166 " --> pdb=" O ASP L 162 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA L 168 " --> pdb=" O ALA L 164 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS L 169 " --> pdb=" O LYS L 165 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY L 170 " --> pdb=" O ALA L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 193 removed outlier: 3.710A pdb=" N LEU L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 210 removed outlier: 3.675A pdb=" N ALA L 208 " --> pdb=" O GLY L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 228 removed outlier: 3.652A pdb=" N LEU L 225 " --> pdb=" O PRO L 221 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU L 226 " --> pdb=" O GLU L 222 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE L 228 " --> pdb=" O ALA L 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 243 removed outlier: 4.144A pdb=" N LEU L 240 " --> pdb=" O GLU L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 265 removed outlier: 4.066A pdb=" N GLY L 260 " --> pdb=" O THR L 256 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR L 261 " --> pdb=" O SER L 257 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG L 264 " --> pdb=" O GLY L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 269 through 284 removed outlier: 4.804A pdb=" N ARG L 274 " --> pdb=" O ASP L 270 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 289 through 298 removed outlier: 3.741A pdb=" N LEU L 294 " --> pdb=" O LYS L 290 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU L 295 " --> pdb=" O GLU L 291 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN L 296 " --> pdb=" O TRP L 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN L 297 " --> pdb=" O SER L 293 " (cutoff:3.500A) Processing helix chain 'L' and resid 301 through 310 removed outlier: 3.740A pdb=" N ARG L 305 " --> pdb=" O PRO L 301 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TRP L 307 " --> pdb=" O PHE L 303 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU L 308 " --> pdb=" O TYR L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 324 removed outlier: 4.002A pdb=" N ALA L 318 " --> pdb=" O GLU L 314 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU L 321 " --> pdb=" O LYS L 317 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU L 322 " --> pdb=" O ALA L 318 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS L 324 " --> pdb=" O LYS L 320 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.733A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 73 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE A 21 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU A 75 " --> pdb=" O ILE A 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 102 through 105 removed outlier: 7.317A pdb=" N ASP A 123 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE A 105 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE A 125 " --> pdb=" O PHE A 105 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 148 through 150 Processing sheet with id= D, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.719A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 73 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE B 21 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU B 75 " --> pdb=" O ILE B 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 102 through 105 removed outlier: 7.288A pdb=" N ASP B 123 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE B 105 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE B 125 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY B 151 " --> pdb=" O MET B 126 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.486A pdb=" N ILE C 18 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY C 44 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL C 20 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 73 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE C 21 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU C 75 " --> pdb=" O ILE C 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 102 through 105 removed outlier: 7.184A pdb=" N ASP C 123 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE C 105 " --> pdb=" O ASP C 123 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE C 125 " --> pdb=" O PHE C 105 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN C 154 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET C 126 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL C 152 " --> pdb=" O MET C 126 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.747A pdb=" N ILE D 18 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLY D 44 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL D 20 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL D 73 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE D 21 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU D 75 " --> pdb=" O ILE D 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'D' and resid 102 through 105 removed outlier: 7.296A pdb=" N ASP D 123 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N PHE D 105 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE D 125 " --> pdb=" O PHE D 105 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN D 154 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N MET D 126 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 152 " --> pdb=" O MET D 126 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA D 128 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU D 150 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 41 through 44 removed outlier: 6.969A pdb=" N ILE E 18 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N GLY E 44 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL E 20 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL E 73 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE E 21 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU E 75 " --> pdb=" O ILE E 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 102 through 105 removed outlier: 7.114A pdb=" N ASP E 123 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N PHE E 105 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE E 125 " --> pdb=" O PHE E 105 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 41 through 44 removed outlier: 6.810A pdb=" N ILE F 18 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLY F 44 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL F 20 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 73 " --> pdb=" O GLY F 19 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE F 21 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU F 75 " --> pdb=" O ILE F 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'F' and resid 102 through 105 removed outlier: 7.307A pdb=" N ASP F 123 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE F 105 " --> pdb=" O ASP F 123 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE F 125 " --> pdb=" O PHE F 105 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'F' and resid 148 through 150 Processing sheet with id= O, first strand: chain 'G' and resid 41 through 44 removed outlier: 6.801A pdb=" N ILE G 18 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLY G 44 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL G 20 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL G 73 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE G 21 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU G 75 " --> pdb=" O ILE G 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 102 through 105 removed outlier: 6.965A pdb=" N ASP G 123 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N PHE G 105 " --> pdb=" O ASP G 123 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE G 125 " --> pdb=" O PHE G 105 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY G 151 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 180 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.850A pdb=" N ILE H 18 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLY H 44 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL H 20 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL H 73 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE H 21 " --> pdb=" O VAL H 73 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU H 75 " --> pdb=" O ILE H 21 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL H 102 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU H 76 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASP H 104 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP H 123 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N PHE H 105 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE H 125 " --> pdb=" O PHE H 105 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'I' and resid 41 through 44 removed outlier: 6.757A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL I 73 " --> pdb=" O GLY I 19 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE I 21 " --> pdb=" O VAL I 73 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU I 75 " --> pdb=" O ILE I 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'I' and resid 102 through 105 removed outlier: 7.286A pdb=" N ASP I 123 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE I 105 " --> pdb=" O ASP I 123 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE I 125 " --> pdb=" O PHE I 105 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN I 154 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N MET I 126 " --> pdb=" O VAL I 152 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL I 152 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA I 128 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU I 150 " --> pdb=" O ALA I 128 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 41 through 44 removed outlier: 6.807A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL J 73 " --> pdb=" O GLY J 19 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE J 21 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU J 75 " --> pdb=" O ILE J 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'J' and resid 102 through 105 removed outlier: 7.322A pdb=" N ASP J 123 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N PHE J 105 " --> pdb=" O ASP J 123 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE J 125 " --> pdb=" O PHE J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'J' and resid 148 through 150 Processing sheet with id= W, first strand: chain 'K' and resid 41 through 44 removed outlier: 6.732A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL K 73 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE K 21 " --> pdb=" O VAL K 73 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU K 75 " --> pdb=" O ILE K 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'K' and resid 102 through 105 removed outlier: 7.309A pdb=" N ASP K 123 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N PHE K 105 " --> pdb=" O ASP K 123 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE K 125 " --> pdb=" O PHE K 105 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY K 151 " --> pdb=" O MET K 126 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 41 through 44 removed outlier: 6.756A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL L 73 " --> pdb=" O GLY L 19 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE L 21 " --> pdb=" O VAL L 73 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU L 75 " --> pdb=" O ILE L 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'L' and resid 102 through 105 removed outlier: 7.318A pdb=" N ASP L 123 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N PHE L 105 " --> pdb=" O ASP L 123 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE L 125 " --> pdb=" O PHE L 105 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY L 151 " --> pdb=" O MET L 126 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 1995 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: 20.16 Time building geometry restraints manager: 40.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 31513 1.05 - 1.26: 5292 1.26 - 1.47: 12514 1.47 - 1.68: 14466 1.68 - 1.89: 252 Bond restraints: 64037 Sorted by residual: bond pdb=" C GLY A 44 " pdb=" N ASN A 45 " ideal model delta sigma weight residual 1.330 1.259 0.071 1.22e-02 6.72e+03 3.38e+01 bond pdb=" CB GLN G 26 " pdb=" CG GLN G 26 " ideal model delta sigma weight residual 1.520 1.636 -0.116 3.00e-02 1.11e+03 1.49e+01 bond pdb=" C4D NDP G 402 " pdb=" O4D NDP G 402 " ideal model delta sigma weight residual 1.419 1.512 -0.093 3.50e-02 8.16e+02 7.00e+00 bond pdb=" C4D NDP G 402 " pdb=" C5D NDP G 402 " ideal model delta sigma weight residual 1.511 1.581 -0.070 3.40e-02 8.65e+02 4.23e+00 bond pdb=" CG GLN G 26 " pdb=" HG3 GLN G 26 " ideal model delta sigma weight residual 0.970 1.010 -0.040 2.00e-02 2.50e+03 3.97e+00 ... (remaining 64032 not shown) Histogram of bond angle deviations from ideal: 59.86 - 74.82: 36 74.82 - 89.78: 2 89.78 - 104.74: 603 104.74 - 119.70: 92509 119.70 - 134.66: 22894 Bond angle restraints: 116044 Sorted by residual: angle pdb=" HG2 GLN G 26 " pdb=" CG GLN G 26 " pdb=" HG3 GLN G 26 " ideal model delta sigma weight residual 110.00 132.63 -22.63 3.00e+00 1.11e-01 5.69e+01 angle pdb=" CD GLN G 26 " pdb=" CG GLN G 26 " pdb=" HG3 GLN G 26 " ideal model delta sigma weight residual 108.00 85.50 22.50 3.00e+00 1.11e-01 5.63e+01 angle pdb=" CD GLN G 26 " pdb=" CG GLN G 26 " pdb=" HG2 GLN G 26 " ideal model delta sigma weight residual 108.00 86.69 21.31 3.00e+00 1.11e-01 5.04e+01 angle pdb=" C2B NDP G 402 " pdb=" O2B NDP G 402 " pdb=" P2B NDP G 402 " ideal model delta sigma weight residual 111.34 124.02 -12.68 2.68e+00 1.40e-01 2.24e+01 angle pdb=" C2B NDP I 402 " pdb=" O2B NDP I 402 " pdb=" P2B NDP I 402 " ideal model delta sigma weight residual 111.34 124.01 -12.67 2.68e+00 1.40e-01 2.24e+01 ... (remaining 116039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.52: 27537 30.52 - 61.04: 931 61.04 - 91.55: 34 91.55 - 122.07: 11 122.07 - 152.59: 1 Dihedral angle restraints: 28514 sinusoidal: 15101 harmonic: 13413 Sorted by residual: dihedral pdb=" CA ASN A 45 " pdb=" C ASN A 45 " pdb=" N VAL A 46 " pdb=" CA VAL A 46 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ASN B 45 " pdb=" C ASN B 45 " pdb=" N VAL B 46 " pdb=" CA VAL B 46 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ARG C 70 " pdb=" C ARG C 70 " pdb=" N SER C 71 " pdb=" CA SER C 71 " ideal model delta harmonic sigma weight residual -180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 28511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4496 0.093 - 0.186: 301 0.186 - 0.278: 1 0.278 - 0.371: 0 0.371 - 0.464: 1 Chirality restraints: 4799 Sorted by residual: chirality pdb=" C4D NDP G 402 " pdb=" C3D NDP G 402 " pdb=" C5D NDP G 402 " pdb=" O4D NDP G 402 " both_signs ideal model delta sigma weight residual False -2.71 -3.18 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA ASP H 11 " pdb=" N ASP H 11 " pdb=" C ASP H 11 " pdb=" CB ASP H 11 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C2B NDP I 402 " pdb=" C1B NDP I 402 " pdb=" C3B NDP I 402 " pdb=" O2B NDP I 402 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 4796 not shown) Planarity restraints: 9344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 44 " 0.022 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" N ASN A 45 " -0.068 2.00e-02 2.50e+03 pdb=" CA ASN A 45 " 0.018 2.00e-02 2.50e+03 pdb=" H ASN A 45 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 44 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C GLY A 44 " 0.062 2.00e-02 2.50e+03 pdb=" O GLY A 44 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A 45 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 220 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO H 221 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO H 221 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 221 " 0.028 5.00e-02 4.00e+02 ... (remaining 9341 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 727 2.07 - 2.70: 103844 2.70 - 3.34: 174559 3.34 - 3.97: 218508 3.97 - 4.60: 361783 Nonbonded interactions: 859421 Sorted by model distance: nonbonded pdb=" HA2 GLY G 22 " pdb="HD22 ASN G 45 " model vdw 1.441 2.270 nonbonded pdb=" HA2 GLY E 22 " pdb="HD22 ASN E 45 " model vdw 1.463 2.270 nonbonded pdb=" HA2 GLY H 22 " pdb="HD22 ASN H 45 " model vdw 1.633 2.270 nonbonded pdb=" HA2 GLY C 22 " pdb="HD22 ASN C 45 " model vdw 1.667 2.270 nonbonded pdb=" CD GLU E 195 " pdb="MG MG E 401 " model vdw 1.670 2.350 ... (remaining 859416 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 'A' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'B' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'C' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'D' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'E' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'F' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'G' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ \ 1 or name HZ2 or name HZ3)) or resid 4 through 331)) selection = (chain 'H' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'I' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'J' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'K' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'L' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) } 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=0.59 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.710 Extract box with map and model: 12.350 Check model and map are aligned: 0.690 Set scattering table: 0.440 Process input model: 148.970 Find NCS groups from input model: 3.270 Set up NCS constraints: 0.200 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 0.116 32512 Z= 0.373 Angle : 0.809 12.677 44029 Z= 0.420 Chirality : 0.045 0.464 4799 Planarity : 0.005 0.049 5530 Dihedral : 15.493 152.588 11973 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -5.41 (0.11), residues: 3935 helix: -4.33 (0.06), residues: 2048 sheet: -3.03 (0.23), residues: 462 loop : -2.15 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 198 HIS 0.013 0.003 HIS I 196 PHE 0.012 0.002 PHE E 184 TYR 0.023 0.002 TYR H 51 ARG 0.003 0.000 ARG H 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 726 time to evaluate : 3.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0 outliers final: 0 residues processed: 726 average time/residue: 0.9385 time to fit residues: 1034.4837 Evaluate side-chains 469 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 3.749 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 332 optimal weight: 0.7980 chunk 298 optimal weight: 0.5980 chunk 165 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 308 optimal weight: 0.2980 chunk 119 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 357 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 297 GLN C 332 ASN E 297 GLN F 154 GLN G 140 HIS G 278 ASN H 25 ASN H 45 ASN J 140 HIS J 154 GLN K 154 GLN L 154 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32512 Z= 0.193 Angle : 0.593 8.431 44029 Z= 0.313 Chirality : 0.040 0.142 4799 Planarity : 0.004 0.043 5530 Dihedral : 9.292 154.423 4463 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.83 % Allowed : 8.21 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -4.86 (0.11), residues: 3935 helix: -3.69 (0.07), residues: 2138 sheet: -2.64 (0.23), residues: 462 loop : -2.12 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 198 HIS 0.003 0.001 HIS J 196 PHE 0.010 0.001 PHE G 303 TYR 0.017 0.001 TYR G 51 ARG 0.005 0.000 ARG J 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 524 time to evaluate : 3.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 59 outliers final: 50 residues processed: 558 average time/residue: 0.8803 time to fit residues: 764.2113 Evaluate side-chains 482 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 432 time to evaluate : 3.732 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.7425 time to fit residues: 65.7781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 198 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 297 optimal weight: 7.9990 chunk 243 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 358 optimal weight: 4.9990 chunk 387 optimal weight: 4.9990 chunk 319 optimal weight: 9.9990 chunk 355 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 287 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 HIS D 154 GLN D 252 HIS ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 32512 Z= 0.389 Angle : 0.666 8.224 44029 Z= 0.355 Chirality : 0.043 0.204 4799 Planarity : 0.004 0.042 5530 Dihedral : 9.426 153.566 4463 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.52 % Allowed : 9.42 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -4.35 (0.12), residues: 3935 helix: -2.91 (0.09), residues: 2148 sheet: -2.51 (0.23), residues: 501 loop : -2.52 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 161 HIS 0.012 0.002 HIS G 253 PHE 0.011 0.001 PHE E 303 TYR 0.014 0.001 TYR C 323 ARG 0.003 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 469 time to evaluate : 3.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 31 residues processed: 482 average time/residue: 0.8497 time to fit residues: 668.9756 Evaluate side-chains 454 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 423 time to evaluate : 3.747 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.6123 time to fit residues: 40.3801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 354 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 240 optimal weight: 5.9990 chunk 359 optimal weight: 0.2980 chunk 380 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 340 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 HIS ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 GLN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32512 Z= 0.170 Angle : 0.528 7.922 44029 Z= 0.273 Chirality : 0.041 0.138 4799 Planarity : 0.003 0.040 5530 Dihedral : 9.041 153.207 4463 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.46 % Allowed : 9.82 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -3.63 (0.12), residues: 3935 helix: -2.41 (0.09), residues: 2170 sheet: -2.18 (0.24), residues: 475 loop : -2.05 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 161 HIS 0.004 0.001 HIS G 253 PHE 0.011 0.001 PHE E 303 TYR 0.009 0.001 TYR G 51 ARG 0.003 0.000 ARG K 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 490 time to evaluate : 3.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 496 average time/residue: 0.7679 time to fit residues: 632.4587 Evaluate side-chains 436 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 431 time to evaluate : 3.723 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5762 time to fit residues: 9.9321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 317 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 324 optimal weight: 0.0970 chunk 263 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 341 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 GLN ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32512 Z= 0.243 Angle : 0.551 7.807 44029 Z= 0.285 Chirality : 0.041 0.167 4799 Planarity : 0.003 0.040 5530 Dihedral : 9.008 153.223 4463 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.77 % Allowed : 11.31 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -3.32 (0.12), residues: 3935 helix: -2.07 (0.10), residues: 2188 sheet: -2.09 (0.24), residues: 475 loop : -2.07 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 161 HIS 0.004 0.001 HIS B 140 PHE 0.009 0.001 PHE E 303 TYR 0.014 0.001 TYR C 62 ARG 0.003 0.000 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 455 time to evaluate : 4.066 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: 25 outliers final: 18 residues processed: 464 average time/residue: 0.7544 time to fit residues: 585.0698 Evaluate side-chains 443 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 425 time to evaluate : 3.740 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.6002 time to fit residues: 24.1538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 128 optimal weight: 0.0470 chunk 342 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 381 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32512 Z= 0.197 Angle : 0.528 7.469 44029 Z= 0.271 Chirality : 0.041 0.195 4799 Planarity : 0.003 0.042 5530 Dihedral : 8.859 153.079 4463 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.90 % Allowed : 11.68 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -2.90 (0.13), residues: 3935 helix: -1.77 (0.10), residues: 2144 sheet: -2.01 (0.24), residues: 475 loop : -1.76 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 161 HIS 0.003 0.001 HIS B 196 PHE 0.008 0.001 PHE E 303 TYR 0.013 0.001 TYR G 282 ARG 0.004 0.000 ARG G 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 456 time to evaluate : 3.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 471 average time/residue: 0.7591 time to fit residues: 589.9648 Evaluate side-chains 448 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 428 time to evaluate : 3.710 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5494 time to fit residues: 24.9757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 367 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 278 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 320 optimal weight: 0.3980 chunk 212 optimal weight: 0.9980 chunk 379 optimal weight: 0.7980 chunk 237 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32512 Z= 0.164 Angle : 0.509 8.205 44029 Z= 0.258 Chirality : 0.040 0.166 4799 Planarity : 0.003 0.039 5530 Dihedral : 8.698 153.006 4463 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.37 % Allowed : 12.52 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -2.48 (0.13), residues: 3935 helix: -1.47 (0.11), residues: 2133 sheet: -1.96 (0.24), residues: 475 loop : -1.44 (0.18), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 161 HIS 0.003 0.001 HIS C 253 PHE 0.008 0.001 PHE I 184 TYR 0.008 0.001 TYR C 62 ARG 0.004 0.000 ARG G 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 449 time to evaluate : 3.754 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: 12 outliers final: 6 residues processed: 459 average time/residue: 0.7615 time to fit residues: 577.4771 Evaluate side-chains 437 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 431 time to evaluate : 3.682 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5726 time to fit residues: 10.9537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 234 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 226 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 32512 Z= 0.237 Angle : 0.539 8.635 44029 Z= 0.277 Chirality : 0.041 0.171 4799 Planarity : 0.003 0.072 5530 Dihedral : 8.701 153.194 4463 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.40 % Allowed : 13.48 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -2.48 (0.13), residues: 3935 helix: -1.38 (0.11), residues: 2128 sheet: -1.92 (0.24), residues: 475 loop : -1.64 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 161 HIS 0.004 0.001 HIS J 196 PHE 0.011 0.001 PHE F 247 TYR 0.008 0.001 TYR H 51 ARG 0.010 0.000 ARG L 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 429 time to evaluate : 3.839 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: 13 outliers final: 11 residues processed: 435 average time/residue: 0.8109 time to fit residues: 581.8413 Evaluate side-chains 430 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 419 time to evaluate : 3.824 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5582 time to fit residues: 16.1564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 345 optimal weight: 3.9990 chunk 363 optimal weight: 5.9990 chunk 331 optimal weight: 8.9990 chunk 353 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 277 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 319 optimal weight: 10.0000 chunk 334 optimal weight: 4.9990 chunk 352 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN G 252 HIS ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 32512 Z= 0.396 Angle : 0.640 9.329 44029 Z= 0.340 Chirality : 0.043 0.153 4799 Planarity : 0.004 0.095 5530 Dihedral : 9.048 153.625 4463 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.53 % Allowed : 13.54 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -3.23 (0.12), residues: 3935 helix: -1.90 (0.09), residues: 2289 sheet: -1.91 (0.24), residues: 489 loop : -2.27 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 161 HIS 0.006 0.002 HIS L 140 PHE 0.021 0.001 PHE B 247 TYR 0.011 0.001 TYR G 217 ARG 0.010 0.001 ARG L 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 394 time to evaluate : 3.743 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 outliers start: 17 outliers final: 15 residues processed: 398 average time/residue: 0.8396 time to fit residues: 544.6235 Evaluate side-chains 403 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 388 time to evaluate : 3.742 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.5742 time to fit residues: 20.6597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 232 optimal weight: 4.9990 chunk 374 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 260 optimal weight: 3.9990 chunk 392 optimal weight: 5.9990 chunk 361 optimal weight: 8.9990 chunk 312 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 241 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32512 Z= 0.198 Angle : 0.538 8.189 44029 Z= 0.275 Chirality : 0.041 0.139 4799 Planarity : 0.003 0.066 5530 Dihedral : 8.811 153.158 4463 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.12 % Allowed : 13.94 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -2.82 (0.13), residues: 3935 helix: -1.56 (0.10), residues: 2251 sheet: -1.93 (0.24), residues: 441 loop : -2.05 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 161 HIS 0.007 0.001 HIS J 140 PHE 0.006 0.001 PHE F 184 TYR 0.009 0.001 TYR B 109 ARG 0.012 0.000 ARG L 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 407 time to evaluate : 3.792 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 outliers start: 4 outliers final: 3 residues processed: 411 average time/residue: 0.7991 time to fit residues: 544.5958 Evaluate side-chains 401 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 398 time to evaluate : 3.754 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5474 time to fit residues: 7.7003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 248 optimal weight: 6.9990 chunk 332 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 131 optimal weight: 0.4980 chunk 321 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 57 optimal weight: 0.0570 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.076230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.062305 restraints weight = 327068.880| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 5.26 r_work: 0.2877 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32512 Z= 0.179 Angle : 0.529 8.096 44029 Z= 0.268 Chirality : 0.040 0.155 4799 Planarity : 0.003 0.069 5530 Dihedral : 8.682 153.070 4463 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.09 % Allowed : 14.41 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -2.47 (0.13), residues: 3935 helix: -1.31 (0.10), residues: 2253 sheet: -1.86 (0.24), residues: 461 loop : -1.79 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 161 HIS 0.006 0.001 HIS J 140 PHE 0.006 0.001 PHE E 303 TYR 0.008 0.001 TYR B 109 ARG 0.013 0.000 ARG L 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11930.60 seconds wall clock time: 207 minutes 27.01 seconds (12447.01 seconds total)