Starting phenix.real_space_refine on Sat Dec 9 14:08:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/12_2023/6jd1_9801_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/12_2023/6jd1_9801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/12_2023/6jd1_9801.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/12_2023/6jd1_9801.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/12_2023/6jd1_9801_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/12_2023/6jd1_9801_trim_updated.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.361 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 24 5.49 5 Mg 36 5.21 5 S 120 5.16 5 C 20413 2.51 5 N 5190 2.21 5 O 6175 1.98 5 H 31469 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 216": "OE1" <-> "OE2" Residue "E TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 274": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 236": "OE1" <-> "OE2" Residue "I TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 60": "OE1" <-> "OE2" Residue "J ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 216": "OE1" <-> "OE2" Residue "J GLU 236": "OE1" <-> "OE2" Residue "J TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 216": "OE1" <-> "OE2" Residue "K ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 236": "OE1" <-> "OE2" Residue "L GLU 243": "OE1" <-> "OE2" Residue "L TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 63427 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 5225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5225 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "B" Number of atoms: 5237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 5237 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} 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: 5225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5225 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "E" Number of atoms: 5211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5211 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 317} Chain: "F" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5223 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "G" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5223 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "H" Number of atoms: 5211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5211 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 317} Chain: "I" Number of atoms: 5189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5189 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "J" Number of atoms: 5211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5211 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 317} Chain: "K" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5184 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "L" Number of atoms: 5188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5188 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {' MG': 4, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "K" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "L" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 20.17, per 1000 atoms: 0.32 Number of scatterers: 63427 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 24 15.00 Mg 36 11.99 O 6175 8.00 N 5190 7.00 C 20413 6.00 H 31469 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=0, symmetry=0 Time building additional restraints: 37.31 Conformation dependent library (CDL) restraints added in 4.8 seconds 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7210 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 205 helices and 23 sheets defined 47.7% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.60 Creating SS restraints... Processing helix chain 'A' and resid 26 through 29 No H-bonds generated for 'chain 'A' and resid 26 through 29' Processing helix chain 'A' and resid 31 through 37 removed outlier: 3.811A pdb=" N ARG A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 52 Processing helix chain 'A' and resid 54 through 57 Processing helix chain 'A' and resid 65 through 68 No H-bonds generated for 'chain 'A' and resid 65 through 68' Processing helix chain 'A' and resid 83 through 89 removed outlier: 3.549A pdb=" N GLU A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 95 Processing helix chain 'A' and resid 135 through 140 removed outlier: 4.172A pdb=" N HIS A 140 " --> pdb=" O MET A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 170 removed outlier: 3.707A pdb=" N ALA A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 193 removed outlier: 3.863A pdb=" N ALA A 188 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU A 189 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A 191 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 192 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 215 removed outlier: 3.522A pdb=" N LEU A 202 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 210 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 228 removed outlier: 3.703A pdb=" N LEU A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 244 removed outlier: 4.509A pdb=" N ALA A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.795A pdb=" N GLY A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 284 removed outlier: 3.698A pdb=" N ARG A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.874A pdb=" N LEU A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'B' and resid 26 through 35 removed outlier: 4.402A pdb=" N GLN B 30 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA B 31 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET B 34 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 35 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 54 No H-bonds generated for 'chain 'B' and resid 51 through 54' Processing helix chain 'B' and resid 65 through 68 No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 83 through 89 removed outlier: 3.774A pdb=" N GLU B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.967A pdb=" N GLN B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.691A 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 134 through 139 removed outlier: 3.864A pdb=" N MET B 137 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 170 removed outlier: 3.862A pdb=" N ALA B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 193 removed outlier: 4.550A pdb=" N LEU B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 215 removed outlier: 3.500A pdb=" N LEU B 202 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 228 removed outlier: 3.805A pdb=" N LEU B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 243 removed outlier: 3.776A pdb=" N LEU B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE B 241 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 255 through 267 removed outlier: 3.801A pdb=" N GLY B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 284 removed outlier: 3.940A pdb=" N ARG B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 282 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.521A pdb=" N LEU B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 310 Processing helix chain 'B' and resid 315 through 323 Processing helix chain 'C' and resid 25 through 34 removed outlier: 3.729A pdb=" N VAL C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE C 33 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.705A pdb=" N LEU C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 83 through 89 removed outlier: 3.800A pdb=" N GLU C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 161 through 170 Processing helix chain 'C' and resid 185 through 193 removed outlier: 4.425A pdb=" N LEU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 216 removed outlier: 3.757A pdb=" N TYR C 210 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 228 removed outlier: 3.842A pdb=" N LEU C 225 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 243 removed outlier: 3.645A pdb=" N ALA C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU C 240 " --> pdb=" O GLU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 252 Processing helix chain 'C' and resid 255 through 267 removed outlier: 4.175A pdb=" N GLY C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 284 removed outlier: 3.587A pdb=" N ARG C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 297 removed outlier: 4.198A pdb=" N LEU C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 310 Processing helix chain 'C' and resid 314 through 323 Processing helix chain 'D' and resid 25 through 34 removed outlier: 3.600A pdb=" N VAL D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE D 33 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 57 removed outlier: 3.611A pdb=" N LEU D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 68 No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 83 through 89 removed outlier: 3.627A pdb=" N GLU D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 134 through 140 removed outlier: 3.903A pdb=" N MET D 137 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS D 140 " --> pdb=" O MET D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 170 removed outlier: 4.004A pdb=" N ALA D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 193 removed outlier: 4.522A pdb=" N LEU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 216 removed outlier: 3.752A pdb=" N TYR D 210 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP D 211 " --> pdb=" O LYS D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 228 removed outlier: 3.877A pdb=" N LEU D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 243 removed outlier: 4.881A pdb=" N LEU D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 255 through 267 removed outlier: 4.263A pdb=" N TYR D 259 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY D 260 " --> pdb=" O SER D 257 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU D 262 " --> pdb=" O TYR D 259 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR D 263 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE D 266 " --> pdb=" O THR D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.945A pdb=" N ARG D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR D 282 " --> pdb=" O ASN D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 removed outlier: 3.783A pdb=" N GLU D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 310 Processing helix chain 'D' and resid 314 through 323 removed outlier: 4.447A pdb=" N GLU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 34 removed outlier: 3.699A pdb=" N THR E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE E 33 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 57 removed outlier: 3.854A pdb=" N LYS E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 89 removed outlier: 3.678A pdb=" N GLU E 88 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 95 No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 135 through 139 Processing helix chain 'E' and resid 161 through 170 removed outlier: 3.586A pdb=" N LYS E 169 " --> pdb=" O LYS E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 193 removed outlier: 4.225A pdb=" N LEU E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 215 removed outlier: 3.741A pdb=" N TYR E 210 " --> pdb=" O ILE E 206 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP E 211 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS E 215 " --> pdb=" O ASP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 228 removed outlier: 3.836A pdb=" N LEU E 225 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU E 226 " --> pdb=" O GLU E 222 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 244 removed outlier: 4.163A pdb=" N ARG E 239 " --> pdb=" O GLU E 236 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU E 240 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU E 244 " --> pdb=" O ILE E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 252 removed outlier: 3.509A pdb=" N VAL E 251 " --> pdb=" O ASN E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.980A pdb=" N GLY E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR E 261 " --> pdb=" O SER E 257 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR E 263 " --> pdb=" O TYR E 259 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG E 264 " --> pdb=" O GLY E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 284 removed outlier: 3.793A pdb=" N ARG E 274 " --> pdb=" O ASP E 270 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE E 275 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU E 279 " --> pdb=" O ILE E 275 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR E 282 " --> pdb=" O ASN E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.902A pdb=" N GLU E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN E 297 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 310 removed outlier: 3.522A pdb=" N TRP E 307 " --> pdb=" O PHE E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 323 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 31 through 36 removed outlier: 3.612A pdb=" N ARG F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 57 Processing helix chain 'F' and resid 65 through 68 No H-bonds generated for 'chain 'F' and resid 65 through 68' Processing helix chain 'F' and resid 83 through 89 removed outlier: 3.609A pdb=" N GLU F 88 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 95 Processing helix chain 'F' and resid 136 through 142 removed outlier: 4.442A pdb=" N LYS F 141 " --> pdb=" O MET F 137 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN F 142 " --> pdb=" O ASP F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 170 removed outlier: 3.983A pdb=" N ALA F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 193 removed outlier: 4.349A pdb=" N LEU F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 216 removed outlier: 3.741A pdb=" N TYR F 210 " --> pdb=" O ILE F 206 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP F 211 " --> pdb=" O LYS F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 228 removed outlier: 3.763A pdb=" N LEU F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU F 226 " --> pdb=" O GLU F 222 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 243 removed outlier: 3.510A pdb=" N ALA F 238 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU F 240 " --> pdb=" O GLU F 236 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE F 241 " --> pdb=" O ILE F 237 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU F 243 " --> pdb=" O ARG F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 252 removed outlier: 3.569A pdb=" N VAL F 251 " --> pdb=" O ASN F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 267 removed outlier: 3.870A pdb=" N GLY F 260 " --> pdb=" O THR F 256 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG F 264 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 284 removed outlier: 3.778A pdb=" N ARG F 274 " --> pdb=" O ASP F 270 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE F 275 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU F 279 " --> pdb=" O ILE F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 295 removed outlier: 3.806A pdb=" N LEU F 294 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 310 Processing helix chain 'F' and resid 314 through 323 Processing helix chain 'G' and resid 27 through 37 removed outlier: 4.798A pdb=" N THR G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE G 33 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 54 No H-bonds generated for 'chain 'G' and resid 51 through 54' Processing helix chain 'G' and resid 83 through 89 removed outlier: 3.706A pdb=" N GLU G 88 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS G 89 " --> pdb=" O GLU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 95 Processing helix chain 'G' and resid 136 through 139 No H-bonds generated for 'chain 'G' and resid 136 through 139' Processing helix chain 'G' and resid 161 through 170 Processing helix chain 'G' and resid 185 through 193 removed outlier: 4.555A pdb=" N LEU G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 216 removed outlier: 3.772A pdb=" N TYR G 210 " --> pdb=" O ILE G 206 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP G 211 " --> pdb=" O LYS G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 228 removed outlier: 3.869A pdb=" N LEU G 225 " --> pdb=" O PRO G 221 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 243 removed outlier: 4.542A pdb=" N LEU G 240 " --> pdb=" O GLU G 236 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE G 241 " --> pdb=" O ILE G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 251 Processing helix chain 'G' and resid 255 through 267 removed outlier: 3.900A pdb=" N GLY G 260 " --> pdb=" O THR G 256 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR G 261 " --> pdb=" O SER G 257 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG G 264 " --> pdb=" O GLY G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 284 removed outlier: 3.972A pdb=" N ARG G 274 " --> pdb=" O ASP G 270 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE G 275 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU G 279 " --> pdb=" O ILE G 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR G 282 " --> pdb=" O ASN G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 298 removed outlier: 4.149A pdb=" N LEU G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN G 297 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 310 Processing helix chain 'G' and resid 314 through 323 Processing helix chain 'H' and resid 27 through 37 removed outlier: 3.656A pdb=" N THR H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG H 35 " --> pdb=" O ALA H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 57 removed outlier: 3.632A pdb=" N LYS H 55 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 70 removed outlier: 3.563A pdb=" N VAL H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 64 through 70' Processing helix chain 'H' and resid 83 through 89 removed outlier: 3.622A pdb=" N GLU H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 97 removed outlier: 4.023A pdb=" N GLN H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLY H 97 " --> pdb=" O PRO H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 139 Processing helix chain 'H' and resid 160 through 170 removed outlier: 3.946A pdb=" N ALA H 164 " --> pdb=" O ALA H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 193 removed outlier: 4.536A pdb=" N LEU H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 215 removed outlier: 3.507A pdb=" N LEU H 202 " --> pdb=" O TRP H 198 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR H 210 " --> pdb=" O ILE H 206 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP H 211 " --> pdb=" O LYS H 207 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS H 215 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 228 removed outlier: 3.808A pdb=" N LEU H 225 " --> pdb=" O PRO H 221 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU H 226 " --> pdb=" O GLU H 222 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU H 227 " --> pdb=" O ALA H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 244 removed outlier: 3.720A pdb=" N ARG H 239 " --> pdb=" O ALA H 235 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU H 240 " --> pdb=" O GLU H 236 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE H 241 " --> pdb=" O ILE H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 removed outlier: 3.652A pdb=" N MET H 250 " --> pdb=" O PHE H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 267 removed outlier: 3.885A pdb=" N GLY H 260 " --> pdb=" O THR H 256 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG H 264 " --> pdb=" O GLY H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 284 removed outlier: 3.992A pdb=" N ILE H 275 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN H 278 " --> pdb=" O ARG H 274 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS H 281 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 298 removed outlier: 3.510A pdb=" N LEU H 294 " --> pdb=" O LYS H 290 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU H 295 " --> pdb=" O GLU H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 310 Processing helix chain 'H' and resid 314 through 326 Processing helix chain 'I' and resid 27 through 37 removed outlier: 4.797A pdb=" N THR I 32 " --> pdb=" O ARG I 28 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE I 33 " --> pdb=" O VAL I 29 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET I 34 " --> pdb=" O GLN I 30 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG I 35 " --> pdb=" O ALA I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 56 removed outlier: 4.202A pdb=" N ALA I 54 " --> pdb=" O TYR I 51 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS I 55 " --> pdb=" O GLU I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 89 removed outlier: 3.602A pdb=" N GLU I 88 " --> pdb=" O LYS I 84 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 95 Processing helix chain 'I' and resid 136 through 142 removed outlier: 4.194A pdb=" N LYS I 141 " --> pdb=" O MET I 137 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN I 142 " --> pdb=" O ASP I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 170 removed outlier: 3.627A pdb=" N ALA I 164 " --> pdb=" O ALA I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 193 removed outlier: 4.316A pdb=" N LEU I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 215 removed outlier: 3.515A pdb=" N LEU I 202 " --> pdb=" O TRP I 198 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR I 210 " --> pdb=" O ILE I 206 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP I 211 " --> pdb=" O LYS I 207 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS I 215 " --> pdb=" O ASP I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 228 removed outlier: 3.800A pdb=" N LEU I 225 " --> pdb=" O PRO I 221 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU I 226 " --> pdb=" O GLU I 222 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU I 227 " --> pdb=" O ALA I 223 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 243 removed outlier: 3.925A pdb=" N LEU I 240 " --> pdb=" O GLU I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 252 Processing helix chain 'I' and resid 255 through 267 removed outlier: 3.956A pdb=" N GLY I 260 " --> pdb=" O THR I 256 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 284 removed outlier: 3.996A pdb=" N ARG I 274 " --> pdb=" O ASP I 270 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE I 275 " --> pdb=" O VAL I 271 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU I 279 " --> pdb=" O ILE I 275 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR I 282 " --> pdb=" O ASN I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 295 removed outlier: 3.866A pdb=" N LEU I 294 " --> pdb=" O LYS I 290 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU I 295 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 310 Processing helix chain 'I' and resid 314 through 323 removed outlier: 3.980A pdb=" N GLU I 321 " --> pdb=" O LYS I 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 28 No H-bonds generated for 'chain 'J' and resid 26 through 28' Processing helix chain 'J' and resid 30 through 34 Processing helix chain 'J' and resid 49 through 57 removed outlier: 3.996A pdb=" N LYS J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS J 56 " --> pdb=" O GLU J 52 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU J 57 " --> pdb=" O LEU J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 89 removed outlier: 3.729A pdb=" N GLU J 88 " --> pdb=" O LYS J 84 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 95 No H-bonds generated for 'chain 'J' and resid 92 through 95' Processing helix chain 'J' and resid 134 through 141 removed outlier: 3.939A pdb=" N ASP J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS J 141 " --> pdb=" O MET J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 170 Processing helix chain 'J' and resid 184 through 193 removed outlier: 3.946A pdb=" N ALA J 188 " --> pdb=" O GLU J 185 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU J 189 " --> pdb=" O GLU J 186 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP J 191 " --> pdb=" O ALA J 188 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU J 192 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 216 removed outlier: 3.761A pdb=" N TYR J 210 " --> pdb=" O ILE J 206 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP J 211 " --> pdb=" O LYS J 207 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 228 removed outlier: 3.812A pdb=" N LEU J 225 " --> pdb=" O PRO J 221 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU J 226 " --> pdb=" O GLU J 222 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU J 227 " --> pdb=" O ALA J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 243 removed outlier: 4.440A pdb=" N LEU J 240 " --> pdb=" O GLU J 236 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE J 241 " --> pdb=" O ILE J 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 251 Processing helix chain 'J' and resid 255 through 267 removed outlier: 3.931A pdb=" N GLY J 260 " --> pdb=" O THR J 256 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR J 261 " --> pdb=" O SER J 257 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG J 264 " --> pdb=" O GLY J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 284 removed outlier: 3.943A pdb=" N ARG J 274 " --> pdb=" O ASP J 270 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE J 275 " --> pdb=" O VAL J 271 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU J 279 " --> pdb=" O ILE J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 295 removed outlier: 3.725A pdb=" N GLU J 295 " --> pdb=" O GLU J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 310 Processing helix chain 'J' and resid 319 through 323 Processing helix chain 'K' and resid 29 through 36 removed outlier: 4.711A pdb=" N MET K 34 " --> pdb=" O GLN K 30 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU K 36 " --> pdb=" O THR K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 52 No H-bonds generated for 'chain 'K' and resid 49 through 52' Processing helix chain 'K' and resid 67 through 70 No H-bonds generated for 'chain 'K' and resid 67 through 70' Processing helix chain 'K' and resid 91 through 97 removed outlier: 3.856A pdb=" N GLN K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLY K 97 " --> pdb=" O PRO K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 140 removed outlier: 3.734A pdb=" N HIS K 140 " --> pdb=" O MET K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 170 removed outlier: 3.573A pdb=" N ALA K 168 " --> pdb=" O LYS K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 193 removed outlier: 4.356A pdb=" N LEU K 190 " --> pdb=" O GLU K 186 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU K 192 " --> pdb=" O ALA K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 215 removed outlier: 3.744A pdb=" N TYR K 210 " --> pdb=" O ILE K 206 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS K 215 " --> pdb=" O ASP K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 228 removed outlier: 3.813A pdb=" N LEU K 225 " --> pdb=" O PRO K 221 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU K 226 " --> pdb=" O GLU K 222 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU K 227 " --> pdb=" O ALA K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 240 through 243 No H-bonds generated for 'chain 'K' and resid 240 through 243' Processing helix chain 'K' and resid 248 through 252 Processing helix chain 'K' and resid 255 through 267 removed outlier: 3.907A pdb=" N GLY K 260 " --> pdb=" O THR K 256 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR K 263 " --> pdb=" O TYR K 259 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG K 264 " --> pdb=" O GLY K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 284 removed outlier: 3.932A pdb=" N ARG K 274 " --> pdb=" O ASP K 270 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE K 275 " --> pdb=" O VAL K 271 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU K 279 " --> pdb=" O ILE K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 297 removed outlier: 3.760A pdb=" N LEU K 294 " --> pdb=" O LYS K 290 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU K 295 " --> pdb=" O GLU K 291 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLN K 297 " --> pdb=" O SER K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 303 through 310 removed outlier: 3.805A pdb=" N GLU K 308 " --> pdb=" O TYR K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 326 Processing helix chain 'L' and resid 26 through 28 No H-bonds generated for 'chain 'L' and resid 26 through 28' Processing helix chain 'L' and resid 32 through 36 Processing helix chain 'L' and resid 49 through 57 removed outlier: 3.857A pdb=" N LEU L 53 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA L 54 " --> pdb=" O TYR L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 70 Processing helix chain 'L' and resid 83 through 89 Processing helix chain 'L' and resid 91 through 97 Processing helix chain 'L' and resid 135 through 139 Processing helix chain 'L' and resid 160 through 170 removed outlier: 3.693A pdb=" N ALA L 164 " --> pdb=" O ALA L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 193 removed outlier: 4.314A pdb=" N LEU L 190 " --> pdb=" O GLU L 186 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU L 192 " --> pdb=" O ALA L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 216 removed outlier: 3.725A pdb=" N TYR L 210 " --> pdb=" O ILE L 206 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP L 211 " --> pdb=" O LYS L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 228 removed outlier: 4.031A pdb=" N LEU L 225 " --> pdb=" O PRO L 221 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU L 226 " --> pdb=" O GLU L 222 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU L 227 " --> pdb=" O ALA L 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 236 No H-bonds generated for 'chain 'L' and resid 233 through 236' Processing helix chain 'L' and resid 238 through 243 Processing helix chain 'L' and resid 247 through 251 removed outlier: 3.626A pdb=" N MET L 250 " --> pdb=" O PHE L 247 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL L 251 " --> pdb=" O ASN L 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 247 through 251' Processing helix chain 'L' and resid 255 through 267 removed outlier: 3.799A pdb=" N GLY L 260 " --> pdb=" O THR L 256 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG L 264 " --> pdb=" O GLY L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 284 removed outlier: 3.926A pdb=" N ARG L 274 " --> pdb=" O ASP L 270 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE L 275 " --> pdb=" O VAL L 271 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU L 279 " --> pdb=" O ILE L 275 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR L 282 " --> pdb=" O ASN L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 295 removed outlier: 3.706A pdb=" N GLU L 295 " --> pdb=" O GLU L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 301 through 310 Processing helix chain 'L' and resid 314 through 323 removed outlier: 3.542A pdb=" N ALA L 318 " --> pdb=" O GLU L 314 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 18 through 21 Processing sheet with id= B, first strand: chain 'A' and resid 73 through 75 removed outlier: 7.168A pdb=" N VAL A 102 " --> pdb=" O ALA A 74 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 18 through 21 Processing sheet with id= D, first strand: chain 'B' and resid 73 through 75 removed outlier: 7.141A pdb=" N VAL B 102 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 105 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 18 through 21 Processing sheet with id= F, first strand: chain 'C' and resid 73 through 75 removed outlier: 6.608A pdb=" N VAL C 102 " --> pdb=" O ALA C 74 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 18 through 21 Processing sheet with id= H, first strand: chain 'D' and resid 73 through 75 removed outlier: 6.723A pdb=" N VAL D 102 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE D 105 " --> pdb=" O ILE D 125 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 18 through 21 Processing sheet with id= J, first strand: chain 'E' and resid 73 through 75 removed outlier: 7.084A pdb=" N VAL E 102 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP E 123 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE E 105 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE E 125 " --> pdb=" O PHE E 105 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN E 154 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N MET E 126 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL E 152 " --> pdb=" O MET E 126 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 18 through 21 Processing sheet with id= L, first strand: chain 'F' and resid 73 through 75 removed outlier: 7.120A pdb=" N VAL F 102 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ASP F 123 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE F 105 " --> pdb=" O ASP F 123 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE F 125 " --> pdb=" O PHE F 105 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'G' and resid 18 through 21 Processing sheet with id= N, first strand: chain 'G' and resid 73 through 75 removed outlier: 7.246A pdb=" N VAL G 102 " --> pdb=" O ALA G 74 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 18 through 21 Processing sheet with id= P, first strand: chain 'H' and resid 73 through 75 removed outlier: 7.041A pdb=" N VAL H 102 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 18 through 21 Processing sheet with id= R, first strand: chain 'I' and resid 73 through 75 removed outlier: 7.512A pdb=" N VAL I 102 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE I 105 " --> pdb=" O ILE I 125 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 18 through 21 Processing sheet with id= T, first strand: chain 'J' and resid 73 through 75 removed outlier: 7.485A pdb=" N VAL J 102 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP J 123 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N PHE J 105 " --> pdb=" O ASP J 123 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE J 125 " --> pdb=" O PHE J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'K' and resid 42 through 44 Processing sheet with id= V, first strand: chain 'K' and resid 102 through 105 removed outlier: 6.241A pdb=" N ASP K 123 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE K 105 " --> pdb=" O ASP K 123 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE K 125 " --> pdb=" O PHE K 105 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY K 151 " --> pdb=" O MET K 126 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 18 through 21 835 hydrogen bonds defined for protein. 2283 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: 18.48 Time building geometry restraints manager: 40.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 31457 1.03 - 1.23: 48 1.23 - 1.42: 13360 1.42 - 1.62: 18726 1.62 - 1.81: 292 Bond restraints: 63883 Sorted by residual: bond pdb=" C1B NAI I 404 " pdb=" C2B NAI I 404 " ideal model delta sigma weight residual 1.528 1.282 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C1B NAI B 404 " pdb=" C2B NAI B 404 " ideal model delta sigma weight residual 1.528 1.284 0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C1B NAI K 404 " pdb=" C2B NAI K 404 " ideal model delta sigma weight residual 1.528 1.285 0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C1B NAI A 404 " pdb=" C2B NAI A 404 " ideal model delta sigma weight residual 1.528 1.286 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1B NAI L 404 " pdb=" C2B NAI L 404 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.45e+02 ... (remaining 63878 not shown) Histogram of bond angle deviations from ideal: 59.92 - 74.75: 36 74.75 - 89.59: 0 89.59 - 104.42: 456 104.42 - 119.25: 89194 119.25 - 134.09: 26081 Bond angle restraints: 115767 Sorted by residual: angle pdb=" O1N NAI H 404 " pdb=" PN NAI H 404 " pdb=" O2N NAI H 404 " ideal model delta sigma weight residual 123.22 108.46 14.76 3.00e+00 1.11e-01 2.42e+01 angle pdb=" O1N NAI B 404 " pdb=" PN NAI B 404 " pdb=" O2N NAI B 404 " ideal model delta sigma weight residual 123.22 108.47 14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" O1N NAI F 405 " pdb=" PN NAI F 405 " pdb=" O2N NAI F 405 " ideal model delta sigma weight residual 123.22 108.53 14.69 3.00e+00 1.11e-01 2.40e+01 angle pdb=" O1N NAI K 404 " pdb=" PN NAI K 404 " pdb=" O2N NAI K 404 " ideal model delta sigma weight residual 123.22 108.63 14.59 3.00e+00 1.11e-01 2.36e+01 angle pdb=" O1N NAI L 404 " pdb=" PN NAI L 404 " pdb=" O2N NAI L 404 " ideal model delta sigma weight residual 123.22 108.64 14.58 3.00e+00 1.11e-01 2.36e+01 ... (remaining 115762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 25644 17.02 - 34.03: 2683 34.03 - 51.05: 584 51.05 - 68.06: 152 68.06 - 85.08: 22 Dihedral angle restraints: 29085 sinusoidal: 15681 harmonic: 13404 Sorted by residual: dihedral pdb=" CA VAL H 41 " pdb=" C VAL H 41 " pdb=" N ILE H 42 " pdb=" CA ILE H 42 " ideal model delta harmonic sigma weight residual 180.00 153.06 26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA VAL D 41 " pdb=" C VAL D 41 " pdb=" N ILE D 42 " pdb=" CA ILE D 42 " ideal model delta harmonic sigma weight residual 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA VAL L 41 " pdb=" C VAL L 41 " pdb=" N ILE L 42 " pdb=" CA ILE L 42 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 29082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3444 0.046 - 0.092: 1020 0.092 - 0.138: 286 0.138 - 0.185: 32 0.185 - 0.231: 10 Chirality restraints: 4792 Sorted by residual: chirality pdb=" C2B NAI J 404 " pdb=" C1B NAI J 404 " pdb=" C3B NAI J 404 " pdb=" O2B NAI J 404 " both_signs ideal model delta sigma weight residual False -2.55 -2.32 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C2B NAI H 404 " pdb=" C1B NAI H 404 " pdb=" C3B NAI H 404 " pdb=" O2B NAI H 404 " both_signs ideal model delta sigma weight residual False -2.55 -2.33 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C2B NAI G 404 " pdb=" C1B NAI G 404 " pdb=" C3B NAI G 404 " pdb=" O2B NAI G 404 " both_signs ideal model delta sigma weight residual False -2.55 -2.33 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 4789 not shown) Planarity restraints: 9307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 128 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO L 129 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO L 129 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 129 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG J 130 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C ARG J 130 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG J 130 " 0.013 2.00e-02 2.50e+03 pdb=" N MET J 131 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 118 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO D 119 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " -0.026 5.00e-02 4.00e+02 ... (remaining 9304 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 3655 2.20 - 2.80: 132491 2.80 - 3.40: 163471 3.40 - 4.00: 215500 4.00 - 4.60: 344040 Nonbonded interactions: 859157 Sorted by model distance: nonbonded pdb=" HH TYR C 268 " pdb=" OE2 GLU D 279 " model vdw 1.596 1.850 nonbonded pdb=" HH TYR A 268 " pdb=" OE2 GLU B 279 " model vdw 1.601 1.850 nonbonded pdb=" HH TYR K 268 " pdb=" OE2 GLU L 279 " model vdw 1.607 1.850 nonbonded pdb=" HH TYR I 229 " pdb=" OE1 GLU I 319 " model vdw 1.611 1.850 nonbonded pdb=" HH TYR E 229 " pdb=" OE1 GLU E 319 " model vdw 1.616 1.850 ... (remaining 859152 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 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 402 through 405)) selection = (chain 'B' 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 195 or (resid 196 and (name N or \ name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or nam \ e CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or na \ me HE1 or name HE2)) or resid 197 through 329 or resid 402 through 405)) selection = (chain 'C' and (resid 3 through 329 or resid 402 through 405)) selection = (chain 'D' and (resid 3 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 402 through 405)) selection = (chain 'E' and (resid 3 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401 through 404)) selection = (chain 'F' 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 195 or (resid 196 and (name N or \ name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or nam \ e CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or na \ me HE1 or name HE2)) or resid 197 through 329 or resid 403 through 406)) 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 195 or (resid 196 and (name N or \ name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or nam \ e CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or na \ me HE1 or name HE2)) or resid 197 through 329 or resid 402 through 405)) selection = (chain 'H' and (resid 3 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 402 through 405)) selection = (chain 'I' and (resid 3 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 402 through 405)) selection = (chain 'J' and (resid 3 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 402 through 405)) selection = (chain 'K' 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 329 or resid 402 through 405)) selection = (chain 'L' and (resid 3 through 329 or resid 402 through 405)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.720 Extract box with map and model: 9.330 Check model and map are aligned: 0.690 Set scattering table: 0.440 Process input model: 145.300 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.170 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:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 : 0.013 0.246 32414 Z= 0.839 Angle : 1.003 14.761 43880 Z= 0.458 Chirality : 0.047 0.231 4792 Planarity : 0.004 0.048 5498 Dihedral : 16.006 85.078 12562 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: -4.95 (0.11), residues: 3929 helix: -3.93 (0.07), residues: 1896 sheet: -2.74 (0.29), residues: 269 loop : -2.43 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 198 HIS 0.004 0.001 HIS B 252 PHE 0.017 0.001 PHE C 101 TYR 0.014 0.002 TYR I 217 ARG 0.006 0.001 ARG H 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 802 time to evaluate : 3.897 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 802 average time/residue: 0.9857 time to fit residues: 1202.6717 Evaluate side-chains 512 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 3.677 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 8.9990 chunk 295 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 354 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 96 GLN A 154 GLN B 154 GLN B 296 GLN C 297 GLN C 332 ASN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN E 154 GLN E 296 GLN F 154 GLN F 296 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 GLN H 296 GLN I 154 GLN ** I 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 GLN J 154 GLN K 154 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN L 296 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 32414 Z= 0.318 Angle : 0.697 7.116 43880 Z= 0.376 Chirality : 0.043 0.163 4792 Planarity : 0.005 0.050 5498 Dihedral : 11.041 88.829 5069 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.58 % Allowed : 11.77 % Favored : 86.65 % 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: -4.13 (0.12), residues: 3929 helix: -2.81 (0.09), residues: 2012 sheet: -2.43 (0.30), residues: 292 loop : -2.50 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 198 HIS 0.006 0.001 HIS G 252 PHE 0.013 0.001 PHE F 228 TYR 0.017 0.001 TYR I 259 ARG 0.011 0.001 ARG F 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 529 time to evaluate : 3.738 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 51 outliers final: 35 residues processed: 552 average time/residue: 0.8841 time to fit residues: 762.8689 Evaluate side-chains 483 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 448 time to evaluate : 3.768 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.5960 time to fit residues: 42.1842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 294 optimal weight: 9.9990 chunk 241 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 354 optimal weight: 5.9990 chunk 383 optimal weight: 9.9990 chunk 315 optimal weight: 2.9990 chunk 351 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 284 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN C 332 ASN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 ASN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 GLN ** I 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 32414 Z= 0.312 Angle : 0.622 6.417 43880 Z= 0.340 Chirality : 0.042 0.149 4792 Planarity : 0.004 0.057 5498 Dihedral : 9.875 84.679 5069 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.71 % Allowed : 14.28 % Favored : 85.00 % 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: -3.81 (0.12), residues: 3929 helix: -2.51 (0.09), residues: 2079 sheet: -2.03 (0.32), residues: 288 loop : -2.42 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 292 HIS 0.005 0.001 HIS F 252 PHE 0.018 0.001 PHE D 288 TYR 0.013 0.001 TYR J 62 ARG 0.014 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 447 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 23 outliers final: 7 residues processed: 458 average time/residue: 0.8742 time to fit residues: 628.6228 Evaluate side-chains 412 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 405 time to evaluate : 3.745 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6047 time to fit residues: 12.1146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 9.9990 chunk 266 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 238 optimal weight: 0.9990 chunk 356 optimal weight: 6.9990 chunk 376 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 337 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 296 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 GLN ** I 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32414 Z= 0.339 Angle : 0.637 7.506 43880 Z= 0.345 Chirality : 0.042 0.146 4792 Planarity : 0.004 0.059 5498 Dihedral : 9.364 84.762 5069 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 1.74 % Allowed : 15.83 % Favored : 82.43 % 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: -3.56 (0.12), residues: 3929 helix: -2.29 (0.10), residues: 2095 sheet: -1.77 (0.32), residues: 292 loop : -2.36 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 198 HIS 0.006 0.002 HIS I 140 PHE 0.011 0.001 PHE F 228 TYR 0.013 0.001 TYR A 217 ARG 0.004 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 434 time to evaluate : 3.897 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 outliers start: 56 outliers final: 39 residues processed: 452 average time/residue: 0.9082 time to fit residues: 652.1356 Evaluate side-chains 431 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 392 time to evaluate : 3.772 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.7090 time to fit residues: 53.1095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 5.9990 chunk 213 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 280 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 321 optimal weight: 3.9990 chunk 260 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 338 optimal weight: 9.9990 chunk 95 optimal weight: 0.2980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 GLN K 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32414 Z= 0.197 Angle : 0.556 8.746 43880 Z= 0.293 Chirality : 0.041 0.140 4792 Planarity : 0.003 0.057 5498 Dihedral : 8.978 84.522 5069 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.75 % Allowed : 17.35 % Favored : 81.90 % 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: -3.04 (0.12), residues: 3929 helix: -1.87 (0.10), residues: 2106 sheet: -1.52 (0.32), residues: 304 loop : -2.11 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 284 HIS 0.004 0.001 HIS I 140 PHE 0.020 0.001 PHE J 266 TYR 0.012 0.001 TYR A 217 ARG 0.008 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 436 time to evaluate : 3.809 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 outliers start: 24 outliers final: 15 residues processed: 446 average time/residue: 0.8270 time to fit residues: 592.2961 Evaluate side-chains 413 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 398 time to evaluate : 3.716 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.6762 time to fit residues: 21.9322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 126 optimal weight: 0.8980 chunk 339 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 221 optimal weight: 0.0370 chunk 93 optimal weight: 0.8980 chunk 377 optimal weight: 6.9990 chunk 313 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 overall best weight: 2.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 40 ASN C 278 ASN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32414 Z= 0.182 Angle : 0.542 8.891 43880 Z= 0.282 Chirality : 0.040 0.142 4792 Planarity : 0.003 0.055 5498 Dihedral : 8.725 85.354 5069 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.43 % Allowed : 19.00 % Favored : 80.57 % 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: -2.61 (0.13), residues: 3929 helix: -1.55 (0.10), residues: 2077 sheet: -1.44 (0.31), residues: 323 loop : -1.84 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 198 HIS 0.003 0.001 HIS I 140 PHE 0.014 0.001 PHE F 288 TYR 0.017 0.001 TYR F 282 ARG 0.005 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 429 time to evaluate : 3.735 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 outliers start: 14 outliers final: 9 residues processed: 434 average time/residue: 0.9138 time to fit residues: 642.5637 Evaluate side-chains 411 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 402 time to evaluate : 3.797 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.7292 time to fit residues: 16.7144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 275 optimal weight: 10.0000 chunk 213 optimal weight: 0.9980 chunk 317 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 375 optimal weight: 0.2980 chunk 235 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 HIS ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32414 Z= 0.208 Angle : 0.547 8.305 43880 Z= 0.287 Chirality : 0.040 0.133 4792 Planarity : 0.003 0.054 5498 Dihedral : 8.576 85.152 5069 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.62 % Allowed : 19.65 % Favored : 79.73 % 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: -2.49 (0.13), residues: 3929 helix: -1.43 (0.11), residues: 2058 sheet: -1.37 (0.31), residues: 323 loop : -1.82 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 198 HIS 0.004 0.001 HIS E 252 PHE 0.013 0.001 PHE I 288 TYR 0.014 0.001 TYR L 282 ARG 0.005 0.000 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 408 time to evaluate : 4.563 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 outliers start: 20 outliers final: 13 residues processed: 413 average time/residue: 0.8393 time to fit residues: 557.5099 Evaluate side-chains 407 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 394 time to evaluate : 3.759 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.5870 time to fit residues: 18.6158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 256 optimal weight: 5.9990 chunk 185 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 295 optimal weight: 4.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32414 Z= 0.291 Angle : 0.589 7.227 43880 Z= 0.316 Chirality : 0.041 0.146 4792 Planarity : 0.004 0.058 5498 Dihedral : 8.529 83.241 5069 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.99 % Allowed : 19.56 % Favored : 79.45 % 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: -2.67 (0.13), residues: 3929 helix: -1.59 (0.11), residues: 2069 sheet: -1.33 (0.31), residues: 334 loop : -1.92 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 198 HIS 0.005 0.001 HIS A 252 PHE 0.014 0.001 PHE G 288 TYR 0.012 0.001 TYR I 217 ARG 0.005 0.001 ARG I 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 406 time to evaluate : 3.799 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 outliers start: 32 outliers final: 19 residues processed: 414 average time/residue: 0.8859 time to fit residues: 591.8692 Evaluate side-chains 406 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 387 time to evaluate : 3.745 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.6934 time to fit residues: 27.9518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 341 optimal weight: 10.0000 chunk 360 optimal weight: 10.0000 chunk 328 optimal weight: 0.7980 chunk 350 optimal weight: 6.9990 chunk 210 optimal weight: 0.0870 chunk 152 optimal weight: 9.9990 chunk 275 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 331 optimal weight: 10.0000 chunk 349 optimal weight: 4.9990 overall best weight: 3.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32414 Z= 0.208 Angle : 0.551 7.784 43880 Z= 0.289 Chirality : 0.041 0.142 4792 Planarity : 0.003 0.057 5498 Dihedral : 8.386 85.815 5069 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.37 % Allowed : 20.43 % Favored : 79.20 % 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: -2.38 (0.13), residues: 3929 helix: -1.40 (0.11), residues: 2049 sheet: -1.22 (0.31), residues: 334 loop : -1.71 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 292 HIS 0.003 0.001 HIS E 252 PHE 0.014 0.001 PHE G 288 TYR 0.011 0.001 TYR I 217 ARG 0.004 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 407 time to evaluate : 3.802 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 outliers start: 12 outliers final: 10 residues processed: 410 average time/residue: 0.8537 time to fit residues: 563.1604 Evaluate side-chains 402 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 392 time to evaluate : 3.720 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.6157 time to fit residues: 15.7397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 230 optimal weight: 9.9990 chunk 370 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 257 optimal weight: 0.5980 chunk 388 optimal weight: 8.9990 chunk 357 optimal weight: 5.9990 chunk 309 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 238 optimal weight: 0.0870 chunk 189 optimal weight: 10.0000 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32414 Z= 0.157 Angle : 0.543 8.414 43880 Z= 0.278 Chirality : 0.041 0.185 4792 Planarity : 0.003 0.057 5498 Dihedral : 8.201 89.734 5069 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.19 % Allowed : 20.93 % Favored : 78.89 % 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: -1.98 (0.13), residues: 3929 helix: -1.05 (0.11), residues: 2052 sheet: -1.22 (0.30), residues: 357 loop : -1.50 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 292 HIS 0.003 0.001 HIS A 252 PHE 0.012 0.001 PHE G 288 TYR 0.014 0.001 TYR E 282 ARG 0.004 0.000 ARG B 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 406 time to evaluate : 3.775 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 outliers start: 6 outliers final: 4 residues processed: 408 average time/residue: 0.8544 time to fit residues: 562.0058 Evaluate side-chains 402 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 398 time to evaluate : 3.775 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5644 time to fit residues: 8.9390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 245 optimal weight: 10.0000 chunk 329 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 309 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 318 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 312 GLN ** 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 = 0.3318 r_free = 0.3318 target = 0.058922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.045628 restraints weight = 424240.749| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 5.99 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32414 Z= 0.217 Angle : 0.553 8.062 43880 Z= 0.291 Chirality : 0.041 0.170 4792 Planarity : 0.003 0.058 5498 Dihedral : 8.145 86.904 5069 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.19 % Allowed : 21.11 % Favored : 78.70 % 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: -2.07 (0.13), residues: 3929 helix: -1.15 (0.11), residues: 2071 sheet: -1.21 (0.30), residues: 357 loop : -1.50 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 292 HIS 0.004 0.001 HIS E 252 PHE 0.012 0.001 PHE F 288 TYR 0.012 0.001 TYR E 282 ARG 0.004 0.000 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12078.48 seconds wall clock time: 210 minutes 28.97 seconds (12628.97 seconds total)