Starting phenix.real_space_refine (version: dev) on Fri Feb 24 07:56:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/02_2023/6jd1_9801_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/02_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_9801/02_2023/6jd1_9801.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/02_2023/6jd1_9801.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/02_2023/6jd1_9801_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/02_2023/6jd1_9801_trim_updated.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.361 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 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-dev-4877/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: 22.77, per 1000 atoms: 0.36 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: 44.63 Conformation dependent library (CDL) restraints added in 4.0 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: 2.81 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: 21.67 Time building geometry restraints manager: 46.75 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: 22289 17.02 - 34.03: 2397 34.03 - 51.05: 352 51.05 - 68.06: 76 68.06 - 85.08: 18 Dihedral angle restraints: 25132 sinusoidal: 11728 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 25129 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 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: 11.110 Check model and map are aligned: 0.710 Process input model: 154.420 Find NCS groups from input model: 3.370 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.440 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 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 : 14.896 85.078 11962 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 % 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 *********************** 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 : 4.204 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: 0.9850 time to fit residues: 1197.8162 Evaluate side-chains 512 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 3.935 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0048 ------------------------------------------------------------------------------- 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: 6.9990 chunk 295 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 354 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 96 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 K 296 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: 0.7256 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 32414 Z= 0.324 Angle : 0.693 6.381 43880 Z= 0.372 Chirality : 0.043 0.132 4792 Planarity : 0.005 0.048 5498 Dihedral : 8.257 86.102 4469 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 1.55 % 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: -4.16 (0.12), residues: 3929 helix: -2.87 (0.09), residues: 2005 sheet: -2.47 (0.30), residues: 292 loop : -2.47 (0.15), residues: 1632 *********************** 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 577 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 527 time to evaluate : 4.017 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 outliers start: 50 outliers final: 35 residues processed: 549 average time/residue: 0.8924 time to fit residues: 769.1866 Evaluate side-chains 482 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 447 time to evaluate : 4.001 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.6038 time to fit residues: 43.3841 ------------------------------------------------------------------------------- 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: 7.9990 chunk 109 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 354 optimal weight: 5.9990 chunk 383 optimal weight: 0.7980 chunk 315 optimal weight: 6.9990 chunk 351 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 284 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN C 332 ASN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 GLN ** I 278 ASN ** 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: 0.7296 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 32414 Z= 0.267 Angle : 0.605 6.590 43880 Z= 0.326 Chirality : 0.041 0.136 4792 Planarity : 0.004 0.063 5498 Dihedral : 7.702 74.290 4469 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 0.62 % 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: -3.66 (0.12), residues: 3929 helix: -2.39 (0.10), residues: 2068 sheet: -2.08 (0.32), residues: 282 loop : -2.33 (0.15), residues: 1579 *********************** 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: 20 poor density : 450 time to evaluate : 3.954 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 outliers start: 20 outliers final: 9 residues processed: 462 average time/residue: 0.8524 time to fit residues: 618.3432 Evaluate side-chains 426 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 417 time to evaluate : 3.993 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.5956 time to fit residues: 14.6076 ------------------------------------------------------------------------------- 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: 10.0000 chunk 184 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 356 optimal weight: 4.9990 chunk 376 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 337 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 GLN ** I 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 32414 Z= 0.333 Angle : 0.632 7.142 43880 Z= 0.341 Chirality : 0.042 0.146 4792 Planarity : 0.004 0.062 5498 Dihedral : 7.528 76.888 4469 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 1.55 % 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: -3.47 (0.12), residues: 3929 helix: -2.23 (0.10), residues: 2081 sheet: -1.71 (0.32), residues: 300 loop : -2.31 (0.15), residues: 1548 *********************** 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 477 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 427 time to evaluate : 4.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 36 residues processed: 440 average time/residue: 0.9395 time to fit residues: 658.5820 Evaluate side-chains 423 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 387 time to evaluate : 3.937 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 36 outliers final: 1 residues processed: 36 average time/residue: 0.6819 time to fit residues: 49.3768 ------------------------------------------------------------------------------- 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: 1.9990 chunk 213 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 321 optimal weight: 1.9990 chunk 260 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 338 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN C 332 ASN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 32414 Z= 0.193 Angle : 0.557 7.495 43880 Z= 0.290 Chirality : 0.040 0.133 4792 Planarity : 0.003 0.060 5498 Dihedral : 7.161 74.571 4469 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.13), residues: 3929 helix: -1.84 (0.10), residues: 2094 sheet: -1.60 (0.33), residues: 293 loop : -2.00 (0.16), residues: 1542 *********************** 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 463 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 440 time to evaluate : 3.934 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 outliers start: 23 outliers final: 15 residues processed: 450 average time/residue: 0.8628 time to fit residues: 619.4690 Evaluate side-chains 418 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 403 time to evaluate : 4.056 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.6712 time to fit residues: 22.7046 ------------------------------------------------------------------------------- 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: 0.6980 chunk 339 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 221 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 377 optimal weight: 5.9990 chunk 313 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN D 297 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 32414 Z= 0.206 Angle : 0.554 8.892 43880 Z= 0.289 Chirality : 0.041 0.145 4792 Planarity : 0.003 0.060 5498 Dihedral : 6.912 75.169 4469 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.13), residues: 3929 helix: -1.56 (0.10), residues: 2082 sheet: -1.37 (0.31), residues: 324 loop : -1.86 (0.16), residues: 1523 *********************** 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 454 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 431 time to evaluate : 3.953 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 outliers start: 23 outliers final: 17 residues processed: 440 average time/residue: 0.8395 time to fit residues: 591.6731 Evaluate side-chains 413 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 396 time to evaluate : 3.941 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.5980 time to fit residues: 23.3947 ------------------------------------------------------------------------------- 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: 0.9980 chunk 214 optimal weight: 6.9990 chunk 275 optimal weight: 9.9990 chunk 213 optimal weight: 0.8980 chunk 317 optimal weight: 9.9990 chunk 210 optimal weight: 9.9990 chunk 375 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 229 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 overall best weight: 5.3786 ------------------------------------------------------------------------------- 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** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 HIS C 296 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 GLN K 297 GLN ** 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: 0.7437 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 32414 Z= 0.323 Angle : 0.607 6.429 43880 Z= 0.326 Chirality : 0.042 0.138 4792 Planarity : 0.004 0.062 5498 Dihedral : 6.915 77.985 4469 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.13), residues: 3929 helix: -1.79 (0.10), residues: 2098 sheet: -1.22 (0.32), residues: 330 loop : -2.01 (0.15), residues: 1501 *********************** 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 438 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 402 time to evaluate : 3.946 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 outliers start: 36 outliers final: 24 residues processed: 413 average time/residue: 0.9114 time to fit residues: 609.2752 Evaluate side-chains 408 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 384 time to evaluate : 3.991 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.6719 time to fit residues: 34.1505 ------------------------------------------------------------------------------- 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: 7.9990 chunk 150 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 238 optimal weight: 0.0980 chunk 256 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 295 optimal weight: 2.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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** ** 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: 0.7386 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 32414 Z= 0.203 Angle : 0.552 7.723 43880 Z= 0.288 Chirality : 0.041 0.134 4792 Planarity : 0.003 0.061 5498 Dihedral : 6.617 77.350 4469 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 0.31 % 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: -2.44 (0.13), residues: 3929 helix: -1.44 (0.11), residues: 2058 sheet: -1.24 (0.31), residues: 334 loop : -1.74 (0.16), residues: 1537 *********************** 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 424 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 414 time to evaluate : 4.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 418 average time/residue: 0.8514 time to fit residues: 571.0034 Evaluate side-chains 403 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 393 time to evaluate : 4.024 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.7533 time to fit residues: 17.3272 ------------------------------------------------------------------------------- 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: 9.9990 chunk 360 optimal weight: 10.0000 chunk 328 optimal weight: 4.9990 chunk 350 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 275 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 316 optimal weight: 9.9990 chunk 331 optimal weight: 8.9990 chunk 349 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** 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** F 37 ASN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 32414 Z= 0.372 Angle : 0.641 6.849 43880 Z= 0.346 Chirality : 0.042 0.147 4792 Planarity : 0.004 0.064 5498 Dihedral : 6.730 82.915 4469 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.13), residues: 3929 helix: -1.91 (0.10), residues: 2078 sheet: -1.18 (0.31), residues: 340 loop : -1.93 (0.16), residues: 1511 *********************** 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 417 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 383 time to evaluate : 4.108 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 outliers start: 34 outliers final: 29 residues processed: 391 average time/residue: 0.8535 time to fit residues: 535.6119 Evaluate side-chains 403 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 374 time to evaluate : 3.986 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.5864 time to fit residues: 36.3211 ------------------------------------------------------------------------------- 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: 10.0000 chunk 226 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 257 optimal weight: 4.9990 chunk 388 optimal weight: 2.9990 chunk 357 optimal weight: 3.9990 chunk 309 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 238 optimal weight: 0.3980 chunk 189 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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** ** 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** H 40 ASN ** 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: 0.7385 moved from start: 0.5461 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= 0.168 Angle : 0.553 7.798 43880 Z= 0.284 Chirality : 0.041 0.179 4792 Planarity : 0.003 0.062 5498 Dihedral : 6.358 79.512 4469 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 0.19 % 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: -2.28 (0.13), residues: 3929 helix: -1.34 (0.11), residues: 2044 sheet: -1.13 (0.31), residues: 334 loop : -1.63 (0.16), residues: 1551 ********************** 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 405 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 399 time to evaluate : 4.162 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 outliers start: 6 outliers final: 4 residues processed: 402 average time/residue: 0.8497 time to fit residues: 551.8055 Evaluate side-chains 394 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 390 time to evaluate : 3.943 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5879 time to fit residues: 9.1882 ------------------------------------------------------------------------------- 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: 0.7980 chunk 94 optimal weight: 6.9990 chunk 285 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 309 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 318 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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** ** 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** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.057972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.044926 restraints weight = 432815.091| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 5.94 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 32414 Z= 0.303 Angle : 0.600 8.207 43880 Z= 0.319 Chirality : 0.042 0.170 4792 Planarity : 0.004 0.063 5498 Dihedral : 6.372 81.040 4469 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer Outliers : 0.34 % 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: -2.50 (0.13), residues: 3929 helix: -1.56 (0.11), residues: 2067 sheet: -1.14 (0.31), residues: 335 loop : -1.69 (0.16), residues: 1527 =============================================================================== Job complete usr+sys time: 11663.56 seconds wall clock time: 203 minutes 7.58 seconds (12187.58 seconds total)