Starting phenix.real_space_refine (version: dev) on Sun Feb 26 09:12:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4i_31712/02_2023/7v4i_31712.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4i_31712/02_2023/7v4i_31712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4i_31712/02_2023/7v4i_31712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4i_31712/02_2023/7v4i_31712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4i_31712/02_2023/7v4i_31712.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4i_31712/02_2023/7v4i_31712.pdb" } resolution = 3.3 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= 0.000 sd= 0.008 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 "J TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 32": "OD1" <-> "OD2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "E ASP 6": "OD1" <-> "OD2" Residue "E ASP 173": "OD1" <-> "OD2" Residue "E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 6": "OD1" <-> "OD2" Residue "G TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 173": "OD1" <-> "OD2" Residue "H ASP 32": "OD1" <-> "OD2" Residue "H PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 122": "OE1" <-> "OE2" Residue "H TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 123": "OE1" <-> "OE2" Residue "I GLU 222": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 27680 Number of models: 1 Model: "" Number of chains: 10 Chain: "J" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "A" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "B" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "C" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "D" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "E" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "F" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "G" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "H" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Chain: "I" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2768 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 332} Time building chain proxies: 15.08, per 1000 atoms: 0.54 Number of scatterers: 27680 At special positions: 0 Unit cell: (138.514, 138.514, 109.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5260 8.00 N 4740 7.00 C 17560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.67 Conformation dependent library (CDL) restraints added in 4.6 seconds 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6320 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 30 sheets defined 33.4% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'J' and resid 11 through 15 removed outlier: 3.898A pdb=" N GLU J 14 " --> pdb=" O ASN J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 50 Processing helix chain 'J' and resid 57 through 61 Processing helix chain 'J' and resid 107 through 115 Processing helix chain 'J' and resid 116 through 123 removed outlier: 3.724A pdb=" N GLU J 123 " --> pdb=" O VAL J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 183 removed outlier: 4.045A pdb=" N VAL J 172 " --> pdb=" O GLY J 168 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY J 183 " --> pdb=" O CYS J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 228 Processing helix chain 'J' and resid 262 through 276 removed outlier: 4.205A pdb=" N LYS J 267 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS J 268 " --> pdb=" O GLU J 264 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS J 276 " --> pdb=" O LYS J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 283 Processing helix chain 'J' and resid 287 through 292 removed outlier: 3.891A pdb=" N ARG J 291 " --> pdb=" O GLY J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 318 through 325 Processing helix chain 'J' and resid 339 through 353 Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.688A pdb=" N CYS A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4 through 9' Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.695A pdb=" N LEU A 50 " --> pdb=" O PRO A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 168 through 183 removed outlier: 4.181A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 229 Processing helix chain 'A' and resid 262 through 276 removed outlier: 4.077A pdb=" N LYS A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.614A pdb=" N ARG A 290 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 325 removed outlier: 3.626A pdb=" N GLU A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 353 Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 116 through 123 Processing helix chain 'B' and resid 168 through 183 removed outlier: 3.983A pdb=" N VAL B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 183 " --> pdb=" O CYS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 228 removed outlier: 3.894A pdb=" N GLY B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 261 through 276 removed outlier: 4.292A pdb=" N VAL B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 283 removed outlier: 3.540A pdb=" N HIS B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 removed outlier: 3.566A pdb=" N ARG B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 339 through 353 Processing helix chain 'C' and resid 46 through 50 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 123 Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.588A pdb=" N VAL C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C 183 " --> pdb=" O CYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 228 removed outlier: 3.976A pdb=" N ASP C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 260 Processing helix chain 'C' and resid 262 through 276 removed outlier: 4.138A pdb=" N LYS C 276 " --> pdb=" O LYS C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 287 through 292 removed outlier: 4.096A pdb=" N ARG C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 325 Processing helix chain 'C' and resid 339 through 353 removed outlier: 3.966A pdb=" N ALA C 348 " --> pdb=" O THR C 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 50 Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 122 Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.967A pdb=" N VAL D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY D 183 " --> pdb=" O CYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 4.281A pdb=" N GLY D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 276 removed outlier: 4.070A pdb=" N LYS D 276 " --> pdb=" O LYS D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 283 Processing helix chain 'D' and resid 287 through 292 removed outlier: 4.136A pdb=" N ARG D 291 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 325 Processing helix chain 'D' and resid 339 through 352 Processing helix chain 'E' and resid 4 through 9 removed outlier: 3.654A pdb=" N CYS E 8 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN E 9 " --> pdb=" O SER E 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4 through 9' Processing helix chain 'E' and resid 46 through 50 removed outlier: 3.728A pdb=" N LEU E 50 " --> pdb=" O PRO E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 61 removed outlier: 3.525A pdb=" N GLY E 61 " --> pdb=" O GLY E 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 57 through 61' Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 116 through 123 Processing helix chain 'E' and resid 169 through 183 Processing helix chain 'E' and resid 208 through 229 Processing helix chain 'E' and resid 262 through 276 removed outlier: 4.094A pdb=" N LYS E 276 " --> pdb=" O LYS E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 284 removed outlier: 3.829A pdb=" N HIS E 280 " --> pdb=" O LYS E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 291 removed outlier: 3.644A pdb=" N ARG E 290 " --> pdb=" O GLY E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 325 removed outlier: 3.605A pdb=" N GLU E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 353 Processing helix chain 'F' and resid 4 through 9 removed outlier: 3.668A pdb=" N ASN F 9 " --> pdb=" O SER F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 15 Processing helix chain 'F' and resid 107 through 115 Processing helix chain 'F' and resid 116 through 123 Processing helix chain 'F' and resid 168 through 183 removed outlier: 3.715A pdb=" N VAL F 172 " --> pdb=" O GLY F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 229 removed outlier: 4.196A pdb=" N ASP F 212 " --> pdb=" O ILE F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 276 removed outlier: 4.393A pdb=" N VAL F 265 " --> pdb=" O GLY F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 284 Processing helix chain 'F' and resid 318 through 325 Processing helix chain 'F' and resid 339 through 353 Processing helix chain 'G' and resid 4 through 9 removed outlier: 3.723A pdb=" N ASN G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 50 removed outlier: 3.600A pdb=" N LEU G 50 " --> pdb=" O PRO G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 115 Processing helix chain 'G' and resid 116 through 123 Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.706A pdb=" N VAL G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 228 Processing helix chain 'G' and resid 262 through 276 removed outlier: 3.647A pdb=" N LYS G 276 " --> pdb=" O LYS G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 283 removed outlier: 3.521A pdb=" N HIS G 280 " --> pdb=" O LYS G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 291 Processing helix chain 'G' and resid 318 through 325 Processing helix chain 'G' and resid 339 through 353 Processing helix chain 'H' and resid 4 through 9 removed outlier: 3.757A pdb=" N ASN H 9 " --> pdb=" O SER H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 50 removed outlier: 3.951A pdb=" N LEU H 50 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 115 Processing helix chain 'H' and resid 116 through 123 Processing helix chain 'H' and resid 168 through 183 removed outlier: 3.729A pdb=" N VAL H 172 " --> pdb=" O GLY H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 229 Processing helix chain 'H' and resid 254 through 259 Processing helix chain 'H' and resid 262 through 276 removed outlier: 3.548A pdb=" N LYS H 276 " --> pdb=" O LYS H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 283 Processing helix chain 'H' and resid 287 through 292 removed outlier: 4.094A pdb=" N ARG H 291 " --> pdb=" O GLY H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 318 through 325 Processing helix chain 'H' and resid 339 through 353 Processing helix chain 'I' and resid 46 through 50 Processing helix chain 'I' and resid 107 through 115 Processing helix chain 'I' and resid 116 through 123 Processing helix chain 'I' and resid 168 through 183 removed outlier: 3.954A pdb=" N VAL I 172 " --> pdb=" O GLY I 168 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY I 183 " --> pdb=" O CYS I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 229 removed outlier: 4.407A pdb=" N GLY I 211 " --> pdb=" O GLY I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 259 Processing helix chain 'I' and resid 262 through 275 removed outlier: 4.257A pdb=" N LYS I 267 " --> pdb=" O PHE I 263 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS I 268 " --> pdb=" O GLU I 264 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 283 Processing helix chain 'I' and resid 287 through 291 removed outlier: 3.564A pdb=" N ARG I 290 " --> pdb=" O GLY I 287 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG I 291 " --> pdb=" O ASN I 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 287 through 291' Processing helix chain 'I' and resid 318 through 325 Processing helix chain 'I' and resid 339 through 353 Processing sheet with id=AA1, first strand: chain 'J' and resid 53 through 56 removed outlier: 4.169A pdb=" N TRP J 53 " --> pdb=" O LEU J 72 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N MET J 91 " --> pdb=" O GLN J 75 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE J 77 " --> pdb=" O LEU J 89 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU J 89 " --> pdb=" O ILE J 77 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE J 20 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL J 90 " --> pdb=" O ILE J 20 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU J 22 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N CYS J 92 " --> pdb=" O GLU J 22 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE J 24 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA J 94 " --> pdb=" O ILE J 24 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ILE J 26 " --> pdb=" O ALA J 94 " (cutoff:3.500A) removed outlier: 9.649A pdb=" N SER J 35 " --> pdb=" O GLY D 191 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY D 191 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N SER D 187 " --> pdb=" O THR J 39 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN D 201 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE D 189 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLU D 199 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLY D 191 " --> pdb=" O GLN D 197 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN D 197 " --> pdb=" O GLY D 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 231 through 233 removed outlier: 3.616A pdb=" N THR J 133 " --> pdb=" O SER J 233 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR J 252 " --> pdb=" O PHE J 329 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE J 329 " --> pdb=" O TYR J 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 231 through 233 removed outlier: 3.616A pdb=" N THR J 133 " --> pdb=" O SER J 233 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER J 205 " --> pdb=" O TYR J 126 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE J 128 " --> pdb=" O GLY J 203 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLY J 203 " --> pdb=" O ILE J 128 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN J 130 " --> pdb=" O GLN J 201 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN J 201 " --> pdb=" O GLN J 130 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TYR J 132 " --> pdb=" O GLU J 199 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU J 199 " --> pdb=" O TYR J 132 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU J 134 " --> pdb=" O GLN J 197 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN J 197 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLN J 197 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLY J 191 " --> pdb=" O GLN J 197 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU J 199 " --> pdb=" O ILE J 189 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE J 189 " --> pdb=" O GLU J 199 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLN J 201 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N SER J 187 " --> pdb=" O THR I 39 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLY J 191 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 9.475A pdb=" N SER I 35 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE I 20 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL I 90 " --> pdb=" O ILE I 20 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU I 22 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N CYS I 92 " --> pdb=" O GLU I 22 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE I 24 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA I 94 " --> pdb=" O ILE I 24 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N ILE I 26 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA I 76 " --> pdb=" O MET I 91 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP I 93 " --> pdb=" O PRO I 74 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR I 95 " --> pdb=" O LEU I 72 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU I 72 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TRP I 53 " --> pdb=" O LEU I 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 36 removed outlier: 6.611A pdb=" N GLU A 22 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N CYS A 92 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 24 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA A 94 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ILE A 26 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 76 " --> pdb=" O MET A 91 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP A 93 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR A 95 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU A 72 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 53 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.649A pdb=" N GLN A 201 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A 189 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU A 199 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 132 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 128 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 205 through 206 removed outlier: 3.573A pdb=" N SER A 205 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 249 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 252 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 329 " --> pdb=" O TYR A 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 56 removed outlier: 4.015A pdb=" N TRP B 53 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET B 91 " --> pdb=" O GLN B 75 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE B 77 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 89 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE B 20 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL B 90 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU B 22 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N CYS B 92 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE B 24 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 94 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE B 26 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP B 25 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N SER B 35 " --> pdb=" O GLY I 191 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLY I 191 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER I 187 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN I 201 " --> pdb=" O SER I 187 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE I 189 " --> pdb=" O GLU I 199 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU I 199 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY I 191 " --> pdb=" O GLN I 197 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN I 197 " --> pdb=" O GLY I 191 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN I 130 " --> pdb=" O PHE I 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.519A pdb=" N TYR B 252 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 329 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 307 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 233 removed outlier: 5.672A pdb=" N TYR B 126 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE B 128 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 130 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLN B 197 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLY B 191 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLU B 199 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE B 189 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN B 201 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N SER B 187 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLY B 191 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N SER C 35 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE C 20 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL C 90 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU C 22 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N CYS C 92 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE C 24 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA C 94 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ILE C 26 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 76 " --> pdb=" O MET C 91 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP C 93 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR C 95 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU C 72 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TRP C 53 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 231 through 233 removed outlier: 3.615A pdb=" N TYR C 252 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE C 329 " --> pdb=" O TYR C 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 231 through 233 removed outlier: 6.118A pdb=" N TYR C 126 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE C 128 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN C 130 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 200 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLN C 197 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY C 191 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLU C 199 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE C 189 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLN C 201 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER C 187 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLY C 191 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N SER D 35 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE D 20 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL D 90 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU D 22 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N CYS D 92 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE D 24 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA D 94 " --> pdb=" O ILE D 24 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ILE D 26 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU D 89 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE D 77 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N MET D 91 " --> pdb=" O GLN D 75 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP D 53 " --> pdb=" O LEU D 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 205 through 206 removed outlier: 3.617A pdb=" N TYR D 252 " --> pdb=" O PHE D 329 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 329 " --> pdb=" O TYR D 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.641A pdb=" N ASP E 93 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA E 76 " --> pdb=" O MET E 91 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE E 20 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL E 90 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU E 22 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS E 92 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE E 24 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA E 94 " --> pdb=" O ILE E 24 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ILE E 26 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG E 38 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N SER E 35 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLY F 191 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY F 188 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR F 126 " --> pdb=" O SER F 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.641A pdb=" N ASP E 93 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA E 76 " --> pdb=" O MET E 91 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE E 20 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL E 90 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU E 22 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS E 92 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE E 24 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA E 94 " --> pdb=" O ILE E 24 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ILE E 26 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG E 38 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N SER E 35 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLY F 191 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY F 188 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS F 249 " --> pdb=" O GLU F 129 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE F 329 " --> pdb=" O TYR F 252 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY F 307 " --> pdb=" O VAL F 317 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 186 through 191 removed outlier: 4.633A pdb=" N GLY E 188 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE E 128 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR E 126 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER E 205 " --> pdb=" O TYR E 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 186 through 191 removed outlier: 4.633A pdb=" N GLY E 188 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE E 128 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS E 249 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR E 252 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE E 329 " --> pdb=" O TYR E 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 133 through 135 Processing sheet with id=AB9, first strand: chain 'F' and resid 33 through 36 removed outlier: 6.263A pdb=" N GLU F 22 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N CYS F 92 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE F 24 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA F 94 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ILE F 26 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA F 76 " --> pdb=" O MET F 91 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP F 93 " --> pdb=" O PRO F 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 133 through 135 removed outlier: 3.505A pdb=" N THR F 133 " --> pdb=" O SER F 233 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 33 through 36 removed outlier: 6.683A pdb=" N GLU G 22 " --> pdb=" O VAL G 90 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N CYS G 92 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE G 24 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA G 94 " --> pdb=" O ILE G 24 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ILE G 26 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA G 76 " --> pdb=" O MET G 91 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP G 93 " --> pdb=" O PRO G 74 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 186 through 189 removed outlier: 6.663A pdb=" N GLN G 201 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE G 128 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER G 205 " --> pdb=" O TYR G 126 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 186 through 189 removed outlier: 6.663A pdb=" N GLN G 201 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE G 128 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE G 329 " --> pdb=" O TYR G 252 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY G 307 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL G 317 " --> pdb=" O GLY G 307 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 133 through 135 removed outlier: 3.622A pdb=" N THR G 133 " --> pdb=" O SER G 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER G 233 " --> pdb=" O THR G 133 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 33 through 36 removed outlier: 3.501A pdb=" N TYR H 23 " --> pdb=" O LYS H 36 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU H 22 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N CYS H 92 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE H 24 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA H 94 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE H 26 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR H 96 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET H 91 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA H 76 " --> pdb=" O MET H 91 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP H 93 " --> pdb=" O PRO H 74 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR H 95 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU H 72 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP H 53 " --> pdb=" O LEU H 72 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 33 through 36 removed outlier: 3.501A pdb=" N TYR H 23 " --> pdb=" O LYS H 36 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU H 22 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N CYS H 92 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE H 24 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA H 94 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE H 26 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR H 96 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 186 through 191 removed outlier: 4.371A pdb=" N GLY H 188 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN H 130 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE H 128 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR H 126 " --> pdb=" O SER H 205 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER H 205 " --> pdb=" O TYR H 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 186 through 191 removed outlier: 4.371A pdb=" N GLY H 188 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN H 130 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE H 128 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE H 329 " --> pdb=" O TYR H 252 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLY H 307 " --> pdb=" O VAL H 317 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 133 through 135 Processing sheet with id=AD2, first strand: chain 'I' and resid 125 through 127 Processing sheet with id=AD3, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.535A pdb=" N GLY I 307 " --> pdb=" O ILE I 315 " (cutoff:3.500A) 1059 hydrogen bonds defined for protein. 2961 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: 10.18 Time building geometry restraints manager: 12.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9083 1.34 - 1.46: 5169 1.46 - 1.58: 13968 1.58 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 28420 Sorted by residual: bond pdb=" N ARG A 84 " pdb=" CA ARG A 84 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.39e+00 bond pdb=" N VAL C 206 " pdb=" CA VAL C 206 " ideal model delta sigma weight residual 1.460 1.474 -0.014 1.23e-02 6.61e+03 1.26e+00 bond pdb=" N ARG J 84 " pdb=" CA ARG J 84 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.07e+00 bond pdb=" C ARG B 333 " pdb=" N PRO B 334 " ideal model delta sigma weight residual 1.332 1.345 -0.013 1.33e-02 5.65e+03 9.96e-01 bond pdb=" CA ARG B 333 " pdb=" C ARG B 333 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.26e-02 6.30e+03 9.81e-01 ... (remaining 28415 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.39: 1091 106.39 - 113.32: 14607 113.32 - 120.25: 10251 120.25 - 127.18: 12187 127.18 - 134.12: 454 Bond angle restraints: 38590 Sorted by residual: angle pdb=" C LYS F 326 " pdb=" CA LYS F 326 " pdb=" CB LYS F 326 " ideal model delta sigma weight residual 116.54 109.51 7.03 1.15e+00 7.56e-01 3.73e+01 angle pdb=" C ARG F 84 " pdb=" CA ARG F 84 " pdb=" CB ARG F 84 " ideal model delta sigma weight residual 115.79 110.14 5.65 1.19e+00 7.06e-01 2.25e+01 angle pdb=" C ARG B 84 " pdb=" CA ARG B 84 " pdb=" CB ARG B 84 " ideal model delta sigma weight residual 115.79 110.21 5.58 1.19e+00 7.06e-01 2.20e+01 angle pdb=" C ARG C 84 " pdb=" CA ARG C 84 " pdb=" CB ARG C 84 " ideal model delta sigma weight residual 115.79 110.60 5.19 1.19e+00 7.06e-01 1.90e+01 angle pdb=" CA LYS F 326 " pdb=" C LYS F 326 " pdb=" N GLY F 327 " ideal model delta sigma weight residual 119.52 116.52 3.00 7.90e-01 1.60e+00 1.44e+01 ... (remaining 38585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 15104 18.01 - 36.01: 1380 36.01 - 54.02: 210 54.02 - 72.02: 48 72.02 - 90.03: 28 Dihedral angle restraints: 16770 sinusoidal: 6730 harmonic: 10040 Sorted by residual: dihedral pdb=" CA GLU F 192 " pdb=" C GLU F 192 " pdb=" N VAL F 193 " pdb=" CA VAL F 193 " ideal model delta harmonic sigma weight residual -180.00 -160.28 -19.72 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LYS F 140 " pdb=" C LYS F 140 " pdb=" N TRP F 141 " pdb=" CA TRP F 141 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA GLU E 192 " pdb=" C GLU E 192 " pdb=" N VAL E 193 " pdb=" CA VAL E 193 " ideal model delta harmonic sigma weight residual -180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 16767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2742 0.041 - 0.082: 893 0.082 - 0.123: 333 0.123 - 0.164: 21 0.164 - 0.204: 1 Chirality restraints: 3990 Sorted by residual: chirality pdb=" CA ARG B 333 " pdb=" N ARG B 333 " pdb=" C ARG B 333 " pdb=" CB ARG B 333 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE J 102 " pdb=" N ILE J 102 " pdb=" C ILE J 102 " pdb=" CB ILE J 102 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ILE C 102 " pdb=" N ILE C 102 " pdb=" C ILE C 102 " pdb=" CB ILE C 102 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 3987 not shown) Planarity restraints: 5070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 354 " -0.029 2.00e-02 2.50e+03 2.69e-02 1.81e+01 pdb=" CG TRP F 354 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP F 354 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP F 354 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP F 354 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 354 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 354 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 354 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 354 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP F 354 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 333 " -0.053 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO B 334 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 334 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 334 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 100 " 0.050 5.00e-02 4.00e+02 7.66e-02 9.40e+00 pdb=" N PRO F 101 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO F 101 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 101 " 0.042 5.00e-02 4.00e+02 ... (remaining 5067 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 337 2.64 - 3.21: 25040 3.21 - 3.77: 42661 3.77 - 4.34: 57223 4.34 - 4.90: 96588 Nonbonded interactions: 221849 Sorted by model distance: nonbonded pdb=" OG1 THR F 39 " pdb=" OH TYR G 176 " model vdw 2.079 2.440 nonbonded pdb=" OH TYR C 176 " pdb=" OG1 THR D 39 " model vdw 2.102 2.440 nonbonded pdb=" OG SER E 233 " pdb=" OD1 ASP E 235 " model vdw 2.131 2.440 nonbonded pdb=" OH TYR A 176 " pdb=" OG1 THR G 39 " model vdw 2.144 2.440 nonbonded pdb=" OH TYR E 176 " pdb=" OG1 THR H 39 " model vdw 2.150 2.440 ... (remaining 221844 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17560 2.51 5 N 4740 2.21 5 O 5260 1.98 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: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 20.680 Check model and map are aligned: 0.420 Process input model: 71.900 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.260 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 : 0.003 0.036 28420 Z= 0.184 Angle : 0.585 8.515 38590 Z= 0.308 Chirality : 0.044 0.204 3990 Planarity : 0.006 0.079 5070 Dihedral : 14.199 90.031 10450 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3540 helix: 1.09 (0.17), residues: 1000 sheet: -1.14 (0.18), residues: 810 loop : -1.70 (0.14), residues: 1730 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 3.011 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.3962 time to fit residues: 224.9825 Evaluate side-chains 269 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 3.274 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 3.9990 chunk 265 optimal weight: 0.7980 chunk 147 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 166 optimal weight: 40.0000 chunk 204 optimal weight: 0.1980 chunk 317 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 28420 Z= 0.204 Angle : 0.568 8.999 38590 Z= 0.295 Chirality : 0.045 0.166 3990 Planarity : 0.005 0.063 5070 Dihedral : 4.186 19.516 3900 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3540 helix: 1.27 (0.17), residues: 950 sheet: -0.95 (0.18), residues: 830 loop : -1.68 (0.14), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 309 time to evaluate : 3.140 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 321 average time/residue: 0.4327 time to fit residues: 218.0211 Evaluate side-chains 276 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 262 time to evaluate : 3.077 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2427 time to fit residues: 10.7402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 264 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 318 optimal weight: 9.9990 chunk 343 optimal weight: 0.7980 chunk 283 optimal weight: 4.9990 chunk 315 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 28420 Z= 0.319 Angle : 0.626 10.637 38590 Z= 0.323 Chirality : 0.047 0.159 3990 Planarity : 0.006 0.063 5070 Dihedral : 4.542 22.690 3900 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3540 helix: 1.16 (0.17), residues: 950 sheet: -0.96 (0.18), residues: 830 loop : -1.76 (0.14), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 293 time to evaluate : 3.301 Fit side-chains outliers start: 37 outliers final: 27 residues processed: 323 average time/residue: 0.4097 time to fit residues: 208.4063 Evaluate side-chains 298 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 271 time to evaluate : 2.997 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2408 time to fit residues: 16.2889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 0.8980 chunk 239 optimal weight: 10.0000 chunk 165 optimal weight: 0.2980 chunk 35 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 213 optimal weight: 0.8980 chunk 319 optimal weight: 10.0000 chunk 338 optimal weight: 0.8980 chunk 166 optimal weight: 9.9990 chunk 302 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 28420 Z= 0.156 Angle : 0.538 8.220 38590 Z= 0.276 Chirality : 0.044 0.151 3990 Planarity : 0.005 0.064 5070 Dihedral : 4.038 18.165 3900 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3540 helix: 1.34 (0.17), residues: 950 sheet: -0.81 (0.18), residues: 830 loop : -1.62 (0.14), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 314 time to evaluate : 3.283 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 330 average time/residue: 0.4241 time to fit residues: 219.9389 Evaluate side-chains 289 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 275 time to evaluate : 3.338 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2662 time to fit residues: 11.4158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 251 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 288 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 chunk 303 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 249 HIS D 249 HIS E 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 28420 Z= 0.378 Angle : 0.668 10.582 38590 Z= 0.343 Chirality : 0.048 0.155 3990 Planarity : 0.006 0.063 5070 Dihedral : 4.725 24.267 3900 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3540 helix: 1.05 (0.17), residues: 950 sheet: -0.95 (0.18), residues: 830 loop : -1.81 (0.14), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 285 time to evaluate : 3.503 Fit side-chains outliers start: 52 outliers final: 33 residues processed: 326 average time/residue: 0.4355 time to fit residues: 224.3482 Evaluate side-chains 304 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 271 time to evaluate : 3.043 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2687 time to fit residues: 20.6743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 0.0770 chunk 304 optimal weight: 6.9990 chunk 66 optimal weight: 0.0070 chunk 198 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 338 optimal weight: 0.7980 chunk 281 optimal weight: 6.9990 chunk 156 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN E 87 ASN H 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 28420 Z= 0.148 Angle : 0.548 9.030 38590 Z= 0.278 Chirality : 0.044 0.168 3990 Planarity : 0.005 0.065 5070 Dihedral : 4.067 18.398 3900 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3540 helix: 1.31 (0.17), residues: 950 sheet: -0.78 (0.18), residues: 830 loop : -1.65 (0.14), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 307 time to evaluate : 3.489 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 317 average time/residue: 0.4297 time to fit residues: 213.5096 Evaluate side-chains 279 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 276 time to evaluate : 3.286 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2663 time to fit residues: 5.9492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 285 optimal weight: 0.9980 chunk 189 optimal weight: 0.0970 chunk 337 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 chunk 155 optimal weight: 0.2980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 28420 Z= 0.167 Angle : 0.546 8.488 38590 Z= 0.278 Chirality : 0.044 0.202 3990 Planarity : 0.005 0.069 5070 Dihedral : 4.001 17.976 3900 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3540 helix: 1.33 (0.17), residues: 950 sheet: -0.74 (0.18), residues: 830 loop : -1.61 (0.14), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 296 time to evaluate : 3.256 Fit side-chains outliers start: 27 outliers final: 18 residues processed: 314 average time/residue: 0.4278 time to fit residues: 212.2335 Evaluate side-chains 293 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 275 time to evaluate : 3.603 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2775 time to fit residues: 14.2188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 0.1980 chunk 214 optimal weight: 0.4980 chunk 229 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN H 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 28420 Z= 0.254 Angle : 0.606 9.132 38590 Z= 0.306 Chirality : 0.046 0.197 3990 Planarity : 0.005 0.065 5070 Dihedral : 4.317 22.291 3900 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.14), residues: 3540 helix: 1.08 (0.17), residues: 970 sheet: -0.79 (0.18), residues: 830 loop : -1.63 (0.14), residues: 1740 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 288 time to evaluate : 3.490 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 294 average time/residue: 0.4257 time to fit residues: 196.7400 Evaluate side-chains 276 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 270 time to evaluate : 3.384 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2728 time to fit residues: 7.5025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 20.0000 chunk 323 optimal weight: 5.9990 chunk 294 optimal weight: 8.9990 chunk 314 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 246 optimal weight: 0.0870 chunk 96 optimal weight: 20.0000 chunk 284 optimal weight: 0.1980 chunk 297 optimal weight: 0.9990 chunk 313 optimal weight: 3.9990 overall best weight: 1.0564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 28420 Z= 0.170 Angle : 0.559 8.230 38590 Z= 0.283 Chirality : 0.044 0.183 3990 Planarity : 0.005 0.067 5070 Dihedral : 4.057 20.679 3900 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3540 helix: 1.18 (0.17), residues: 970 sheet: -0.73 (0.18), residues: 830 loop : -1.54 (0.14), residues: 1740 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 292 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 303 average time/residue: 0.4504 time to fit residues: 213.4963 Evaluate side-chains 287 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 276 time to evaluate : 3.394 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2749 time to fit residues: 10.2924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 1.9990 chunk 332 optimal weight: 6.9990 chunk 202 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 348 optimal weight: 5.9990 chunk 320 optimal weight: 10.0000 chunk 277 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 41 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 28420 Z= 0.312 Angle : 0.651 11.193 38590 Z= 0.329 Chirality : 0.047 0.196 3990 Planarity : 0.005 0.066 5070 Dihedral : 4.533 23.295 3900 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3540 helix: 0.96 (0.17), residues: 970 sheet: -0.83 (0.19), residues: 830 loop : -1.68 (0.14), residues: 1740 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 282 time to evaluate : 3.271 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 290 average time/residue: 0.4376 time to fit residues: 197.2552 Evaluate side-chains 278 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 272 time to evaluate : 3.379 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2756 time to fit residues: 7.3815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 0.0370 chunk 295 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 256 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 278 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 285 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.215177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.169371 restraints weight = 34553.969| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.87 r_work: 0.4121 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 28420 Z= 0.160 Angle : 0.567 9.582 38590 Z= 0.286 Chirality : 0.044 0.165 3990 Planarity : 0.005 0.068 5070 Dihedral : 4.053 18.400 3900 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3540 helix: 1.11 (0.17), residues: 970 sheet: -0.75 (0.18), residues: 830 loop : -1.55 (0.14), residues: 1740 =============================================================================== Job complete usr+sys time: 5563.21 seconds wall clock time: 103 minutes 23.67 seconds (6203.67 seconds total)