Starting phenix.real_space_refine on Wed Mar 20 15:11:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4i_31712/03_2024/7v4i_31712.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4i_31712/03_2024/7v4i_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_31712/03_2024/7v4i_31712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4i_31712/03_2024/7v4i_31712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4i_31712/03_2024/7v4i_31712.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4i_31712/03_2024/7v4i_31712.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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-5265/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: 13.61, per 1000 atoms: 0.49 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: 10.12 Conformation dependent library (CDL) restraints added in 5.1 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: 2.98 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: 9.04 Time building geometry restraints manager: 11.10 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 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: 4.890 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: 0.030 Extract box with map and model: 19.360 Check model and map are aligned: 0.440 Set scattering table: 0.250 Process input model: 68.380 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 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 : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP F 354 HIS 0.018 0.001 HIS I 175 PHE 0.007 0.001 PHE G 329 TYR 0.025 0.001 TYR I 176 ARG 0.012 0.001 ARG G 278 *********************** 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 : 3.132 Fit side-chains revert: symmetry clash REVERT: J 16 THR cc_start: 0.8168 (t) cc_final: 0.7781 (p) REVERT: C 221 LEU cc_start: 0.7483 (tt) cc_final: 0.7238 (tt) REVERT: D 257 MET cc_start: 0.8381 (mtp) cc_final: 0.8150 (mtp) REVERT: F 31 MET cc_start: 0.6997 (tpp) cc_final: 0.6713 (tpt) REVERT: F 326 LYS cc_start: 0.7766 (mmtt) cc_final: 0.7447 (mmmt) REVERT: G 31 MET cc_start: 0.7144 (tpp) cc_final: 0.6675 (tpt) REVERT: H 216 MET cc_start: 0.7309 (mmm) cc_final: 0.7100 (mmm) REVERT: I 91 MET cc_start: 0.5793 (tpt) cc_final: 0.5559 (tpt) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.3824 time to fit residues: 216.7499 Evaluate side-chains 268 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.881 ------------------------------------------------------------------------------- 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: 0.0970 chunk 147 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 274 optimal weight: 7.9990 chunk 106 optimal weight: 0.0970 chunk 166 optimal weight: 40.0000 chunk 204 optimal weight: 0.1980 chunk 317 optimal weight: 8.9990 overall best weight: 1.0780 ------------------------------------------------------------------------------- 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: 0.7100 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28420 Z= 0.172 Angle : 0.549 8.424 38590 Z= 0.284 Chirality : 0.044 0.165 3990 Planarity : 0.005 0.063 5070 Dihedral : 4.059 18.105 3900 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.73 % Allowed : 7.99 % Favored : 91.28 % 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: -0.98 (0.14), residues: 3540 helix: 1.31 (0.17), residues: 950 sheet: -0.90 (0.18), residues: 830 loop : -1.65 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP F 354 HIS 0.012 0.001 HIS J 175 PHE 0.013 0.001 PHE F 329 TYR 0.019 0.001 TYR I 252 ARG 0.007 0.000 ARG J 258 *********************** 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 343 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 322 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 49 LYS cc_start: 0.8935 (mttt) cc_final: 0.8484 (mttp) REVERT: J 255 LYS cc_start: 0.7551 (tptt) cc_final: 0.7137 (tptp) REVERT: A 31 MET cc_start: 0.7391 (tpp) cc_final: 0.7128 (tpt) REVERT: A 257 MET cc_start: 0.5883 (OUTLIER) cc_final: 0.5353 (mtm) REVERT: A 306 TRP cc_start: 0.7631 (p-90) cc_final: 0.7293 (p-90) REVERT: B 125 TRP cc_start: 0.5725 (m-10) cc_final: 0.5491 (m-10) REVERT: B 145 TRP cc_start: 0.7997 (t-100) cc_final: 0.7413 (t-100) REVERT: C 316 ARG cc_start: 0.6853 (ttp80) cc_final: 0.6208 (tmm-80) REVERT: D 213 GLN cc_start: 0.6137 (OUTLIER) cc_final: 0.4621 (mp-120) REVERT: D 252 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.7163 (t80) REVERT: E 31 MET cc_start: 0.7569 (tpp) cc_final: 0.7189 (tpt) REVERT: H 216 MET cc_start: 0.7318 (mmm) cc_final: 0.7078 (mmm) REVERT: I 91 MET cc_start: 0.5879 (tpt) cc_final: 0.5531 (tpt) REVERT: I 129 GLU cc_start: 0.5829 (mt-10) cc_final: 0.5260 (mt-10) REVERT: I 175 HIS cc_start: 0.7567 (t-90) cc_final: 0.7278 (t70) outliers start: 21 outliers final: 10 residues processed: 334 average time/residue: 0.4017 time to fit residues: 211.3644 Evaluate side-chains 286 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 273 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain I residue 346 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 318 optimal weight: 10.0000 chunk 343 optimal weight: 0.0170 chunk 283 optimal weight: 5.9990 chunk 315 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 overall best weight: 2.9624 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 28420 Z= 0.308 Angle : 0.616 10.460 38590 Z= 0.318 Chirality : 0.046 0.156 3990 Planarity : 0.006 0.062 5070 Dihedral : 4.480 23.607 3900 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.59 % Allowed : 11.38 % Favored : 87.02 % 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: -1.08 (0.14), residues: 3540 helix: 1.21 (0.17), residues: 950 sheet: -0.91 (0.18), residues: 830 loop : -1.74 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP F 354 HIS 0.011 0.001 HIS B 175 PHE 0.018 0.002 PHE F 329 TYR 0.028 0.002 TYR C 176 ARG 0.008 0.000 ARG A 278 *********************** 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 339 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 293 time to evaluate : 3.199 Fit side-chains revert: symmetry clash REVERT: A 257 MET cc_start: 0.5907 (OUTLIER) cc_final: 0.5383 (mtm) REVERT: A 286 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6946 (pm20) REVERT: B 289 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7118 (pp20) REVERT: C 125 TRP cc_start: 0.5688 (m-10) cc_final: 0.5422 (m-10) REVERT: C 222 GLU cc_start: 0.7780 (tt0) cc_final: 0.7297 (tt0) REVERT: D 107 ARG cc_start: 0.5331 (ttt180) cc_final: 0.4829 (ttt180) REVERT: D 213 GLN cc_start: 0.6315 (OUTLIER) cc_final: 0.5109 (mp-120) REVERT: E 346 MET cc_start: 0.7133 (mtp) cc_final: 0.6842 (mtp) REVERT: H 1 MET cc_start: 0.3394 (pmm) cc_final: 0.1546 (ptt) REVERT: H 286 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6918 (pm20) REVERT: I 91 MET cc_start: 0.5884 (tpt) cc_final: 0.5562 (tpt) REVERT: I 129 GLU cc_start: 0.5920 (mt-10) cc_final: 0.5249 (mt-10) REVERT: I 213 GLN cc_start: 0.6438 (OUTLIER) cc_final: 0.4791 (mp-120) outliers start: 46 outliers final: 33 residues processed: 324 average time/residue: 0.4078 time to fit residues: 207.1140 Evaluate side-chains 311 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 274 time to evaluate : 3.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 213 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 319 optimal weight: 0.9990 chunk 338 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 302 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** B 41 ASN D 213 GLN ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 28420 Z= 0.305 Angle : 0.613 10.346 38590 Z= 0.316 Chirality : 0.046 0.159 3990 Planarity : 0.005 0.064 5070 Dihedral : 4.558 24.623 3900 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.32 % Allowed : 13.08 % Favored : 84.60 % 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: 1.14 (0.17), residues: 950 sheet: -0.94 (0.18), residues: 830 loop : -1.77 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP F 354 HIS 0.012 0.001 HIS B 175 PHE 0.018 0.002 PHE F 329 TYR 0.020 0.002 TYR G 252 ARG 0.009 0.000 ARG A 278 *********************** 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 358 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 291 time to evaluate : 3.092 Fit side-chains REVERT: A 286 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6892 (pm20) REVERT: C 125 TRP cc_start: 0.5722 (m-10) cc_final: 0.5478 (m-10) REVERT: C 222 GLU cc_start: 0.7804 (tt0) cc_final: 0.7308 (tt0) REVERT: C 316 ARG cc_start: 0.6797 (ttp80) cc_final: 0.6483 (tmm-80) REVERT: D 107 ARG cc_start: 0.5285 (ttt180) cc_final: 0.4719 (ttt180) REVERT: D 129 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6221 (pt0) REVERT: H 242 ASP cc_start: 0.7053 (t0) cc_final: 0.6835 (t0) REVERT: H 286 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6817 (pm20) REVERT: I 91 MET cc_start: 0.5799 (tpt) cc_final: 0.5514 (tpt) REVERT: I 213 GLN cc_start: 0.6393 (OUTLIER) cc_final: 0.4778 (mp-120) outliers start: 67 outliers final: 49 residues processed: 339 average time/residue: 0.4054 time to fit residues: 215.6899 Evaluate side-chains 329 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 278 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 249 HIS Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 306 TRP Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 233 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 6.9990 chunk 192 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 251 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 288 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 303 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 D 213 GLN ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28420 Z= 0.258 Angle : 0.599 9.958 38590 Z= 0.307 Chirality : 0.045 0.188 3990 Planarity : 0.005 0.064 5070 Dihedral : 4.457 23.488 3900 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.70 % Allowed : 14.15 % Favored : 83.15 % 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: -1.11 (0.14), residues: 3540 helix: 1.16 (0.17), residues: 950 sheet: -0.91 (0.18), residues: 830 loop : -1.75 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP F 354 HIS 0.012 0.001 HIS B 175 PHE 0.015 0.002 PHE F 329 TYR 0.022 0.001 TYR G 252 ARG 0.009 0.000 ARG E 278 *********************** 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 370 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 292 time to evaluate : 3.395 Fit side-chains revert: symmetry clash REVERT: A 131 GLU cc_start: 0.7766 (pm20) cc_final: 0.7563 (pm20) REVERT: A 286 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6776 (pm20) REVERT: B 123 GLU cc_start: 0.8242 (mp0) cc_final: 0.8020 (mp0) REVERT: B 125 TRP cc_start: 0.5657 (m-10) cc_final: 0.5400 (m-10) REVERT: C 125 TRP cc_start: 0.5705 (m-10) cc_final: 0.5456 (m-10) REVERT: C 222 GLU cc_start: 0.7770 (tt0) cc_final: 0.7309 (tt0) REVERT: C 316 ARG cc_start: 0.6815 (ttp80) cc_final: 0.6486 (tmm-80) REVERT: D 107 ARG cc_start: 0.5351 (OUTLIER) cc_final: 0.4679 (ttt180) REVERT: D 125 TRP cc_start: 0.5305 (m-10) cc_final: 0.5083 (m-10) REVERT: D 129 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.6077 (pt0) REVERT: D 213 GLN cc_start: 0.6387 (OUTLIER) cc_final: 0.5236 (mp-120) REVERT: E 252 TYR cc_start: 0.7357 (t80) cc_final: 0.7153 (t80) REVERT: E 257 MET cc_start: 0.5170 (mtp) cc_final: 0.4227 (mtp) REVERT: F 131 GLU cc_start: 0.7625 (pm20) cc_final: 0.6970 (pm20) REVERT: F 317 VAL cc_start: 0.7936 (t) cc_final: 0.7639 (p) REVERT: H 242 ASP cc_start: 0.7001 (t0) cc_final: 0.6670 (t0) REVERT: H 286 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6799 (pm20) REVERT: I 91 MET cc_start: 0.5764 (tpt) cc_final: 0.5515 (tpt) REVERT: I 213 GLN cc_start: 0.6329 (OUTLIER) cc_final: 0.4722 (mp-120) outliers start: 78 outliers final: 55 residues processed: 352 average time/residue: 0.3971 time to fit residues: 222.1593 Evaluate side-chains 335 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 276 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 249 HIS Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 249 HIS Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 338 MET Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 306 TRP Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 230 VAL Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 346 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 2.9990 chunk 304 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 338 optimal weight: 0.9990 chunk 281 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 28 optimal weight: 0.0370 chunk 112 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 overall best weight: 0.9464 ------------------------------------------------------------------------------- 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 D 213 GLN E 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.1641 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= 0.163 Angle : 0.550 9.431 38590 Z= 0.279 Chirality : 0.044 0.166 3990 Planarity : 0.005 0.064 5070 Dihedral : 4.060 19.534 3900 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.08 % Allowed : 15.47 % Favored : 82.46 % 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: -0.94 (0.14), residues: 3540 helix: 1.30 (0.17), residues: 950 sheet: -0.80 (0.18), residues: 830 loop : -1.65 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.001 TRP F 354 HIS 0.012 0.001 HIS B 175 PHE 0.016 0.001 PHE C 108 TYR 0.025 0.001 TYR G 252 ARG 0.009 0.000 ARG G 278 *********************** 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 367 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 307 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 49 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8229 (mttp) REVERT: J 125 TRP cc_start: 0.5381 (m-10) cc_final: 0.5153 (m-10) REVERT: A 6 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6563 (m-30) REVERT: A 31 MET cc_start: 0.7280 (tpp) cc_final: 0.6832 (tpt) REVERT: A 286 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6696 (pm20) REVERT: C 12 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7607 (pp) REVERT: C 125 TRP cc_start: 0.5732 (m-10) cc_final: 0.5481 (m-10) REVERT: C 222 GLU cc_start: 0.7753 (tt0) cc_final: 0.7278 (tt0) REVERT: D 107 ARG cc_start: 0.5288 (OUTLIER) cc_final: 0.4997 (ttt180) REVERT: D 129 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.6128 (pt0) REVERT: E 31 MET cc_start: 0.7458 (tpp) cc_final: 0.6968 (tpt) REVERT: E 257 MET cc_start: 0.5067 (mtp) cc_final: 0.4018 (mtp) REVERT: F 31 MET cc_start: 0.7186 (tpp) cc_final: 0.6763 (tpt) REVERT: G 31 MET cc_start: 0.7237 (tpp) cc_final: 0.6818 (tpt) REVERT: H 31 MET cc_start: 0.7406 (tpp) cc_final: 0.6969 (tpt) REVERT: H 242 ASP cc_start: 0.6916 (t0) cc_final: 0.6593 (t0) REVERT: H 286 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6703 (pm20) REVERT: I 91 MET cc_start: 0.5747 (tpt) cc_final: 0.5502 (tpt) REVERT: I 123 GLU cc_start: 0.8446 (mp0) cc_final: 0.8079 (mp0) REVERT: I 213 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.4715 (mp-120) outliers start: 60 outliers final: 41 residues processed: 350 average time/residue: 0.3916 time to fit residues: 214.4134 Evaluate side-chains 325 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 279 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 249 HIS Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 249 HIS Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 306 TRP Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 230 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 285 optimal weight: 0.9990 chunk 189 optimal weight: 0.0010 chunk 337 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 overall best weight: 1.5592 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1703 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= 0.197 Angle : 0.563 8.643 38590 Z= 0.286 Chirality : 0.044 0.210 3990 Planarity : 0.005 0.063 5070 Dihedral : 4.087 20.246 3900 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.15 % Allowed : 16.51 % Favored : 81.35 % 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: -0.93 (0.14), residues: 3540 helix: 1.29 (0.17), residues: 950 sheet: -0.77 (0.18), residues: 830 loop : -1.64 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP F 354 HIS 0.013 0.001 HIS D 175 PHE 0.013 0.001 PHE F 329 TYR 0.021 0.001 TYR G 252 ARG 0.010 0.000 ARG G 278 *********************** 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 352 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 290 time to evaluate : 3.290 Fit side-chains revert: symmetry clash REVERT: J 49 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8232 (mttp) REVERT: J 125 TRP cc_start: 0.5409 (m-10) cc_final: 0.5149 (m-10) REVERT: J 284 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.7300 (m-10) REVERT: A 6 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6558 (m-30) REVERT: A 286 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6701 (pm20) REVERT: B 125 TRP cc_start: 0.5539 (m-10) cc_final: 0.5323 (m-10) REVERT: C 12 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7637 (pp) REVERT: C 125 TRP cc_start: 0.5747 (m-10) cc_final: 0.5490 (m-10) REVERT: C 222 GLU cc_start: 0.7724 (tt0) cc_final: 0.7276 (tt0) REVERT: C 316 ARG cc_start: 0.6853 (ttp80) cc_final: 0.6514 (tmm-80) REVERT: D 107 ARG cc_start: 0.5314 (OUTLIER) cc_final: 0.4954 (ttt180) REVERT: D 125 TRP cc_start: 0.5433 (m-10) cc_final: 0.5201 (m-10) REVERT: D 129 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.6086 (pt0) REVERT: D 213 GLN cc_start: 0.6225 (OUTLIER) cc_final: 0.5196 (mp10) REVERT: E 257 MET cc_start: 0.5081 (mtp) cc_final: 0.4235 (mtp) REVERT: E 326 LYS cc_start: 0.7874 (pttt) cc_final: 0.7321 (ptpt) REVERT: F 131 GLU cc_start: 0.7530 (pm20) cc_final: 0.7312 (pm20) REVERT: F 317 VAL cc_start: 0.7769 (t) cc_final: 0.7467 (p) REVERT: H 31 MET cc_start: 0.7444 (tpp) cc_final: 0.6846 (tpt) REVERT: H 242 ASP cc_start: 0.6962 (t0) cc_final: 0.6632 (t0) REVERT: H 286 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6736 (pm20) REVERT: I 91 MET cc_start: 0.5748 (tpt) cc_final: 0.5508 (tpt) REVERT: I 123 GLU cc_start: 0.8440 (mp0) cc_final: 0.8074 (mp0) REVERT: I 213 GLN cc_start: 0.6296 (OUTLIER) cc_final: 0.4750 (mp-120) outliers start: 62 outliers final: 48 residues processed: 340 average time/residue: 0.4039 time to fit residues: 216.1483 Evaluate side-chains 338 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 283 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 249 HIS Chi-restraints excluded: chain J residue 284 TYR Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 249 HIS Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 230 VAL Chi-restraints excluded: chain I residue 233 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 66 optimal weight: 0.0040 chunk 65 optimal weight: 2.9990 chunk 214 optimal weight: 0.1980 chunk 229 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 chunk 265 optimal weight: 6.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- 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 D 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1795 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= 0.162 Angle : 0.551 8.957 38590 Z= 0.278 Chirality : 0.044 0.192 3990 Planarity : 0.005 0.063 5070 Dihedral : 3.918 18.431 3900 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.42 % Allowed : 16.26 % Favored : 81.31 % 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: -0.86 (0.14), residues: 3540 helix: 1.35 (0.17), residues: 950 sheet: -0.74 (0.18), residues: 830 loop : -1.60 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP F 354 HIS 0.014 0.001 HIS D 175 PHE 0.012 0.001 PHE H 234 TYR 0.019 0.001 TYR I 132 ARG 0.011 0.000 ARG A 278 *********************** 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 368 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 298 time to evaluate : 3.289 Fit side-chains revert: symmetry clash REVERT: J 284 TYR cc_start: 0.7592 (OUTLIER) cc_final: 0.7315 (m-80) REVERT: A 10 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7578 (tt) REVERT: A 31 MET cc_start: 0.7259 (tpp) cc_final: 0.6702 (tpt) REVERT: A 286 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6628 (pm20) REVERT: A 319 ARG cc_start: 0.7499 (mtp85) cc_final: 0.6609 (mtp85) REVERT: B 125 TRP cc_start: 0.5500 (m-10) cc_final: 0.5275 (m-10) REVERT: B 161 ILE cc_start: 0.8387 (pt) cc_final: 0.8101 (pt) REVERT: C 12 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7607 (pp) REVERT: C 125 TRP cc_start: 0.5757 (m-10) cc_final: 0.5495 (m-10) REVERT: C 222 GLU cc_start: 0.7709 (tt0) cc_final: 0.7199 (tt0) REVERT: C 284 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.7308 (m-10) REVERT: C 316 ARG cc_start: 0.6884 (ttp80) cc_final: 0.6546 (tmm-80) REVERT: D 107 ARG cc_start: 0.5205 (OUTLIER) cc_final: 0.4976 (ttt180) REVERT: D 129 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.6118 (pt0) REVERT: D 213 GLN cc_start: 0.6332 (OUTLIER) cc_final: 0.4916 (mp-120) REVERT: E 31 MET cc_start: 0.7458 (tpp) cc_final: 0.6885 (tpt) REVERT: E 257 MET cc_start: 0.5009 (mtp) cc_final: 0.4204 (mtp) REVERT: E 326 LYS cc_start: 0.7896 (pttt) cc_final: 0.7266 (ptpt) REVERT: F 31 MET cc_start: 0.7127 (tpp) cc_final: 0.6737 (tpt) REVERT: F 131 GLU cc_start: 0.7484 (pm20) cc_final: 0.7242 (pm20) REVERT: F 317 VAL cc_start: 0.7713 (t) cc_final: 0.7399 (p) REVERT: G 31 MET cc_start: 0.7074 (tpp) cc_final: 0.6852 (tpt) REVERT: H 31 MET cc_start: 0.7395 (tpp) cc_final: 0.6935 (tpt) REVERT: H 242 ASP cc_start: 0.6968 (t0) cc_final: 0.6690 (t0) REVERT: H 257 MET cc_start: 0.6601 (mtt) cc_final: 0.6301 (mtt) REVERT: H 286 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6619 (pm20) REVERT: I 91 MET cc_start: 0.5714 (tpt) cc_final: 0.5491 (tpt) REVERT: I 123 GLU cc_start: 0.8465 (mp0) cc_final: 0.8114 (mp0) REVERT: I 213 GLN cc_start: 0.6276 (OUTLIER) cc_final: 0.4761 (mp-120) outliers start: 70 outliers final: 51 residues processed: 355 average time/residue: 0.3887 time to fit residues: 219.0764 Evaluate side-chains 338 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 279 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 249 HIS Chi-restraints excluded: chain J residue 284 TYR Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 284 TYR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 249 HIS Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 306 TRP Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 230 VAL 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: 7.9990 chunk 294 optimal weight: 8.9990 chunk 314 optimal weight: 5.9990 chunk 189 optimal weight: 0.1980 chunk 136 optimal weight: 0.0060 chunk 246 optimal weight: 0.1980 chunk 96 optimal weight: 20.0000 chunk 284 optimal weight: 5.9990 chunk 297 optimal weight: 2.9990 chunk 313 optimal weight: 0.9980 overall best weight: 0.8798 ------------------------------------------------------------------------------- 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** D 213 GLN ** I 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1860 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 : 0.552 11.158 38590 Z= 0.278 Chirality : 0.044 0.180 3990 Planarity : 0.005 0.063 5070 Dihedral : 3.846 18.751 3900 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.25 % Allowed : 16.71 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3540 helix: 1.36 (0.17), residues: 950 sheet: -0.71 (0.18), residues: 830 loop : -1.56 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP F 354 HIS 0.014 0.001 HIS D 175 PHE 0.012 0.001 PHE H 234 TYR 0.027 0.001 TYR G 252 ARG 0.012 0.000 ARG F 278 *********************** 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 360 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 295 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 173 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: J 284 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.7233 (m-80) REVERT: A 10 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7572 (tt) REVERT: A 31 MET cc_start: 0.7289 (tpp) cc_final: 0.6765 (tpt) REVERT: A 286 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6626 (pm20) REVERT: B 125 TRP cc_start: 0.5464 (m-10) cc_final: 0.5218 (m-10) REVERT: B 161 ILE cc_start: 0.8383 (pt) cc_final: 0.8098 (pt) REVERT: C 12 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7599 (pp) REVERT: C 125 TRP cc_start: 0.5763 (m-10) cc_final: 0.5507 (m-10) REVERT: C 222 GLU cc_start: 0.7690 (tt0) cc_final: 0.7180 (tt0) REVERT: C 284 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.7278 (m-10) REVERT: C 316 ARG cc_start: 0.6905 (ttp80) cc_final: 0.6554 (tmm-80) REVERT: D 107 ARG cc_start: 0.5236 (OUTLIER) cc_final: 0.4564 (ttt180) REVERT: D 129 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6136 (pt0) REVERT: E 31 MET cc_start: 0.7464 (tpp) cc_final: 0.6928 (tpt) REVERT: E 326 LYS cc_start: 0.7867 (pttt) cc_final: 0.7244 (ptpt) REVERT: F 31 MET cc_start: 0.7199 (tpp) cc_final: 0.6824 (tpt) REVERT: F 131 GLU cc_start: 0.7480 (pm20) cc_final: 0.6830 (pm20) REVERT: G 31 MET cc_start: 0.7096 (tpp) cc_final: 0.6889 (tpt) REVERT: G 216 MET cc_start: 0.7215 (mmm) cc_final: 0.7008 (mmm) REVERT: H 31 MET cc_start: 0.7395 (tpp) cc_final: 0.7001 (tpt) REVERT: H 123 GLU cc_start: 0.7992 (mp0) cc_final: 0.7246 (mp0) REVERT: H 242 ASP cc_start: 0.6931 (t0) cc_final: 0.6663 (t0) REVERT: H 257 MET cc_start: 0.6609 (mtt) cc_final: 0.6310 (mtt) REVERT: H 286 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6605 (pm20) REVERT: I 91 MET cc_start: 0.5716 (tpt) cc_final: 0.5479 (tpt) REVERT: I 123 GLU cc_start: 0.8453 (mp0) cc_final: 0.8125 (mp0) REVERT: I 213 GLN cc_start: 0.6285 (OUTLIER) cc_final: 0.4768 (mp-120) outliers start: 65 outliers final: 53 residues processed: 348 average time/residue: 0.3980 time to fit residues: 217.4553 Evaluate side-chains 338 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 277 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 249 HIS Chi-restraints excluded: chain J residue 284 TYR Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 284 TYR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 249 HIS Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 306 TRP Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 230 VAL Chi-restraints excluded: chain I residue 233 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 5.9990 chunk 332 optimal weight: 6.9990 chunk 202 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 348 optimal weight: 7.9990 chunk 320 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 214 optimal weight: 0.0070 chunk 170 optimal weight: 0.2980 overall best weight: 1.2200 ------------------------------------------------------------------------------- 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** D 213 GLN H 249 HIS ** I 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1901 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= 0.177 Angle : 0.559 11.112 38590 Z= 0.282 Chirality : 0.044 0.195 3990 Planarity : 0.005 0.065 5070 Dihedral : 3.896 18.627 3900 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.32 % Allowed : 16.64 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3540 helix: 1.35 (0.17), residues: 950 sheet: -0.72 (0.18), residues: 830 loop : -1.57 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP F 354 HIS 0.015 0.001 HIS D 175 PHE 0.012 0.001 PHE F 329 TYR 0.040 0.001 TYR A 252 ARG 0.012 0.000 ARG G 278 ********************** 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 353 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 286 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 125 TRP cc_start: 0.5348 (m-10) cc_final: 0.5074 (m-10) REVERT: J 173 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.8056 (m-30) REVERT: J 284 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.7256 (m-80) REVERT: A 10 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7579 (tt) REVERT: A 31 MET cc_start: 0.7328 (tpp) cc_final: 0.6752 (tpt) REVERT: A 286 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6622 (pm20) REVERT: A 319 ARG cc_start: 0.7490 (mtp85) cc_final: 0.7205 (mtp85) REVERT: B 125 TRP cc_start: 0.5453 (m-10) cc_final: 0.5211 (m-10) REVERT: B 161 ILE cc_start: 0.8404 (pt) cc_final: 0.8124 (pt) REVERT: C 12 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7609 (pp) REVERT: C 125 TRP cc_start: 0.5765 (m-10) cc_final: 0.5501 (m-10) REVERT: C 222 GLU cc_start: 0.7696 (tt0) cc_final: 0.7177 (tt0) REVERT: C 284 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.7247 (m-10) REVERT: C 316 ARG cc_start: 0.6927 (ttp80) cc_final: 0.6577 (tmm-80) REVERT: D 129 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6091 (pt0) REVERT: D 213 GLN cc_start: 0.6578 (OUTLIER) cc_final: 0.5729 (mt0) REVERT: E 31 MET cc_start: 0.7472 (tpp) cc_final: 0.6928 (tpt) REVERT: E 326 LYS cc_start: 0.7845 (pttt) cc_final: 0.7245 (ptpt) REVERT: F 31 MET cc_start: 0.7177 (tpp) cc_final: 0.6781 (tpt) REVERT: F 131 GLU cc_start: 0.7490 (pm20) cc_final: 0.7272 (pm20) REVERT: G 31 MET cc_start: 0.7140 (tpp) cc_final: 0.6754 (tpt) REVERT: G 216 MET cc_start: 0.7260 (mmm) cc_final: 0.7049 (mmm) REVERT: H 31 MET cc_start: 0.7402 (tpp) cc_final: 0.7017 (tpt) REVERT: H 242 ASP cc_start: 0.6966 (t0) cc_final: 0.6699 (t0) REVERT: H 257 MET cc_start: 0.6615 (mtt) cc_final: 0.6318 (mtt) REVERT: H 286 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6621 (pm20) REVERT: I 91 MET cc_start: 0.5731 (tpt) cc_final: 0.5431 (tpt) REVERT: I 123 GLU cc_start: 0.8457 (mp0) cc_final: 0.8122 (mp0) REVERT: I 213 GLN cc_start: 0.6306 (OUTLIER) cc_final: 0.4806 (mp-120) outliers start: 67 outliers final: 55 residues processed: 341 average time/residue: 0.3952 time to fit residues: 211.8522 Evaluate side-chains 342 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 279 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 249 HIS Chi-restraints excluded: chain J residue 284 TYR Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 284 TYR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 249 HIS Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 306 TRP Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 53 TRP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 230 VAL Chi-restraints excluded: chain I residue 233 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 3.9990 chunk 295 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 285 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 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** B 41 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS D 75 GLN ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.212493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.167144 restraints weight = 34704.299| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 3.12 r_work: 0.4069 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1916 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= 0.201 Angle : 0.572 11.041 38590 Z= 0.289 Chirality : 0.045 0.216 3990 Planarity : 0.005 0.066 5070 Dihedral : 3.984 19.413 3900 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.35 % Allowed : 16.71 % Favored : 80.93 % 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: -0.87 (0.14), residues: 3540 helix: 1.29 (0.17), residues: 950 sheet: -0.73 (0.18), residues: 830 loop : -1.57 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP F 354 HIS 0.017 0.001 HIS D 175 PHE 0.013 0.001 PHE F 329 TYR 0.034 0.001 TYR A 252 ARG 0.012 0.000 ARG A 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5743.60 seconds wall clock time: 105 minutes 11.20 seconds (6311.20 seconds total)