Starting phenix.real_space_refine on Mon Mar 25 14:56:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5adx_2856/03_2024/5adx_2856_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5adx_2856/03_2024/5adx_2856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5adx_2856/03_2024/5adx_2856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5adx_2856/03_2024/5adx_2856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5adx_2856/03_2024/5adx_2856_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5adx_2856/03_2024/5adx_2856_neut.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 138 5.16 5 C 30953 2.51 5 N 8910 2.21 5 O 9391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49392 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2957 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "B" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2957 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "C" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2957 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "D" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2957 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "E" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2957 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "F" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2957 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "G" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2957 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "H" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2957 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "J" Number of atoms: 2879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2879 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 344} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2242 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 264} Chain: "L" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2137 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 258} Chain: "M" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 2855 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 571} Link IDs: {'CIS': 1, 'TRANS': 569} Chain breaks: 5 Unresolved non-hydrogen bonds: 1142 Unresolved non-hydrogen angles: 1713 Unresolved non-hydrogen dihedrals: 571 Planarities with less than four sites: {'UNK:plan-1': 571} Unresolved non-hydrogen planarities: 571 Chain: "N" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 3010 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 602} Link IDs: {'CIS': 2, 'TRANS': 599} Chain breaks: 5 Unresolved non-hydrogen bonds: 1204 Unresolved non-hydrogen angles: 1806 Unresolved non-hydrogen dihedrals: 602 Planarities with less than four sites: {'UNK:plan-1': 602} Unresolved non-hydrogen planarities: 602 Chain: "O" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 323 Classifications: {'peptide': 65} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 63} Link IDs: {'TRANS': 64} Chain breaks: 3 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 65} Unresolved non-hydrogen planarities: 65 Chain: "P" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 323 Classifications: {'peptide': 65} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 63} Link IDs: {'TRANS': 64} Chain breaks: 3 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 65} Unresolved non-hydrogen planarities: 65 Chain: "Q" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 435 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'TRANS': 86} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'UNK:plan-1': 87} Unresolved non-hydrogen planarities: 87 Chain: "R" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 435 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'TRANS': 86} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'UNK:plan-1': 87} Unresolved non-hydrogen planarities: 87 Chain: "U" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 831 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PTRANS': 10, 'TRANS': 158} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 609 Unresolved non-hydrogen dihedrals: 378 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 12, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 227 Chain: "V" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 812 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 10, 'TRANS': 154} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 394 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 8, 'HIS:plan': 4, 'PHE:plan': 9, 'GLU:plan': 6, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 228 Chain: "Y" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1215 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 243} Link IDs: {'TRANS': 242} Chain breaks: 12 Unresolved non-hydrogen bonds: 486 Unresolved non-hydrogen angles: 729 Unresolved non-hydrogen dihedrals: 243 Planarities with less than four sites: {'UNK:plan-1': 243} Unresolved non-hydrogen planarities: 243 Chain: "Z" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 2095 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 419} Link IDs: {'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 838 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 419 Planarities with less than four sites: {'UNK:plan-1': 419} Unresolved non-hydrogen planarities: 419 Chain: "a" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 341 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "b" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 517 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "c" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 179 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 3, 'TRANS': 27} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'UNK:plan-1': 11, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 Chain: "d" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 127 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 16} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "z" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 2095 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 419} Link IDs: {'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 838 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 419 Planarities with less than four sites: {'UNK:plan-1': 419} Unresolved non-hydrogen planarities: 419 Time building chain proxies: 27.02, per 1000 atoms: 0.55 Number of scatterers: 49392 At special positions: 0 Unit cell: (284.08, 215.74, 328.3, 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 138 16.00 O 9391 8.00 N 8910 7.00 C 30953 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: 20.86 Conformation dependent library (CDL) restraints added in 7.2 seconds 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13916 Finding SS restraints... Secondary structure from input PDB file: 244 helices and 68 sheets defined 90.1% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.38 Creating SS restraints... Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 82 through 95 removed outlier: 3.581A pdb=" N MET A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 removed outlier: 3.683A pdb=" N ARG A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 151 removed outlier: 3.902A pdb=" N LEU A 145 " --> pdb=" O MET A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 202 Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.871A pdb=" N VAL A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 286 removed outlier: 3.862A pdb=" N SER A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.729A pdb=" N THR A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 338 through 350 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.735A pdb=" N MET A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 357' Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 367 through 376 removed outlier: 4.000A pdb=" N ILE A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 82 through 95 removed outlier: 3.532A pdb=" N MET B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 141 through 151 removed outlier: 3.994A pdb=" N LEU B 145 " --> pdb=" O MET B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 202 Processing helix chain 'B' and resid 210 through 221 removed outlier: 4.076A pdb=" N VAL B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 286 removed outlier: 3.517A pdb=" N SER B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.641A pdb=" N THR B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 360 through 366 Processing helix chain 'B' and resid 367 through 376 removed outlier: 3.935A pdb=" N ILE B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 82 through 95 removed outlier: 3.514A pdb=" N MET C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 131 removed outlier: 3.558A pdb=" N ARG C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 151 removed outlier: 3.893A pdb=" N LEU C 145 " --> pdb=" O MET C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.631A pdb=" N ILE C 180 " --> pdb=" O PRO C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 202 Processing helix chain 'C' and resid 207 through 221 removed outlier: 3.828A pdb=" N GLU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE C 213 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 286 removed outlier: 3.692A pdb=" N SER C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 290 through 297 Processing helix chain 'C' and resid 303 through 307 removed outlier: 4.052A pdb=" N PHE C 307 " --> pdb=" O SER C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.530A pdb=" N ARG C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 350 removed outlier: 3.617A pdb=" N ILE C 342 " --> pdb=" O TYR C 338 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 343 " --> pdb=" O SER C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.529A pdb=" N MET C 356 " --> pdb=" O THR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 366 Processing helix chain 'C' and resid 367 through 376 removed outlier: 3.995A pdb=" N ILE C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE C 376 " --> pdb=" O HIS C 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.532A pdb=" N MET D 86 " --> pdb=" O ASP D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 130 Processing helix chain 'D' and resid 141 through 151 removed outlier: 3.813A pdb=" N LEU D 145 " --> pdb=" O MET D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'D' and resid 186 through 202 Processing helix chain 'D' and resid 207 through 221 removed outlier: 3.938A pdb=" N GLU D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE D 213 " --> pdb=" O SER D 209 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL D 214 " --> pdb=" O GLU D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.720A pdb=" N THR D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 322 Processing helix chain 'D' and resid 338 through 350 Processing helix chain 'D' and resid 352 through 357 removed outlier: 3.557A pdb=" N TRP D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 366 Processing helix chain 'D' and resid 367 through 376 removed outlier: 4.011A pdb=" N ILE D 371 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE D 376 " --> pdb=" O HIS D 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 65 Processing helix chain 'E' and resid 82 through 95 removed outlier: 3.671A pdb=" N MET E 86 " --> pdb=" O ASP E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 131 Processing helix chain 'E' and resid 142 through 151 Processing helix chain 'E' and resid 186 through 202 Processing helix chain 'E' and resid 210 through 221 removed outlier: 3.936A pdb=" N VAL E 214 " --> pdb=" O GLU E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 286 removed outlier: 3.526A pdb=" N SER E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 290 through 297 Processing helix chain 'E' and resid 309 through 322 Processing helix chain 'E' and resid 338 through 350 Processing helix chain 'E' and resid 352 through 357 removed outlier: 3.503A pdb=" N MET E 356 " --> pdb=" O THR E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 366 Processing helix chain 'E' and resid 367 through 376 removed outlier: 3.987A pdb=" N ILE E 371 " --> pdb=" O GLY E 367 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE E 376 " --> pdb=" O HIS E 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 65 Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.536A pdb=" N MET F 86 " --> pdb=" O ASP F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 131 Processing helix chain 'F' and resid 141 through 151 removed outlier: 3.709A pdb=" N LEU F 145 " --> pdb=" O MET F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 Processing helix chain 'F' and resid 207 through 221 removed outlier: 3.941A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE F 213 " --> pdb=" O SER F 209 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL F 214 " --> pdb=" O GLU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 253 through 258 Processing helix chain 'F' and resid 259 through 264 removed outlier: 4.198A pdb=" N PHE F 263 " --> pdb=" O PRO F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 286 removed outlier: 3.593A pdb=" N SER F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 290 through 297 Processing helix chain 'F' and resid 302 through 306 removed outlier: 3.804A pdb=" N THR F 305 " --> pdb=" O GLY F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 322 Processing helix chain 'F' and resid 338 through 350 Processing helix chain 'F' and resid 352 through 357 removed outlier: 3.505A pdb=" N TRP F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 366 Processing helix chain 'F' and resid 367 through 376 removed outlier: 4.038A pdb=" N ILE F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE F 376 " --> pdb=" O HIS F 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 65 Processing helix chain 'G' and resid 82 through 95 Processing helix chain 'G' and resid 117 through 131 removed outlier: 3.590A pdb=" N ARG G 121 " --> pdb=" O PRO G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 151 Processing helix chain 'G' and resid 176 through 180 removed outlier: 3.654A pdb=" N ILE G 180 " --> pdb=" O PRO G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 202 Processing helix chain 'G' and resid 207 through 221 removed outlier: 3.988A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE G 213 " --> pdb=" O SER G 209 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 253 through 258 Processing helix chain 'G' and resid 259 through 263 Processing helix chain 'G' and resid 274 through 286 removed outlier: 3.697A pdb=" N SER G 286 " --> pdb=" O ALA G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 289 No H-bonds generated for 'chain 'G' and resid 287 through 289' Processing helix chain 'G' and resid 290 through 297 Processing helix chain 'G' and resid 302 through 306 removed outlier: 3.807A pdb=" N THR G 305 " --> pdb=" O GLY G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 322 Processing helix chain 'G' and resid 338 through 350 Processing helix chain 'G' and resid 352 through 357 Processing helix chain 'G' and resid 360 through 366 Processing helix chain 'G' and resid 367 through 375 removed outlier: 3.896A pdb=" N ILE G 371 " --> pdb=" O GLY G 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 61 Processing helix chain 'H' and resid 78 through 91 Processing helix chain 'H' and resid 112 through 125 removed outlier: 4.076A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 171 through 175 removed outlier: 3.511A pdb=" N ILE H 175 " --> pdb=" O PRO H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 196 removed outlier: 3.590A pdb=" N ARG H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 216 removed outlier: 3.991A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 233 Processing helix chain 'H' and resid 252 through 257 Processing helix chain 'H' and resid 258 through 263 removed outlier: 4.180A pdb=" N PHE H 262 " --> pdb=" O PRO H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 285 removed outlier: 3.672A pdb=" N PHE H 279 " --> pdb=" O HIS H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 289 Processing helix chain 'H' and resid 290 through 296 Processing helix chain 'H' and resid 301 through 305 removed outlier: 3.535A pdb=" N THR H 304 " --> pdb=" O GLY H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 321 Processing helix chain 'H' and resid 337 through 349 Processing helix chain 'H' and resid 350 through 355 removed outlier: 3.535A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 365 Processing helix chain 'H' and resid 366 through 368 No H-bonds generated for 'chain 'H' and resid 366 through 368' Processing helix chain 'H' and resid 369 through 375 removed outlier: 4.012A pdb=" N PHE H 375 " --> pdb=" O HIS H 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 65 Processing helix chain 'I' and resid 82 through 95 removed outlier: 3.607A pdb=" N MET I 86 " --> pdb=" O ASP I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 131 removed outlier: 3.534A pdb=" N ARG I 121 " --> pdb=" O PRO I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 151 removed outlier: 3.795A pdb=" N LEU I 145 " --> pdb=" O MET I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 202 removed outlier: 3.539A pdb=" N LYS I 200 " --> pdb=" O LEU I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 221 removed outlier: 3.797A pdb=" N GLU I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE I 213 " --> pdb=" O SER I 209 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL I 214 " --> pdb=" O GLU I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 234 Processing helix chain 'I' and resid 253 through 258 Processing helix chain 'I' and resid 259 through 263 Processing helix chain 'I' and resid 264 through 268 removed outlier: 3.836A pdb=" N LEU I 267 " --> pdb=" O ARG I 264 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 286 removed outlier: 3.634A pdb=" N SER I 286 " --> pdb=" O ALA I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 289 No H-bonds generated for 'chain 'I' and resid 287 through 289' Processing helix chain 'I' and resid 290 through 297 Processing helix chain 'I' and resid 302 through 306 removed outlier: 3.745A pdb=" N THR I 305 " --> pdb=" O GLY I 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 322 Processing helix chain 'I' and resid 338 through 350 Processing helix chain 'I' and resid 352 through 357 removed outlier: 3.514A pdb=" N MET I 356 " --> pdb=" O THR I 352 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP I 357 " --> pdb=" O PHE I 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 352 through 357' Processing helix chain 'I' and resid 360 through 366 Processing helix chain 'I' and resid 367 through 376 removed outlier: 3.977A pdb=" N ILE I 371 " --> pdb=" O GLY I 367 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE I 376 " --> pdb=" O HIS I 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 79 removed outlier: 4.044A pdb=" N PHE J 77 " --> pdb=" O HIS J 73 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG J 78 " --> pdb=" O ILE J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 111 Processing helix chain 'J' and resid 122 through 132 removed outlier: 3.786A pdb=" N MET J 126 " --> pdb=" O PRO J 122 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU J 131 " --> pdb=" O ALA J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 182 removed outlier: 3.510A pdb=" N LEU J 171 " --> pdb=" O GLY J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 214 Processing helix chain 'J' and resid 219 through 231 removed outlier: 3.529A pdb=" N PHE J 231 " --> pdb=" O GLN J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 269 removed outlier: 4.165A pdb=" N ARG J 263 " --> pdb=" O LEU J 259 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP J 264 " --> pdb=" O GLY J 260 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE J 269 " --> pdb=" O SER J 265 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 272 No H-bonds generated for 'chain 'J' and resid 270 through 272' Processing helix chain 'J' and resid 279 through 291 removed outlier: 3.948A pdb=" N ILE J 284 " --> pdb=" O VAL J 280 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU J 285 " --> pdb=" O ALA J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 302 removed outlier: 4.554A pdb=" N LYS J 297 " --> pdb=" O ILE J 293 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLN J 298 " --> pdb=" O ASP J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 309 through 312 Processing helix chain 'J' and resid 315 through 329 Processing helix chain 'J' and resid 329 through 334 removed outlier: 3.866A pdb=" N LYS J 334 " --> pdb=" O PRO J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 352 through 365 removed outlier: 3.748A pdb=" N LEU J 356 " --> pdb=" O CYS J 352 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU J 364 " --> pdb=" O ILE J 360 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN J 365 " --> pdb=" O PHE J 361 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 382 removed outlier: 4.040A pdb=" N GLN J 380 " --> pdb=" O GLU J 376 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 23 removed outlier: 3.647A pdb=" N PHE K 20 " --> pdb=" O ILE K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 40 Processing helix chain 'K' and resid 43 through 62 removed outlier: 3.577A pdb=" N GLY K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE K 62 " --> pdb=" O ASN K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 136 removed outlier: 3.843A pdb=" N TRP K 120 " --> pdb=" O SER K 116 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG K 121 " --> pdb=" O LEU K 117 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS K 124 " --> pdb=" O TRP K 120 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA K 130 " --> pdb=" O SER K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 259 removed outlier: 3.873A pdb=" N ILE K 229 " --> pdb=" O ALA K 225 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS K 230 " --> pdb=" O LYS K 226 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR K 247 " --> pdb=" O ILE K 243 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR K 249 " --> pdb=" O GLU K 245 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP K 252 " --> pdb=" O GLN K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 275 Processing helix chain 'L' and resid 2 through 14 Processing helix chain 'L' and resid 17 through 19 No H-bonds generated for 'chain 'L' and resid 17 through 19' Processing helix chain 'L' and resid 20 through 32 Processing helix chain 'L' and resid 35 through 43 Processing helix chain 'L' and resid 90 through 112 Processing helix chain 'L' and resid 208 through 237 removed outlier: 3.545A pdb=" N ASN L 212 " --> pdb=" O PRO L 208 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU L 216 " --> pdb=" O ASN L 212 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS L 235 " --> pdb=" O ILE L 231 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 245 Processing helix chain 'L' and resid 247 through 271 Proline residue: L 253 - end of helix removed outlier: 3.589A pdb=" N GLN L 270 " --> pdb=" O LEU L 266 " (cutoff:3.500A) Processing helix chain 'M' and resid 1 through 44 removed outlier: 3.625A pdb=" N UNK M 36 " --> pdb=" O UNK M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 72 removed outlier: 3.504A pdb=" N UNK M 49 " --> pdb=" O UNK M 45 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N UNK M 69 " --> pdb=" O UNK M 65 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N UNK M 70 " --> pdb=" O UNK M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 166 removed outlier: 3.569A pdb=" N UNK M 137 " --> pdb=" O UNK M 133 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N UNK M 138 " --> pdb=" O UNK M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 238 removed outlier: 3.629A pdb=" N UNK M 234 " --> pdb=" O UNK M 230 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N UNK M 235 " --> pdb=" O UNK M 231 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N UNK M 236 " --> pdb=" O UNK M 232 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N UNK M 238 " --> pdb=" O UNK M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 263 removed outlier: 3.690A pdb=" N UNK M 246 " --> pdb=" O UNK M 242 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N UNK M 247 " --> pdb=" O UNK M 243 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N UNK M 254 " --> pdb=" O UNK M 250 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N UNK M 257 " --> pdb=" O UNK M 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 266 through 362 removed outlier: 3.825A pdb=" N UNK M 270 " --> pdb=" O UNK M 266 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N UNK M 288 " --> pdb=" O UNK M 284 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N UNK M 291 " --> pdb=" O UNK M 287 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N UNK M 295 " --> pdb=" O UNK M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 401 through 438 Processing helix chain 'M' and resid 443 through 460 Processing helix chain 'M' and resid 465 through 553 removed outlier: 4.234A pdb=" N UNK M 469 " --> pdb=" O UNK M 465 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N UNK M 470 " --> pdb=" O UNK M 466 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N UNK M 472 " --> pdb=" O UNK M 468 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N UNK M 486 " --> pdb=" O UNK M 482 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N UNK M 492 " --> pdb=" O UNK M 488 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N UNK M 495 " --> pdb=" O UNK M 491 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N UNK M 499 " --> pdb=" O UNK M 495 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N UNK M 502 " --> pdb=" O UNK M 498 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N UNK M 503 " --> pdb=" O UNK M 499 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N UNK M 506 " --> pdb=" O UNK M 502 " (cutoff:3.500A) Processing helix chain 'M' and resid 601 through 625 Processing helix chain 'M' and resid 701 through 741 Processing helix chain 'M' and resid 801 through 824 Processing helix chain 'N' and resid 1 through 39 removed outlier: 3.562A pdb=" N UNK N 35 " --> pdb=" O UNK N 31 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N UNK N 39 " --> pdb=" O UNK N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 74 Processing helix chain 'N' and resid 77 through 167 removed outlier: 4.104A pdb=" N UNK N 81 " --> pdb=" O UNK N 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N UNK N 104 " --> pdb=" O UNK N 100 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N UNK N 118 " --> pdb=" O UNK N 114 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N UNK N 161 " --> pdb=" O UNK N 157 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 240 removed outlier: 3.644A pdb=" N UNK N 238 " --> pdb=" O UNK N 234 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N UNK N 239 " --> pdb=" O UNK N 235 " (cutoff:3.500A) Processing helix chain 'N' and resid 241 through 269 removed outlier: 3.676A pdb=" N UNK N 245 " --> pdb=" O UNK N 241 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N UNK N 246 " --> pdb=" O UNK N 242 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N UNK N 249 " --> pdb=" O UNK N 245 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N UNK N 250 " --> pdb=" O UNK N 246 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N UNK N 267 " --> pdb=" O UNK N 263 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N UNK N 268 " --> pdb=" O UNK N 264 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N UNK N 269 " --> pdb=" O UNK N 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 363 removed outlier: 3.617A pdb=" N UNK N 289 " --> pdb=" O UNK N 285 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N UNK N 292 " --> pdb=" O UNK N 288 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N UNK N 311 " --> pdb=" O UNK N 307 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N UNK N 312 " --> pdb=" O UNK N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 401 through 434 Processing helix chain 'N' and resid 435 through 437 No H-bonds generated for 'chain 'N' and resid 435 through 437' Processing helix chain 'N' and resid 439 through 464 removed outlier: 3.513A pdb=" N UNK N 444 " --> pdb=" O UNK N 440 " (cutoff:3.500A) Processing helix chain 'N' and resid 466 through 553 removed outlier: 3.567A pdb=" N UNK N 470 " --> pdb=" O UNK N 466 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N UNK N 475 " --> pdb=" O UNK N 471 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N UNK N 491 " --> pdb=" O UNK N 487 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N UNK N 492 " --> pdb=" O UNK N 488 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N UNK N 498 " --> pdb=" O UNK N 494 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N UNK N 499 " --> pdb=" O UNK N 495 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N UNK N 505 " --> pdb=" O UNK N 501 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N UNK N 506 " --> pdb=" O UNK N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 602 through 626 removed outlier: 3.627A pdb=" N UNK N 623 " --> pdb=" O UNK N 619 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N UNK N 624 " --> pdb=" O UNK N 620 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N UNK N 626 " --> pdb=" O UNK N 622 " (cutoff:3.500A) Processing helix chain 'N' and resid 701 through 745 removed outlier: 3.719A pdb=" N UNK N 708 " --> pdb=" O UNK N 704 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N UNK N 727 " --> pdb=" O UNK N 723 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N UNK N 728 " --> pdb=" O UNK N 724 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N UNK N 744 " --> pdb=" O UNK N 740 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N UNK N 745 " --> pdb=" O UNK N 741 " (cutoff:3.500A) Processing helix chain 'N' and resid 760 through 768 removed outlier: 3.892A pdb=" N UNK N 766 " --> pdb=" O UNK N 762 " (cutoff:3.500A) Processing helix chain 'N' and resid 801 through 818 Processing helix chain 'O' and resid 80 through 94 Processing helix chain 'O' and resid 96 through 112 Processing helix chain 'P' and resid 80 through 94 Processing helix chain 'P' and resid 96 through 112 Processing helix chain 'Q' and resid 1 through 38 Processing helix chain 'Q' and resid 42 through 62 Processing helix chain 'Q' and resid 64 through 91 Processing helix chain 'R' and resid 1 through 38 Processing helix chain 'R' and resid 42 through 62 Processing helix chain 'R' and resid 64 through 91 Processing helix chain 'U' and resid 158 through 181 Proline residue: U 168 - end of helix Processing helix chain 'V' and resid 158 through 177 removed outlier: 3.516A pdb=" N GLN V 162 " --> pdb=" O PRO V 158 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS V 175 " --> pdb=" O SER V 171 " (cutoff:3.500A) Processing helix chain 'Y' and resid 442 through 467 removed outlier: 3.686A pdb=" N UNK Y 454 " --> pdb=" O UNK Y 450 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N UNK Y 455 " --> pdb=" O UNK Y 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 146 through 230 removed outlier: 3.546A pdb=" N UNK Z 168 " --> pdb=" O UNK Z 164 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N UNK Z 172 " --> pdb=" O UNK Z 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N UNK Z 185 " --> pdb=" O UNK Z 181 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N UNK Z 189 " --> pdb=" O UNK Z 185 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N UNK Z 214 " --> pdb=" O UNK Z 210 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N UNK Z 228 " --> pdb=" O UNK Z 224 " (cutoff:3.500A) Processing helix chain 'Z' and resid 236 through 400 removed outlier: 3.510A pdb=" N UNK Z 307 " --> pdb=" O UNK Z 303 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N UNK Z 325 " --> pdb=" O UNK Z 321 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N UNK Z 339 " --> pdb=" O UNK Z 335 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N UNK Z 343 " --> pdb=" O UNK Z 339 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N UNK Z 352 " --> pdb=" O UNK Z 348 " (cutoff:3.500A) Processing helix chain 'Z' and resid 801 through 912 removed outlier: 3.703A pdb=" N UNK Z 836 " --> pdb=" O UNK Z 832 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N UNK Z 837 " --> pdb=" O UNK Z 833 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N UNK Z 838 " --> pdb=" O UNK Z 834 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1001 through 1037 removed outlier: 4.264A pdb=" N UNK Z1033 " --> pdb=" O UNK Z1029 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 61 removed outlier: 3.985A pdb=" N ASP a 57 " --> pdb=" O ASN a 53 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS a 58 " --> pdb=" O ALA a 54 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE a 59 " --> pdb=" O ALA a 55 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASP a 61 " --> pdb=" O ASP a 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 61 removed outlier: 3.984A pdb=" N ASP b 57 " --> pdb=" O ASN b 53 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS b 58 " --> pdb=" O ALA b 54 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP b 61 " --> pdb=" O ASP b 57 " (cutoff:3.500A) Processing helix chain 'z' and resid 147 through 238 removed outlier: 3.613A pdb=" N UNK z 191 " --> pdb=" O UNK z 187 " (cutoff:3.500A) Processing helix chain 'z' and resid 245 through 400 removed outlier: 3.992A pdb=" N UNK z 249 " --> pdb=" O UNK z 245 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N UNK z 273 " --> pdb=" O UNK z 269 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N UNK z 289 " --> pdb=" O UNK z 285 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N UNK z 290 " --> pdb=" O UNK z 286 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N UNK z 291 " --> pdb=" O UNK z 287 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N UNK z 293 " --> pdb=" O UNK z 289 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N UNK z 294 " --> pdb=" O UNK z 290 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N UNK z 295 " --> pdb=" O UNK z 291 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N UNK z 296 " --> pdb=" O UNK z 292 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N UNK z 297 " --> pdb=" O UNK z 293 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N UNK z 300 " --> pdb=" O UNK z 296 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N UNK z 301 " --> pdb=" O UNK z 297 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N UNK z 302 " --> pdb=" O UNK z 298 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N UNK z 304 " --> pdb=" O UNK z 300 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N UNK z 347 " --> pdb=" O UNK z 343 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N UNK z 350 " --> pdb=" O UNK z 346 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N UNK z 356 " --> pdb=" O UNK z 352 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N UNK z 357 " --> pdb=" O UNK z 353 " (cutoff:3.500A) Processing helix chain 'z' and resid 801 through 912 Processing helix chain 'z' and resid 1001 through 1042 removed outlier: 3.729A pdb=" N UNK z1042 " --> pdb=" O UNK z1038 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 12 through 14 removed outlier: 3.697A pdb=" N THR A 111 " --> pdb=" O ILE A 14 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 20 through 23 Processing sheet with id= AC, first strand: chain 'A' and resid 39 through 42 removed outlier: 3.793A pdb=" N ARG A 72 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 41 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 75 through 76 Processing sheet with id= AE, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.684A pdb=" N THR A 165 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS A 166 " --> pdb=" O ASP A 159 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 159 " --> pdb=" O HIS A 166 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 240 through 242 Processing sheet with id= BA, first strand: chain 'B' and resid 12 through 14 removed outlier: 3.688A pdb=" N THR B 111 " --> pdb=" O ILE B 14 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'B' and resid 20 through 23 Processing sheet with id= BC, first strand: chain 'B' and resid 75 through 76 Processing sheet with id= BD, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.655A pdb=" N HIS B 166 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP B 159 " --> pdb=" O HIS B 166 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'B' and resid 240 through 242 Processing sheet with id= CA, first strand: chain 'C' and resid 33 through 36 removed outlier: 3.595A pdb=" N THR C 111 " --> pdb=" O ILE C 14 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.695A pdb=" N ARG C 41 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'C' and resid 75 through 76 Processing sheet with id= CD, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.536A pdb=" N HIS C 166 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 168 " --> pdb=" O VAL C 157 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'C' and resid 240 through 242 Processing sheet with id= DA, first strand: chain 'D' and resid 12 through 14 removed outlier: 3.579A pdb=" N THR D 111 " --> pdb=" O ILE D 14 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'D' and resid 20 through 23 Processing sheet with id= DC, first strand: chain 'D' and resid 39 through 42 removed outlier: 3.559A pdb=" N VAL D 39 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG D 72 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG D 41 " --> pdb=" O SER D 70 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'D' and resid 75 through 76 Processing sheet with id= DE, first strand: chain 'D' and resid 165 through 170 Processing sheet with id= DF, first strand: chain 'D' and resid 240 through 242 Processing sheet with id= EA, first strand: chain 'E' and resid 33 through 36 removed outlier: 3.621A pdb=" N THR E 111 " --> pdb=" O ILE E 14 " (cutoff:3.500A) Processing sheet with id= EB, first strand: chain 'E' and resid 41 through 42 removed outlier: 3.603A pdb=" N ARG E 41 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing sheet with id= EC, first strand: chain 'E' and resid 75 through 76 Processing sheet with id= ED, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.516A pdb=" N ARG a 14 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id= EE, first strand: chain 'E' and resid 240 through 242 Processing sheet with id= FA, first strand: chain 'F' and resid 12 through 14 removed outlier: 3.573A pdb=" N THR F 111 " --> pdb=" O ILE F 14 " (cutoff:3.500A) Processing sheet with id= FB, first strand: chain 'F' and resid 20 through 23 Processing sheet with id= FC, first strand: chain 'F' and resid 39 through 42 removed outlier: 3.629A pdb=" N VAL F 39 " --> pdb=" O ARG F 72 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG F 41 " --> pdb=" O SER F 70 " (cutoff:3.500A) Processing sheet with id= FD, first strand: chain 'F' and resid 75 through 76 Processing sheet with id= FE, first strand: chain 'F' and resid 181 through 183 removed outlier: 3.687A pdb=" N MET F 181 " --> pdb=" O ALA F 167 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS F 166 " --> pdb=" O ASP F 159 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL F 168 " --> pdb=" O VAL F 157 " (cutoff:3.500A) Processing sheet with id= GA, first strand: chain 'G' and resid 33 through 36 removed outlier: 3.542A pdb=" N THR G 111 " --> pdb=" O ILE G 14 " (cutoff:3.500A) Processing sheet with id= GB, first strand: chain 'G' and resid 41 through 42 removed outlier: 3.579A pdb=" N ARG G 41 " --> pdb=" O SER G 70 " (cutoff:3.500A) Processing sheet with id= GC, first strand: chain 'G' and resid 75 through 76 Processing sheet with id= GD, first strand: chain 'G' and resid 181 through 183 removed outlier: 3.516A pdb=" N HIS G 166 " --> pdb=" O ASP G 159 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL G 168 " --> pdb=" O VAL G 157 " (cutoff:3.500A) Processing sheet with id= GE, first strand: chain 'G' and resid 240 through 242 Processing sheet with id= HA, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.989A pdb=" N THR H 106 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET H 132 " --> pdb=" O ILE H 357 " (cutoff:3.500A) Processing sheet with id= HB, first strand: chain 'H' and resid 176 through 178 removed outlier: 3.514A pdb=" N SER H 300 " --> pdb=" O MET H 153 " (cutoff:3.500A) Processing sheet with id= HC, first strand: chain 'H' and resid 238 through 241 removed outlier: 3.992A pdb=" N LYS H 238 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE H 250 " --> pdb=" O LYS H 238 " (cutoff:3.500A) Processing sheet with id= IA, first strand: chain 'I' and resid 12 through 14 removed outlier: 3.632A pdb=" N THR I 111 " --> pdb=" O ILE I 14 " (cutoff:3.500A) Processing sheet with id= IB, first strand: chain 'I' and resid 20 through 23 Processing sheet with id= IC, first strand: chain 'I' and resid 39 through 42 removed outlier: 3.574A pdb=" N ARG I 41 " --> pdb=" O SER I 70 " (cutoff:3.500A) Processing sheet with id= ID, first strand: chain 'I' and resid 181 through 183 removed outlier: 3.528A pdb=" N THR I 165 " --> pdb=" O ILE I 183 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS I 166 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL I 168 " --> pdb=" O VAL I 157 " (cutoff:3.500A) Processing sheet with id= IE, first strand: chain 'I' and resid 240 through 242 Processing sheet with id= JA, first strand: chain 'J' and resid 26 through 29 Processing sheet with id= JB, first strand: chain 'J' and resid 42 through 43 removed outlier: 3.762A pdb=" N ILE J 52 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing sheet with id= JC, first strand: chain 'J' and resid 155 through 156 removed outlier: 3.547A pdb=" N ILE J 155 " --> pdb=" O TYR J 152 " (cutoff:3.500A) No H-bonds generated for sheet with id= JC Processing sheet with id= JD, first strand: chain 'J' and resid 162 through 164 removed outlier: 3.664A pdb=" N GLY J 162 " --> pdb=" O VAL J 148 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU J 164 " --> pdb=" O SER J 146 " (cutoff:3.500A) Processing sheet with id= JE, first strand: chain 'J' and resid 303 through 307 removed outlier: 3.522A pdb=" N VAL J 138 " --> pdb=" O LEU J 149 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE J 155 " --> pdb=" O PRO J 150 " (cutoff:3.500A) Processing sheet with id= JF, first strand: chain 'J' and resid 303 through 307 removed outlier: 3.522A pdb=" N VAL J 138 " --> pdb=" O LEU J 149 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU J 164 " --> pdb=" O SER J 146 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY J 162 " --> pdb=" O VAL J 148 " (cutoff:3.500A) Processing sheet with id= KA, first strand: chain 'K' and resid 64 through 66 removed outlier: 3.574A pdb=" N VAL K 65 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL K 74 " --> pdb=" O VAL K 65 " (cutoff:3.500A) No H-bonds generated for sheet with id= KA Processing sheet with id= KB, first strand: chain 'K' and resid 86 through 87 removed outlier: 6.526A pdb=" N SER K 95 " --> pdb=" O PRO K 108 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS K 97 " --> pdb=" O SER K 106 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER K 106 " --> pdb=" O LYS K 97 " (cutoff:3.500A) Processing sheet with id= KC, first strand: chain 'K' and resid 140 through 148 removed outlier: 3.884A pdb=" N PHE K 140 " --> pdb=" O GLU K 159 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS K 146 " --> pdb=" O THR K 153 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR K 153 " --> pdb=" O LYS K 146 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN K 187 " --> pdb=" O THR K 180 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU L 193 " --> pdb=" O VAL L 173 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP L 149 " --> pdb=" O MET L 174 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TRP L 176 " --> pdb=" O CYS L 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE L 134 " --> pdb=" O SER L 150 " (cutoff:3.500A) Processing sheet with id= LA, first strand: chain 'L' and resid 48 through 52 removed outlier: 4.295A pdb=" N LYS L 48 " --> pdb=" O LEU L 61 " (cutoff:3.500A) Processing sheet with id= LB, first strand: chain 'L' and resid 66 through 67 removed outlier: 3.733A pdb=" N SER L 70 " --> pdb=" O ASP L 67 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR L 71 " --> pdb=" O ASP L 80 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP L 80 " --> pdb=" O TYR L 71 " (cutoff:3.500A) Processing sheet with id= OA, first strand: chain 'O' and resid 26 through 27 Processing sheet with id= PA, first strand: chain 'P' and resid 26 through 27 Processing sheet with id= UA, first strand: chain 'U' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 85 through 86 current: chain 'U' and resid 119 through 121 removed outlier: 3.855A pdb=" N ILE U 120 " --> pdb=" O THR U 137 " (cutoff:3.500A) Processing sheet with id= UB, first strand: chain 'U' and resid 22 through 29 removed outlier: 3.570A pdb=" N ASP U 26 " --> pdb=" O ALA U 43 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA U 45 " --> pdb=" O ASP U 26 " (cutoff:3.500A) removed outlier: 12.496A pdb=" N THR U 28 " --> pdb=" O ALA U 45 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN U 93 " --> pdb=" O VAL U 109 " (cutoff:3.500A) Processing sheet with id= UC, first strand: chain 'U' and resid 96 through 97 Processing sheet with id= VA, first strand: chain 'V' and resid 21 through 22 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 62 through 63 current: chain 'V' and resid 109 through 110 Processing sheet with id= VB, first strand: chain 'V' and resid 34 through 36 Processing sheet with id= VC, first strand: chain 'V' and resid 47 through 48 Processing sheet with id= VD, first strand: chain 'V' and resid 86 through 87 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 86 through 87 current: chain 'V' and resid 120 through 122 No H-bonds generated for sheet with id= VD Processing sheet with id= VE, first strand: chain 'V' and resid 127 through 128 removed outlier: 6.793A pdb=" N VAL V 145 " --> pdb=" O SER V 154 " (cutoff:3.500A) Processing sheet with id= YA, first strand: chain 'Y' and resid 513 through 520 removed outlier: 6.620A pdb=" N UNK Y 514 " --> pdb=" O UNK Y 529 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N UNK Y 529 " --> pdb=" O UNK Y 514 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N UNK Y 516 " --> pdb=" O UNK Y 527 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N UNK Y 527 " --> pdb=" O UNK Y 516 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N UNK Y 518 " --> pdb=" O UNK Y 525 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N UNK Y 525 " --> pdb=" O UNK Y 518 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N UNK Y 520 " --> pdb=" O UNK Y 523 " (cutoff:3.500A) Processing sheet with id= YB, first strand: chain 'Y' and resid 583 through 584 3545 hydrogen bonds defined for protein. 10293 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: 22.22 Time building geometry restraints manager: 22.21 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: 16249 1.34 - 1.46: 4724 1.46 - 1.57: 28918 1.57 - 1.69: 0 1.69 - 1.81: 236 Bond restraints: 50127 Sorted by residual: bond pdb=" C LEU a 9 " pdb=" N PRO a 10 " ideal model delta sigma weight residual 1.335 1.407 -0.071 1.36e-02 5.41e+03 2.75e+01 bond pdb=" N PRO a 10 " pdb=" CD PRO a 10 " ideal model delta sigma weight residual 1.473 1.545 -0.072 1.40e-02 5.10e+03 2.62e+01 bond pdb=" CA ASN b 51 " pdb=" CB ASN b 51 " ideal model delta sigma weight residual 1.522 1.555 -0.033 7.00e-03 2.04e+04 2.17e+01 bond pdb=" C ARG I 41 " pdb=" N PRO I 42 " ideal model delta sigma weight residual 1.332 1.390 -0.059 1.30e-02 5.92e+03 2.03e+01 bond pdb=" CA ASP K 107 " pdb=" CB ASP K 107 " ideal model delta sigma weight residual 1.525 1.559 -0.034 8.30e-03 1.45e+04 1.71e+01 ... (remaining 50122 not shown) Histogram of bond angle deviations from ideal: 99.05 - 107.35: 1421 107.35 - 115.64: 29908 115.64 - 123.94: 36042 123.94 - 132.24: 936 132.24 - 140.54: 52 Bond angle restraints: 68359 Sorted by residual: angle pdb=" C PHE V 83 " pdb=" N PRO V 84 " pdb=" CA PRO V 84 " ideal model delta sigma weight residual 119.84 131.90 -12.06 1.25e+00 6.40e-01 9.32e+01 angle pdb=" C PRO V 71 " pdb=" N PRO V 72 " pdb=" CA PRO V 72 " ideal model delta sigma weight residual 118.97 128.93 -9.96 1.04e+00 9.25e-01 9.18e+01 angle pdb=" CA PRO L 253 " pdb=" N PRO L 253 " pdb=" CD PRO L 253 " ideal model delta sigma weight residual 112.00 99.05 12.95 1.40e+00 5.10e-01 8.56e+01 angle pdb=" C HIS U 36 " pdb=" N PRO U 37 " pdb=" CA PRO U 37 " ideal model delta sigma weight residual 119.76 128.14 -8.38 1.03e+00 9.43e-01 6.62e+01 angle pdb=" C THR U 71 " pdb=" N PRO U 72 " pdb=" CA PRO U 72 " ideal model delta sigma weight residual 119.84 129.59 -9.75 1.25e+00 6.40e-01 6.09e+01 ... (remaining 68354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.98: 28837 22.98 - 45.96: 1150 45.96 - 68.95: 175 68.95 - 91.93: 7 91.93 - 114.91: 1 Dihedral angle restraints: 30170 sinusoidal: 8851 harmonic: 21319 Sorted by residual: dihedral pdb=" CA UNK N 271 " pdb=" C UNK N 271 " pdb=" N UNK N 272 " pdb=" CA UNK N 272 " ideal model delta harmonic sigma weight residual -180.00 -65.09 -114.91 0 5.00e+00 4.00e-02 5.28e+02 dihedral pdb=" CA UNK N 270 " pdb=" C UNK N 270 " pdb=" N UNK N 271 " pdb=" CA UNK N 271 " ideal model delta harmonic sigma weight residual 180.00 -128.74 -51.26 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA THR G 375 " pdb=" C THR G 375 " pdb=" N PHE G 376 " pdb=" CA PHE G 376 " ideal model delta harmonic sigma weight residual 180.00 144.86 35.14 0 5.00e+00 4.00e-02 4.94e+01 ... (remaining 30167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 7676 0.126 - 0.253: 444 0.253 - 0.379: 12 0.379 - 0.506: 3 0.506 - 0.632: 1 Chirality restraints: 8136 Sorted by residual: chirality pdb=" CA UNK M 462 " pdb=" N UNK M 462 " pdb=" C UNK M 462 " pdb=" CB UNK M 462 " both_signs ideal model delta sigma weight residual False 2.52 1.89 0.63 2.00e-01 2.50e+01 9.99e+00 chirality pdb=" CA UNK M 461 " pdb=" N UNK M 461 " pdb=" C UNK M 461 " pdb=" CB UNK M 461 " both_signs ideal model delta sigma weight residual False 2.52 2.02 0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CA UNK M 463 " pdb=" N UNK M 463 " pdb=" C UNK M 463 " pdb=" CB UNK M 463 " both_signs ideal model delta sigma weight residual False 2.52 2.11 0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 8133 not shown) Planarity restraints: 9100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN L 252 " -0.112 5.00e-02 4.00e+02 1.56e-01 3.91e+01 pdb=" N PRO L 253 " 0.270 5.00e-02 4.00e+02 pdb=" CA PRO L 253 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO L 253 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN J 83 " -0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO J 84 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO J 84 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO J 84 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA UNK N 74 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C UNK N 74 " 0.050 2.00e-02 2.50e+03 pdb=" O UNK N 74 " -0.019 2.00e-02 2.50e+03 pdb=" N UNK N 75 " -0.017 2.00e-02 2.50e+03 ... (remaining 9097 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.90: 4 1.90 - 2.65: 179 2.65 - 3.40: 65431 3.40 - 4.15: 111575 4.15 - 4.90: 201022 Nonbonded interactions: 378211 Sorted by model distance: nonbonded pdb=" O LYS I 43 " pdb=" ND2 ASN J 275 " model vdw 1.155 2.520 nonbonded pdb=" CG ARG G 373 " pdb=" OD1 ASP b 70 " model vdw 1.510 3.440 nonbonded pdb=" O LYS I 43 " pdb=" CG ASN J 275 " model vdw 1.646 3.270 nonbonded pdb=" CD ARG G 373 " pdb=" OD1 ASP b 70 " model vdw 1.772 3.440 nonbonded pdb=" O ASP L 251 " pdb=" CD2 PHE L 255 " model vdw 1.935 3.340 ... (remaining 378206 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 'I' } ncs_group { reference = chain 'M' selection = (chain 'N' and resid 32 through 818) } ncs_group { reference = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'Z' selection = chain 'z' } 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 group one per residue 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: 3.490 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: 0.050 Extract box with map and model: 20.120 Check model and map are aligned: 0.780 Set scattering table: 0.480 Process input model: 128.020 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.460 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: 0.020 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 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 : 0.008 0.072 50127 Z= 0.479 Angle : 1.046 17.177 68359 Z= 0.671 Chirality : 0.063 0.632 8136 Planarity : 0.004 0.156 9100 Dihedral : 12.823 114.909 16254 Min Nonbonded Distance : 1.155 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.26 % Favored : 93.46 % Rotamer: Outliers : 1.97 % Allowed : 8.38 % Favored : 89.66 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.10), residues: 4693 helix: -1.16 (0.09), residues: 1782 sheet: -2.05 (0.18), residues: 602 loop : -2.38 (0.11), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 148 HIS 0.009 0.001 HIS K 79 PHE 0.040 0.002 PHE b 71 TYR 0.028 0.002 TYR K 247 ARG 0.018 0.001 ARG K 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 868 time to evaluate : 5.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8306 (ttt) cc_final: 0.8018 (ttm) REVERT: A 100 GLN cc_start: 0.8987 (mt0) cc_final: 0.8554 (mp-120) REVERT: A 141 MET cc_start: 0.7538 (mmm) cc_final: 0.7278 (mmp) REVERT: A 184 ASP cc_start: 0.8718 (m-30) cc_final: 0.8407 (p0) REVERT: A 189 ASP cc_start: 0.8163 (t0) cc_final: 0.7593 (t70) REVERT: A 227 ASN cc_start: 0.8901 (m-40) cc_final: 0.8576 (t0) REVERT: A 245 ASP cc_start: 0.8788 (t70) cc_final: 0.8492 (t0) REVERT: B 75 MET cc_start: 0.8356 (ttt) cc_final: 0.7933 (tpt) REVERT: B 85 ASP cc_start: 0.8342 (m-30) cc_final: 0.7447 (m-30) REVERT: B 86 MET cc_start: 0.8514 (mmm) cc_final: 0.8127 (mmm) REVERT: B 89 ILE cc_start: 0.9234 (mt) cc_final: 0.8989 (mm) REVERT: B 174 PHE cc_start: 0.7103 (m-80) cc_final: 0.6886 (m-80) REVERT: C 68 LEU cc_start: 0.8921 (mt) cc_final: 0.8697 (mt) REVERT: C 89 ILE cc_start: 0.9338 (mt) cc_final: 0.9121 (mm) REVERT: C 140 SER cc_start: 0.9300 (p) cc_final: 0.9062 (p) REVERT: C 176 MET cc_start: 0.8024 (mtt) cc_final: 0.7541 (mtt) REVERT: C 227 ASN cc_start: 0.8488 (m-40) cc_final: 0.8042 (t0) REVERT: C 373 ARG cc_start: 0.8891 (ttm110) cc_final: 0.7001 (tpt170) REVERT: D 227 ASN cc_start: 0.8732 (m-40) cc_final: 0.8322 (p0) REVERT: D 289 ASP cc_start: 0.7975 (m-30) cc_final: 0.7732 (t0) REVERT: D 369 ARG cc_start: 0.8912 (mtm180) cc_final: 0.8690 (mmt-90) REVERT: E 55 ASP cc_start: 0.7673 (m-30) cc_final: 0.7387 (t70) REVERT: E 112 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7824 (mm-30) REVERT: E 141 MET cc_start: 0.8567 (mmm) cc_final: 0.8228 (mmm) REVERT: E 176 MET cc_start: 0.8633 (mtt) cc_final: 0.8258 (mtm) REVERT: E 183 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8905 (mm) REVERT: E 297 ASN cc_start: 0.8708 (m-40) cc_final: 0.8498 (m-40) REVERT: E 355 LYS cc_start: 0.8869 (mttt) cc_final: 0.8495 (mmmt) REVERT: F 48 MET cc_start: 0.8199 (ttt) cc_final: 0.7684 (ttp) REVERT: F 94 TYR cc_start: 0.8273 (m-80) cc_final: 0.7176 (m-10) REVERT: F 116 ASN cc_start: 0.7777 (m-40) cc_final: 0.7062 (m110) REVERT: F 248 THR cc_start: 0.9156 (m) cc_final: 0.8892 (p) REVERT: F 353 PHE cc_start: 0.8731 (t80) cc_final: 0.8303 (t80) REVERT: F 369 ARG cc_start: 0.8235 (mtm180) cc_final: 0.7362 (mmt90) REVERT: G 86 MET cc_start: 0.7442 (mmm) cc_final: 0.5996 (tpt) REVERT: G 116 ASN cc_start: 0.8306 (m-40) cc_final: 0.8080 (m-40) REVERT: G 189 ASP cc_start: 0.7891 (t0) cc_final: 0.7506 (t70) REVERT: G 197 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.7662 (t80) REVERT: G 250 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7937 (tm-30) REVERT: G 362 GLU cc_start: 0.8165 (tp30) cc_final: 0.7921 (tp30) REVERT: H 75 ILE cc_start: 0.9403 (mm) cc_final: 0.9157 (mm) REVERT: H 142 LEU cc_start: 0.9218 (tp) cc_final: 0.8852 (tp) REVERT: H 190 MET cc_start: 0.7770 (ttp) cc_final: 0.7564 (ttm) REVERT: H 269 MET cc_start: 0.8560 (mtp) cc_final: 0.8078 (mtp) REVERT: H 281 SER cc_start: 0.8801 (m) cc_final: 0.8582 (t) REVERT: H 352 PHE cc_start: 0.8886 (t80) cc_final: 0.8408 (t80) REVERT: I 75 MET cc_start: 0.8122 (ttt) cc_final: 0.7385 (mmm) REVERT: I 79 ILE cc_start: 0.9154 (mt) cc_final: 0.8676 (mm) REVERT: J 19 ASP cc_start: 0.7987 (t0) cc_final: 0.7608 (t0) REVERT: J 44 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8909 (tptp) REVERT: J 48 MET cc_start: 0.7378 (tpt) cc_final: 0.6949 (tpt) REVERT: J 64 LEU cc_start: 0.9593 (mt) cc_final: 0.9227 (tp) REVERT: J 71 PHE cc_start: 0.9359 (t80) cc_final: 0.8994 (t80) REVERT: J 160 CYS cc_start: 0.8022 (m) cc_final: 0.7703 (m) REVERT: J 176 GLU cc_start: 0.9202 (tt0) cc_final: 0.8693 (tm-30) REVERT: J 208 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8509 (mm-30) REVERT: J 273 GLN cc_start: 0.8235 (mt0) cc_final: 0.7732 (tp40) REVERT: J 274 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6669 (t0) REVERT: J 283 LEU cc_start: 0.8800 (tp) cc_final: 0.8540 (tp) REVERT: J 322 GLU cc_start: 0.8820 (tp30) cc_final: 0.8196 (tp30) REVERT: a 1 MET cc_start: 0.7182 (mmm) cc_final: 0.6698 (mmt) REVERT: b 79 LYS cc_start: 0.7982 (tmtt) cc_final: 0.7215 (ptmt) outliers start: 74 outliers final: 16 residues processed: 915 average time/residue: 0.6251 time to fit residues: 919.5285 Evaluate side-chains 434 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 414 time to evaluate : 5.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 44 LYS Chi-restraints excluded: chain J residue 274 ASP Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 243 ILE Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 245 SER Chi-restraints excluded: chain L residue 268 GLN Chi-restraints excluded: chain a residue 53 ASN Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain c residue 14 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 607 optimal weight: 10.0000 chunk 544 optimal weight: 8.9990 chunk 302 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 367 optimal weight: 0.0000 chunk 291 optimal weight: 1.9990 chunk 563 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 chunk 342 optimal weight: 0.6980 chunk 419 optimal weight: 0.9980 chunk 652 optimal weight: 10.0000 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 116 ASN A 120 ASN B 37 ASN ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 98 GLN C 229 GLN D 44 HIS D 98 GLN E 16 ASN E 98 GLN E 166 HIS F 37 ASN F 98 GLN G 98 GLN ** G 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN H 246 GLN I 29 GLN I 37 ASN I 84 ASN I 98 GLN I 229 GLN J 58 ASN J 73 HIS J 178 GLN ** J 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 HIS K 41 ASN K 84 ASN K 152 GLN K 164 GLN K 197 HIS K 248 GLN L 178 GLN L 264 GLN L 268 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 50127 Z= 0.265 Angle : 0.663 14.008 68359 Z= 0.336 Chirality : 0.041 0.208 8136 Planarity : 0.005 0.067 9100 Dihedral : 4.942 56.117 7715 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.48 % Rotamer: Outliers : 3.14 % Allowed : 14.54 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.11), residues: 4693 helix: 0.88 (0.12), residues: 1774 sheet: -1.54 (0.18), residues: 699 loop : -1.83 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 357 HIS 0.015 0.002 HIS K 23 PHE 0.025 0.002 PHE K 255 TYR 0.024 0.002 TYR K 247 ARG 0.008 0.001 ARG L 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 403 time to evaluate : 4.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8900 (mmm) cc_final: 0.8228 (mmm) REVERT: A 100 GLN cc_start: 0.8988 (mt0) cc_final: 0.8614 (mp10) REVERT: A 184 ASP cc_start: 0.8813 (m-30) cc_final: 0.8605 (p0) REVERT: A 189 ASP cc_start: 0.8199 (t0) cc_final: 0.7786 (t70) REVERT: A 227 ASN cc_start: 0.8774 (m-40) cc_final: 0.8362 (t0) REVERT: A 325 ASP cc_start: 0.8237 (m-30) cc_final: 0.7724 (t0) REVERT: B 86 MET cc_start: 0.8693 (mmm) cc_final: 0.8406 (mmm) REVERT: B 174 PHE cc_start: 0.7633 (m-80) cc_final: 0.7271 (m-80) REVERT: B 197 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: B 279 LEU cc_start: 0.9037 (tt) cc_final: 0.8795 (tp) REVERT: C 68 LEU cc_start: 0.9087 (mt) cc_final: 0.8782 (mt) REVERT: C 86 MET cc_start: 0.9098 (tpt) cc_final: 0.8867 (tpt) REVERT: C 141 MET cc_start: 0.8264 (mtt) cc_final: 0.8045 (mtt) REVERT: C 164 VAL cc_start: 0.9460 (OUTLIER) cc_final: 0.9119 (m) REVERT: C 373 ARG cc_start: 0.9244 (ttm110) cc_final: 0.7434 (tpt170) REVERT: D 100 GLN cc_start: 0.9045 (mt0) cc_final: 0.8351 (mp10) REVERT: D 197 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7845 (t80) REVERT: D 227 ASN cc_start: 0.8381 (m-40) cc_final: 0.7558 (p0) REVERT: D 279 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8815 (mt) REVERT: E 55 ASP cc_start: 0.8025 (m-30) cc_final: 0.7453 (t70) REVERT: E 158 LEU cc_start: 0.9311 (tm) cc_final: 0.9101 (tp) REVERT: E 197 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.8282 (t80) REVERT: E 215 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9077 (ttmt) REVERT: E 353 PHE cc_start: 0.9228 (t80) cc_final: 0.8987 (t80) REVERT: E 355 LYS cc_start: 0.8965 (mttt) cc_final: 0.8526 (mmmt) REVERT: F 48 MET cc_start: 0.7514 (ttt) cc_final: 0.6488 (ttt) REVERT: F 89 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9230 (tt) REVERT: F 317 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8645 (mm-30) REVERT: F 353 PHE cc_start: 0.8880 (t80) cc_final: 0.8454 (t80) REVERT: G 86 MET cc_start: 0.7997 (mmm) cc_final: 0.7737 (tpt) REVERT: G 100 GLN cc_start: 0.9123 (mt0) cc_final: 0.8841 (mp10) REVERT: G 197 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.7926 (t80) REVERT: H 16 MET cc_start: 0.8168 (mmm) cc_final: 0.6446 (pmm) REVERT: H 57 GLU cc_start: 0.8605 (mp0) cc_final: 0.8190 (mp0) REVERT: H 123 MET cc_start: 0.9229 (mmp) cc_final: 0.8834 (mmt) REVERT: H 132 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8365 (ppp) REVERT: H 142 LEU cc_start: 0.9278 (tp) cc_final: 0.8960 (tp) REVERT: H 153 MET cc_start: 0.8749 (tmm) cc_final: 0.8305 (tmm) REVERT: H 352 PHE cc_start: 0.8963 (t80) cc_final: 0.8624 (t80) REVERT: I 75 MET cc_start: 0.8299 (ttt) cc_final: 0.7729 (mmm) REVERT: I 79 ILE cc_start: 0.8917 (mt) cc_final: 0.8521 (mm) REVERT: I 366 ASP cc_start: 0.8640 (m-30) cc_final: 0.7805 (t70) REVERT: J 128 LEU cc_start: 0.9570 (tp) cc_final: 0.9225 (tp) REVERT: J 160 CYS cc_start: 0.8231 (m) cc_final: 0.7971 (m) REVERT: J 273 GLN cc_start: 0.7850 (mt0) cc_final: 0.7524 (tp40) REVERT: J 274 ASP cc_start: 0.6634 (OUTLIER) cc_final: 0.6276 (t0) REVERT: J 322 GLU cc_start: 0.8907 (tp30) cc_final: 0.8453 (tp30) REVERT: a 1 MET cc_start: 0.7409 (mmm) cc_final: 0.7118 (mmt) REVERT: b 79 LYS cc_start: 0.7899 (tmtt) cc_final: 0.7140 (ptmt) outliers start: 118 outliers final: 57 residues processed: 498 average time/residue: 0.5637 time to fit residues: 481.5735 Evaluate side-chains 375 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 308 time to evaluate : 4.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 340 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 252 ASN Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 297 ASN Chi-restraints excluded: chain I residue 358 VAL Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 274 ASP Chi-restraints excluded: chain K residue 152 GLN Chi-restraints excluded: chain K residue 243 ILE Chi-restraints excluded: chain K residue 245 GLU Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain a residue 53 ASN Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 61 ASP Chi-restraints excluded: chain b residue 63 ARG Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 72 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 362 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 543 optimal weight: 10.0000 chunk 444 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 654 optimal weight: 10.0000 chunk 706 optimal weight: 40.0000 chunk 582 optimal weight: 20.0000 chunk 648 optimal weight: 90.0000 chunk 222 optimal weight: 4.9990 chunk 524 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN A 206 HIS A 227 ASN ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN C 100 GLN ** E 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 ASN ** E 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 ASN G 100 GLN G 229 GLN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 ASN ** J 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 GLN ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.138 50127 Z= 0.783 Angle : 1.086 20.945 68359 Z= 0.537 Chirality : 0.052 0.316 8136 Planarity : 0.007 0.076 9100 Dihedral : 5.678 58.866 7693 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.31 % Favored : 92.61 % Rotamer: Outliers : 6.62 % Allowed : 15.61 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.69 (0.12), residues: 4693 helix: -0.10 (0.11), residues: 1791 sheet: -1.73 (0.17), residues: 857 loop : -1.70 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D 83 HIS 0.017 0.003 HIS J 344 PHE 0.034 0.004 PHE G 256 TYR 0.054 0.004 TYR E 38 ARG 0.038 0.002 ARG K 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 287 time to evaluate : 4.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9321 (mmm) cc_final: 0.8786 (mmm) REVERT: A 174 PHE cc_start: 0.8418 (m-80) cc_final: 0.8215 (m-80) REVERT: A 210 GLU cc_start: 0.8580 (tt0) cc_final: 0.8167 (pt0) REVERT: A 227 ASN cc_start: 0.8864 (m110) cc_final: 0.8475 (t0) REVERT: A 325 ASP cc_start: 0.8576 (m-30) cc_final: 0.8375 (t0) REVERT: A 357 TRP cc_start: 0.8350 (OUTLIER) cc_final: 0.6425 (p90) REVERT: B 197 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.8186 (m-80) REVERT: B 357 TRP cc_start: 0.8760 (p90) cc_final: 0.8216 (p90) REVERT: C 184 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8649 (t70) REVERT: C 189 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8134 (t70) REVERT: C 227 ASN cc_start: 0.8665 (m-40) cc_final: 0.8160 (t0) REVERT: D 179 SER cc_start: 0.9469 (m) cc_final: 0.9182 (p) REVERT: D 197 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: E 55 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7634 (t70) REVERT: E 197 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.8188 (t80) REVERT: E 215 LYS cc_start: 0.9519 (OUTLIER) cc_final: 0.9115 (ttmt) REVERT: E 355 LYS cc_start: 0.8862 (mttt) cc_final: 0.8507 (mmmt) REVERT: E 357 TRP cc_start: 0.9386 (OUTLIER) cc_final: 0.8302 (p90) REVERT: E 373 ARG cc_start: 0.8747 (ptp-170) cc_final: 0.8336 (ptt180) REVERT: F 48 MET cc_start: 0.7767 (ttt) cc_final: 0.7393 (ttm) REVERT: F 89 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9242 (tp) REVERT: G 100 GLN cc_start: 0.9044 (mt0) cc_final: 0.8839 (mp10) REVERT: G 116 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7835 (m-40) REVERT: G 197 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.8466 (t80) REVERT: H 25 ASP cc_start: 0.8040 (p0) cc_final: 0.7769 (p0) REVERT: H 123 MET cc_start: 0.9346 (mmp) cc_final: 0.8922 (mmt) REVERT: H 132 MET cc_start: 0.9096 (ppp) cc_final: 0.8606 (ppp) REVERT: H 142 LEU cc_start: 0.9489 (tp) cc_final: 0.9042 (tp) REVERT: H 153 MET cc_start: 0.9008 (tmm) cc_final: 0.8756 (tmm) REVERT: H 311 ASP cc_start: 0.8572 (m-30) cc_final: 0.8310 (t0) REVERT: I 75 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8165 (tpp) REVERT: I 87 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.8929 (pt0) REVERT: I 227 ASN cc_start: 0.9317 (OUTLIER) cc_final: 0.9107 (p0) REVERT: I 270 GLU cc_start: 0.7471 (tt0) cc_final: 0.7116 (tt0) REVERT: J 48 MET cc_start: 0.6766 (tpt) cc_final: 0.6513 (tpp) REVERT: J 274 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6884 (t0) REVERT: J 322 GLU cc_start: 0.9206 (tp30) cc_final: 0.8720 (tp30) REVERT: a 1 MET cc_start: 0.7253 (mmm) cc_final: 0.6387 (mmt) REVERT: a 47 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.6985 (p-80) REVERT: b 79 LYS cc_start: 0.8077 (tmtt) cc_final: 0.7619 (ttpt) REVERT: c 1 MET cc_start: 0.6145 (mmp) cc_final: 0.5650 (mmp) REVERT: d 1 MET cc_start: 0.4785 (mmt) cc_final: 0.4213 (mmm) outliers start: 249 outliers final: 131 residues processed: 507 average time/residue: 0.6020 time to fit residues: 521.1403 Evaluate side-chains 376 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 228 time to evaluate : 5.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 357 TRP Chi-restraints excluded: chain E residue 366 ASP Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 340 THR Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 252 ASN Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 75 MET Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 227 ASN Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 297 ASN Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 176 GLU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 274 ASP Chi-restraints excluded: chain J residue 282 THR Chi-restraints excluded: chain J residue 311 MET Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 152 GLN Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 163 PHE Chi-restraints excluded: chain K residue 245 GLU Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 247 ASP Chi-restraints excluded: chain a residue 47 HIS Chi-restraints excluded: chain a residue 50 VAL Chi-restraints excluded: chain a residue 53 ASN Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain b residue 42 SER Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 61 ASP Chi-restraints excluded: chain b residue 63 ARG Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 646 optimal weight: 70.0000 chunk 491 optimal weight: 3.9990 chunk 339 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 312 optimal weight: 0.6980 chunk 439 optimal weight: 10.0000 chunk 656 optimal weight: 20.0000 chunk 694 optimal weight: 90.0000 chunk 342 optimal weight: 0.9980 chunk 622 optimal weight: 20.0000 chunk 187 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 77 HIS ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN C 16 ASN ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** E 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 ASN ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN H 59 GLN I 16 ASN I 120 ASN ** J 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN L 77 ASN L 209 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 50127 Z= 0.221 Angle : 0.609 13.466 68359 Z= 0.304 Chirality : 0.040 0.187 8136 Planarity : 0.004 0.071 9100 Dihedral : 4.743 56.901 7688 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.90 % Favored : 96.08 % Rotamer: Outliers : 3.56 % Allowed : 18.88 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.81 (0.12), residues: 4693 helix: 0.78 (0.12), residues: 1787 sheet: -1.31 (0.17), residues: 824 loop : -1.33 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 341 HIS 0.008 0.001 HIS C 178 PHE 0.017 0.001 PHE K 33 TYR 0.025 0.002 TYR K 247 ARG 0.011 0.001 ARG L 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 306 time to evaluate : 4.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9117 (mmm) cc_final: 0.8830 (mmm) REVERT: A 174 PHE cc_start: 0.8393 (m-80) cc_final: 0.7977 (m-10) REVERT: A 210 GLU cc_start: 0.8295 (tt0) cc_final: 0.7896 (pt0) REVERT: A 227 ASN cc_start: 0.8770 (m110) cc_final: 0.8335 (t0) REVERT: A 325 ASP cc_start: 0.8512 (m-30) cc_final: 0.8309 (t0) REVERT: B 197 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: B 357 TRP cc_start: 0.8517 (p90) cc_final: 0.7993 (p90) REVERT: C 227 ASN cc_start: 0.8414 (m-40) cc_final: 0.7933 (t0) REVERT: C 373 ARG cc_start: 0.9486 (ttm110) cc_final: 0.7828 (tpt170) REVERT: D 48 MET cc_start: 0.8790 (ptm) cc_final: 0.8488 (ptm) REVERT: D 100 GLN cc_start: 0.9123 (mt0) cc_final: 0.8476 (mp10) REVERT: D 197 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: E 55 ASP cc_start: 0.8057 (m-30) cc_final: 0.7726 (t70) REVERT: E 69 LEU cc_start: 0.9188 (mt) cc_final: 0.8979 (mt) REVERT: E 197 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7958 (t80) REVERT: E 355 LYS cc_start: 0.8733 (mttt) cc_final: 0.8387 (mmmt) REVERT: E 357 TRP cc_start: 0.9209 (OUTLIER) cc_final: 0.8219 (p90) REVERT: F 48 MET cc_start: 0.7800 (ttt) cc_final: 0.6951 (ttm) REVERT: F 86 MET cc_start: 0.8324 (tpp) cc_final: 0.8093 (tpp) REVERT: G 75 MET cc_start: 0.9149 (mmm) cc_final: 0.8847 (tpp) REVERT: G 80 VAL cc_start: 0.9263 (OUTLIER) cc_final: 0.9035 (p) REVERT: G 197 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.8238 (t80) REVERT: G 376 PHE cc_start: 0.5587 (OUTLIER) cc_final: 0.5347 (m-80) REVERT: H 16 MET cc_start: 0.8553 (mmm) cc_final: 0.5981 (pmm) REVERT: H 25 ASP cc_start: 0.7802 (p0) cc_final: 0.7506 (p0) REVERT: H 132 MET cc_start: 0.8967 (ppp) cc_final: 0.8499 (ppp) REVERT: H 142 LEU cc_start: 0.9148 (tp) cc_final: 0.8707 (tp) REVERT: I 75 MET cc_start: 0.8695 (ttt) cc_final: 0.8028 (tpp) REVERT: I 112 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8210 (pp20) REVERT: I 184 ASP cc_start: 0.8581 (m-30) cc_final: 0.8364 (t0) REVERT: I 227 ASN cc_start: 0.9201 (OUTLIER) cc_final: 0.9001 (p0) REVERT: I 294 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9009 (mm) REVERT: J 128 LEU cc_start: 0.9576 (tp) cc_final: 0.9326 (tp) REVERT: J 220 LEU cc_start: 0.9040 (pt) cc_final: 0.8507 (tp) REVERT: J 274 ASP cc_start: 0.6733 (OUTLIER) cc_final: 0.6510 (t0) REVERT: J 322 GLU cc_start: 0.8952 (tp30) cc_final: 0.8220 (tp30) REVERT: K 234 HIS cc_start: 0.6180 (OUTLIER) cc_final: 0.5918 (p-80) REVERT: L 179 THR cc_start: 0.5368 (p) cc_final: 0.5021 (m) REVERT: a 1 MET cc_start: 0.6823 (mmm) cc_final: 0.6345 (mmt) REVERT: a 47 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.6764 (p-80) REVERT: c 1 MET cc_start: 0.6197 (mmp) cc_final: 0.5698 (mmp) REVERT: d 1 MET cc_start: 0.5157 (mmt) cc_final: 0.4603 (mmm) outliers start: 134 outliers final: 76 residues processed: 415 average time/residue: 0.5531 time to fit residues: 399.1623 Evaluate side-chains 349 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 261 time to evaluate : 4.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 120 ASN Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 357 TRP Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 340 THR Chi-restraints excluded: chain G residue 376 PHE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 252 ASN Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 227 ASN Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain J residue 274 ASP Chi-restraints excluded: chain K residue 234 HIS Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 247 ASP Chi-restraints excluded: chain a residue 47 HIS Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 61 ASP Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 69 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 578 optimal weight: 40.0000 chunk 394 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 517 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 chunk 593 optimal weight: 0.0870 chunk 480 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 354 optimal weight: 9.9990 chunk 623 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 ASN ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 ASN L 77 ASN L 209 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 50127 Z= 0.319 Angle : 0.639 14.399 68359 Z= 0.314 Chirality : 0.040 0.186 8136 Planarity : 0.004 0.069 9100 Dihedral : 4.544 56.236 7686 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.88 % Favored : 94.10 % Rotamer: Outliers : 3.96 % Allowed : 19.54 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.60 (0.12), residues: 4693 helix: 0.92 (0.12), residues: 1788 sheet: -1.19 (0.17), residues: 855 loop : -1.18 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 357 HIS 0.008 0.001 HIS J 344 PHE 0.029 0.002 PHE L 255 TYR 0.020 0.002 TYR H 143 ARG 0.007 0.001 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 265 time to evaluate : 5.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9160 (mmm) cc_final: 0.8808 (mmm) REVERT: A 97 GLU cc_start: 0.8006 (tp30) cc_final: 0.7760 (tm-30) REVERT: A 174 PHE cc_start: 0.8392 (m-80) cc_final: 0.8079 (m-10) REVERT: A 210 GLU cc_start: 0.8396 (tt0) cc_final: 0.7869 (pt0) REVERT: A 227 ASN cc_start: 0.8788 (m110) cc_final: 0.8339 (t0) REVERT: A 325 ASP cc_start: 0.8588 (m-30) cc_final: 0.8279 (t0) REVERT: B 197 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: B 321 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9059 (mm) REVERT: B 357 TRP cc_start: 0.8540 (p90) cc_final: 0.8020 (p90) REVERT: C 270 GLU cc_start: 0.8662 (tt0) cc_final: 0.8438 (tt0) REVERT: D 100 GLN cc_start: 0.9132 (mt0) cc_final: 0.8386 (mp10) REVERT: D 197 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: D 354 LYS cc_start: 0.9409 (mttt) cc_final: 0.9083 (mtpp) REVERT: E 55 ASP cc_start: 0.8184 (m-30) cc_final: 0.7686 (t70) REVERT: E 69 LEU cc_start: 0.9270 (mt) cc_final: 0.9006 (mt) REVERT: E 197 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8058 (t80) REVERT: E 335 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8744 (pm20) REVERT: E 355 LYS cc_start: 0.8787 (mttt) cc_final: 0.8413 (mmmt) REVERT: E 373 ARG cc_start: 0.8621 (ptp-170) cc_final: 0.8343 (ptt180) REVERT: F 48 MET cc_start: 0.7939 (ttt) cc_final: 0.7371 (ttm) REVERT: F 86 MET cc_start: 0.8388 (tpp) cc_final: 0.8113 (mmm) REVERT: F 116 ASN cc_start: 0.7972 (m-40) cc_final: 0.7661 (m110) REVERT: G 197 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.8429 (t80) REVERT: H 25 ASP cc_start: 0.7864 (p0) cc_final: 0.7583 (p0) REVERT: H 132 MET cc_start: 0.8995 (ppp) cc_final: 0.8572 (ppp) REVERT: H 142 LEU cc_start: 0.9298 (tp) cc_final: 0.8741 (tp) REVERT: I 75 MET cc_start: 0.7847 (ttt) cc_final: 0.7529 (mmm) REVERT: I 87 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.9022 (pp20) REVERT: I 112 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8301 (pp20) REVERT: I 294 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9077 (mm) REVERT: J 128 LEU cc_start: 0.9600 (tp) cc_final: 0.9287 (tp) REVERT: J 220 LEU cc_start: 0.9025 (pt) cc_final: 0.8499 (tp) REVERT: J 322 GLU cc_start: 0.8984 (tp30) cc_final: 0.8231 (tp30) REVERT: K 245 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: a 1 MET cc_start: 0.6867 (mmm) cc_final: 0.6334 (mmt) REVERT: a 47 HIS cc_start: 0.7449 (OUTLIER) cc_final: 0.6802 (p-80) REVERT: c 1 MET cc_start: 0.6137 (mmp) cc_final: 0.5575 (mmp) REVERT: d 1 MET cc_start: 0.5287 (mmt) cc_final: 0.4794 (mmm) outliers start: 149 outliers final: 102 residues processed: 392 average time/residue: 0.5319 time to fit residues: 365.2301 Evaluate side-chains 363 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 251 time to evaluate : 4.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 120 ASN Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 340 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 252 ASN Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 297 ASN Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain K residue 163 PHE Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 245 GLU Chi-restraints excluded: chain L residue 147 CYS Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 247 ASP Chi-restraints excluded: chain a residue 47 HIS Chi-restraints excluded: chain a residue 50 VAL Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 61 ASP Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 69 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 233 optimal weight: 0.5980 chunk 625 optimal weight: 70.0000 chunk 137 optimal weight: 0.9990 chunk 408 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 695 optimal weight: 60.0000 chunk 577 optimal weight: 50.0000 chunk 322 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 365 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS B 44 HIS ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN C 240 GLN ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 HIS ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN ** H 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 50127 Z= 0.220 Angle : 0.567 14.928 68359 Z= 0.279 Chirality : 0.038 0.220 8136 Planarity : 0.004 0.066 9100 Dihedral : 4.274 57.241 7682 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.07 % Favored : 95.91 % Rotamer: Outliers : 3.46 % Allowed : 20.05 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.31 (0.12), residues: 4693 helix: 1.17 (0.13), residues: 1782 sheet: -0.98 (0.17), residues: 845 loop : -1.04 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 357 HIS 0.006 0.001 HIS C 178 PHE 0.015 0.001 PHE K 33 TYR 0.033 0.001 TYR K 247 ARG 0.005 0.000 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 290 time to evaluate : 5.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8980 (ptm) cc_final: 0.8366 (ppp) REVERT: A 86 MET cc_start: 0.9108 (mmm) cc_final: 0.8853 (mmm) REVERT: A 97 GLU cc_start: 0.7998 (tp30) cc_final: 0.7744 (tm-30) REVERT: A 174 PHE cc_start: 0.8437 (m-80) cc_final: 0.8092 (m-10) REVERT: A 210 GLU cc_start: 0.8423 (tt0) cc_final: 0.7817 (pt0) REVERT: A 227 ASN cc_start: 0.8773 (m110) cc_final: 0.8319 (t0) REVERT: A 325 ASP cc_start: 0.8534 (m-30) cc_final: 0.8251 (t0) REVERT: B 101 THR cc_start: 0.9375 (OUTLIER) cc_final: 0.9147 (t) REVERT: B 197 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: B 321 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9092 (mm) REVERT: B 357 TRP cc_start: 0.8459 (p90) cc_final: 0.7965 (p90) REVERT: C 145 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8665 (mp) REVERT: C 270 GLU cc_start: 0.8559 (tt0) cc_final: 0.8312 (tt0) REVERT: C 373 ARG cc_start: 0.9501 (ttm110) cc_final: 0.7812 (tpt170) REVERT: D 100 GLN cc_start: 0.9176 (mt0) cc_final: 0.8414 (mp10) REVERT: D 179 SER cc_start: 0.9217 (m) cc_final: 0.8987 (p) REVERT: D 197 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: E 55 ASP cc_start: 0.8164 (m-30) cc_final: 0.7690 (t70) REVERT: E 69 LEU cc_start: 0.9214 (mt) cc_final: 0.9003 (mt) REVERT: E 197 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8065 (t80) REVERT: E 335 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8690 (pm20) REVERT: E 355 LYS cc_start: 0.8758 (mttt) cc_final: 0.8384 (mmmt) REVERT: F 48 MET cc_start: 0.7834 (ttt) cc_final: 0.7246 (ttm) REVERT: F 86 MET cc_start: 0.8416 (tpp) cc_final: 0.8067 (mmm) REVERT: F 116 ASN cc_start: 0.7932 (m-40) cc_final: 0.7572 (m110) REVERT: F 210 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8287 (mt-10) REVERT: G 22 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8781 (mtmt) REVERT: G 197 TYR cc_start: 0.8962 (OUTLIER) cc_final: 0.8304 (t80) REVERT: H 16 MET cc_start: 0.8534 (mmm) cc_final: 0.6369 (pmm) REVERT: H 25 ASP cc_start: 0.7816 (p0) cc_final: 0.7495 (p0) REVERT: H 132 MET cc_start: 0.8997 (ppp) cc_final: 0.8552 (ppp) REVERT: H 142 LEU cc_start: 0.9210 (tp) cc_final: 0.8679 (tp) REVERT: H 374 CYS cc_start: 0.8521 (t) cc_final: 0.8198 (p) REVERT: I 75 MET cc_start: 0.7769 (ttt) cc_final: 0.7476 (mmm) REVERT: I 87 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.8987 (pp20) REVERT: I 112 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8263 (pp20) REVERT: I 184 ASP cc_start: 0.8640 (m-30) cc_final: 0.8428 (t0) REVERT: J 43 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6894 (pp) REVERT: J 128 LEU cc_start: 0.9591 (tp) cc_final: 0.9246 (tp) REVERT: J 220 LEU cc_start: 0.9023 (pt) cc_final: 0.8506 (tp) REVERT: J 322 GLU cc_start: 0.8948 (tp30) cc_final: 0.8198 (tp30) REVERT: K 234 HIS cc_start: 0.6141 (OUTLIER) cc_final: 0.5828 (p-80) REVERT: L 88 MET cc_start: 0.4428 (mmm) cc_final: 0.4000 (mmm) REVERT: a 1 MET cc_start: 0.6650 (mmm) cc_final: 0.6068 (mmt) REVERT: a 47 HIS cc_start: 0.7384 (OUTLIER) cc_final: 0.6761 (p-80) REVERT: b 79 LYS cc_start: 0.8483 (tppt) cc_final: 0.6975 (ttpp) REVERT: d 1 MET cc_start: 0.5312 (mmt) cc_final: 0.4387 (mmt) outliers start: 130 outliers final: 90 residues processed: 401 average time/residue: 0.5460 time to fit residues: 381.9537 Evaluate side-chains 366 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 262 time to evaluate : 5.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 120 ASN Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 340 THR Chi-restraints excluded: chain G residue 376 PHE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 252 ASN Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain J residue 43 ILE Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 234 HIS Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 247 ASP Chi-restraints excluded: chain a residue 47 HIS Chi-restraints excluded: chain a residue 50 VAL Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain d residue 6 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 670 optimal weight: 8.9990 chunk 78 optimal weight: 0.0470 chunk 396 optimal weight: 0.8980 chunk 508 optimal weight: 5.9990 chunk 393 optimal weight: 5.9990 chunk 585 optimal weight: 30.0000 chunk 388 optimal weight: 0.9990 chunk 692 optimal weight: 9.9990 chunk 433 optimal weight: 9.9990 chunk 422 optimal weight: 0.9990 chunk 319 optimal weight: 0.5980 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 HIS ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN E 240 GLN ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 257 HIS ** J 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 50127 Z= 0.195 Angle : 0.547 13.942 68359 Z= 0.268 Chirality : 0.038 0.179 8136 Planarity : 0.003 0.065 9100 Dihedral : 4.095 57.442 7682 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.28 % Favored : 95.70 % Rotamer: Outliers : 3.56 % Allowed : 20.10 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.13 (0.12), residues: 4693 helix: 1.24 (0.13), residues: 1794 sheet: -0.75 (0.17), residues: 839 loop : -0.93 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 357 HIS 0.006 0.001 HIS F 166 PHE 0.035 0.001 PHE L 255 TYR 0.024 0.001 TYR K 247 ARG 0.005 0.000 ARG d 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 293 time to evaluate : 5.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8957 (ptm) cc_final: 0.8259 (ppp) REVERT: A 86 MET cc_start: 0.9088 (mmm) cc_final: 0.8851 (mmm) REVERT: A 174 PHE cc_start: 0.8306 (m-80) cc_final: 0.7942 (m-10) REVERT: A 210 GLU cc_start: 0.8390 (tt0) cc_final: 0.8107 (pt0) REVERT: A 227 ASN cc_start: 0.8764 (m110) cc_final: 0.8311 (t0) REVERT: A 325 ASP cc_start: 0.8497 (m-30) cc_final: 0.8246 (t0) REVERT: B 101 THR cc_start: 0.9392 (OUTLIER) cc_final: 0.9179 (t) REVERT: B 197 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: B 321 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9135 (mm) REVERT: B 357 TRP cc_start: 0.8412 (p90) cc_final: 0.7936 (p90) REVERT: C 270 GLU cc_start: 0.8536 (tt0) cc_final: 0.8260 (tt0) REVERT: C 373 ARG cc_start: 0.9503 (ttm110) cc_final: 0.7756 (tpt170) REVERT: D 48 MET cc_start: 0.8582 (ptm) cc_final: 0.8269 (ptt) REVERT: D 100 GLN cc_start: 0.9164 (mt0) cc_final: 0.8403 (mp10) REVERT: D 164 VAL cc_start: 0.9470 (OUTLIER) cc_final: 0.9091 (m) REVERT: D 197 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: E 22 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8399 (mtmm) REVERT: E 55 ASP cc_start: 0.8121 (m-30) cc_final: 0.7638 (t70) REVERT: E 69 LEU cc_start: 0.9178 (mt) cc_final: 0.8955 (mt) REVERT: E 94 TYR cc_start: 0.8550 (m-80) cc_final: 0.8343 (m-80) REVERT: E 197 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.8101 (t80) REVERT: E 335 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8670 (pm20) REVERT: E 355 LYS cc_start: 0.8783 (mttt) cc_final: 0.8388 (mmmt) REVERT: F 48 MET cc_start: 0.7791 (ttt) cc_final: 0.7256 (ttm) REVERT: F 86 MET cc_start: 0.8378 (tpp) cc_final: 0.8021 (mmm) REVERT: G 22 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8656 (mtmt) REVERT: G 30 ILE cc_start: 0.9540 (OUTLIER) cc_final: 0.9320 (tp) REVERT: G 145 LEU cc_start: 0.9183 (mt) cc_final: 0.8981 (mt) REVERT: G 197 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.8341 (t80) REVERT: H 16 MET cc_start: 0.8518 (mmm) cc_final: 0.6760 (pmm) REVERT: H 25 ASP cc_start: 0.7797 (p0) cc_final: 0.7455 (p0) REVERT: H 132 MET cc_start: 0.9019 (ppp) cc_final: 0.8575 (ppp) REVERT: H 142 LEU cc_start: 0.9189 (tp) cc_final: 0.8669 (tp) REVERT: H 374 CYS cc_start: 0.8443 (t) cc_final: 0.8207 (p) REVERT: I 87 GLU cc_start: 0.9324 (OUTLIER) cc_final: 0.8969 (pp20) REVERT: I 184 ASP cc_start: 0.8627 (m-30) cc_final: 0.8415 (t0) REVERT: J 79 HIS cc_start: 0.7354 (m90) cc_final: 0.7011 (m90) REVERT: J 128 LEU cc_start: 0.9573 (tp) cc_final: 0.9176 (tp) REVERT: J 220 LEU cc_start: 0.9174 (pt) cc_final: 0.8671 (tp) REVERT: J 322 GLU cc_start: 0.8940 (tp30) cc_final: 0.8290 (tp30) REVERT: K 234 HIS cc_start: 0.6493 (OUTLIER) cc_final: 0.6199 (p-80) REVERT: a 1 MET cc_start: 0.6426 (mmm) cc_final: 0.5873 (mmt) REVERT: b 79 LYS cc_start: 0.8341 (tppt) cc_final: 0.7088 (tttp) REVERT: d 1 MET cc_start: 0.5202 (mmt) cc_final: 0.4368 (mmt) outliers start: 134 outliers final: 95 residues processed: 405 average time/residue: 0.5167 time to fit residues: 366.8278 Evaluate side-chains 372 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 264 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 120 ASN Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 340 THR Chi-restraints excluded: chain G residue 376 PHE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 353 GLN Chi-restraints excluded: chain H residue 355 MET Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 384 ILE Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 234 HIS Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 147 CYS Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain a residue 50 VAL Chi-restraints excluded: chain b residue 42 SER Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain d residue 6 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 428 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 chunk 413 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 440 optimal weight: 7.9990 chunk 472 optimal weight: 20.0000 chunk 342 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 544 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** E 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 ASN L 209 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 50127 Z= 0.395 Angle : 0.685 16.736 68359 Z= 0.334 Chirality : 0.041 0.194 8136 Planarity : 0.004 0.065 9100 Dihedral : 4.390 56.093 7682 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.92 % Favored : 94.05 % Rotamer: Outliers : 3.86 % Allowed : 20.18 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.36 (0.12), residues: 4693 helix: 0.97 (0.12), residues: 1791 sheet: -0.84 (0.17), residues: 829 loop : -1.00 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 271 HIS 0.009 0.002 HIS J 344 PHE 0.020 0.002 PHE J 71 TYR 0.047 0.002 TYR A 148 ARG 0.010 0.001 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 255 time to evaluate : 4.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9184 (mmm) cc_final: 0.8864 (mmm) REVERT: A 174 PHE cc_start: 0.8369 (m-80) cc_final: 0.8024 (m-10) REVERT: A 227 ASN cc_start: 0.8775 (m110) cc_final: 0.8324 (t0) REVERT: A 325 ASP cc_start: 0.8544 (m-30) cc_final: 0.8244 (t0) REVERT: B 101 THR cc_start: 0.9479 (OUTLIER) cc_final: 0.9243 (t) REVERT: B 197 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: B 225 SER cc_start: 0.8679 (p) cc_final: 0.8478 (t) REVERT: B 227 ASN cc_start: 0.8237 (m-40) cc_final: 0.7936 (t0) REVERT: B 321 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9105 (mm) REVERT: B 357 TRP cc_start: 0.8570 (p90) cc_final: 0.8048 (p90) REVERT: C 178 HIS cc_start: 0.7512 (m90) cc_final: 0.7115 (m90) REVERT: C 270 GLU cc_start: 0.8781 (tt0) cc_final: 0.8580 (tt0) REVERT: D 100 GLN cc_start: 0.9144 (mt0) cc_final: 0.8414 (mp10) REVERT: D 164 VAL cc_start: 0.9503 (OUTLIER) cc_final: 0.9193 (m) REVERT: D 197 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: E 55 ASP cc_start: 0.8237 (m-30) cc_final: 0.7768 (t70) REVERT: E 69 LEU cc_start: 0.9317 (mt) cc_final: 0.9060 (mt) REVERT: E 197 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.8125 (t80) REVERT: E 335 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8964 (pm20) REVERT: E 355 LYS cc_start: 0.8945 (mttt) cc_final: 0.8552 (mmmt) REVERT: F 48 MET cc_start: 0.7964 (ttt) cc_final: 0.7501 (ttm) REVERT: F 116 ASN cc_start: 0.7876 (m-40) cc_final: 0.7558 (m110) REVERT: G 48 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7498 (tmm) REVERT: G 196 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9230 (tt) REVERT: G 197 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8400 (t80) REVERT: H 16 MET cc_start: 0.8513 (mmm) cc_final: 0.6031 (pmm) REVERT: H 25 ASP cc_start: 0.7882 (p0) cc_final: 0.7523 (p0) REVERT: H 132 MET cc_start: 0.9042 (ppp) cc_final: 0.8618 (ppp) REVERT: H 142 LEU cc_start: 0.9348 (tp) cc_final: 0.8819 (tp) REVERT: I 87 GLU cc_start: 0.9350 (OUTLIER) cc_final: 0.8989 (pp20) REVERT: J 220 LEU cc_start: 0.9147 (pt) cc_final: 0.8605 (tp) REVERT: J 322 GLU cc_start: 0.9039 (tp30) cc_final: 0.8401 (tp30) REVERT: K 234 HIS cc_start: 0.6506 (OUTLIER) cc_final: 0.6228 (p-80) REVERT: L 126 HIS cc_start: 0.6566 (OUTLIER) cc_final: 0.6262 (t70) REVERT: a 1 MET cc_start: 0.6663 (mmm) cc_final: 0.6231 (mmt) REVERT: a 47 HIS cc_start: 0.7136 (OUTLIER) cc_final: 0.6659 (p-80) REVERT: d 1 MET cc_start: 0.5417 (mmt) cc_final: 0.4624 (mmp) outliers start: 145 outliers final: 104 residues processed: 377 average time/residue: 0.5230 time to fit residues: 347.9993 Evaluate side-chains 364 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 246 time to evaluate : 4.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 340 THR Chi-restraints excluded: chain G residue 376 PHE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 276 GLU Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 355 MET Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 384 ILE Chi-restraints excluded: chain K residue 163 PHE Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 234 HIS Chi-restraints excluded: chain K residue 245 GLU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 126 HIS Chi-restraints excluded: chain L residue 147 CYS Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 247 ASP Chi-restraints excluded: chain a residue 47 HIS Chi-restraints excluded: chain a residue 50 VAL Chi-restraints excluded: chain b residue 42 SER Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain d residue 6 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 630 optimal weight: 20.0000 chunk 663 optimal weight: 8.9990 chunk 605 optimal weight: 30.0000 chunk 645 optimal weight: 90.0000 chunk 388 optimal weight: 0.9980 chunk 281 optimal weight: 4.9990 chunk 507 optimal weight: 7.9990 chunk 198 optimal weight: 0.7980 chunk 583 optimal weight: 20.0000 chunk 610 optimal weight: 9.9990 chunk 643 optimal weight: 100.0000 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS B 229 GLN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN ** E 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 HIS J 60 ASN J 379 ASN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 209 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.6367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.102 50127 Z= 0.773 Angle : 1.064 22.060 68359 Z= 0.524 Chirality : 0.050 0.431 8136 Planarity : 0.007 0.064 9100 Dihedral : 5.692 52.740 7682 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.16 % Favored : 90.79 % Rotamer: Outliers : 4.36 % Allowed : 20.18 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.74 (0.12), residues: 4693 helix: -0.38 (0.12), residues: 1798 sheet: -1.34 (0.17), residues: 892 loop : -1.68 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP D 83 HIS 0.015 0.003 HIS J 344 PHE 0.042 0.004 PHE J 71 TYR 0.041 0.004 TYR H 143 ARG 0.009 0.001 ARG E 292 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 230 time to evaluate : 5.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.9145 (ptm) cc_final: 0.8818 (ppp) REVERT: A 174 PHE cc_start: 0.8826 (m-80) cc_final: 0.8490 (m-10) REVERT: A 181 MET cc_start: 0.8529 (mmp) cc_final: 0.8247 (mpp) REVERT: A 210 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8398 (pt0) REVERT: A 227 ASN cc_start: 0.8885 (m110) cc_final: 0.8529 (t0) REVERT: A 325 ASP cc_start: 0.8880 (m-30) cc_final: 0.8492 (t0) REVERT: A 357 TRP cc_start: 0.8710 (OUTLIER) cc_final: 0.7021 (p90) REVERT: B 48 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8201 (tmm) REVERT: B 101 THR cc_start: 0.9518 (OUTLIER) cc_final: 0.9301 (p) REVERT: B 197 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.8265 (m-80) REVERT: B 227 ASN cc_start: 0.8209 (m-40) cc_final: 0.7929 (t0) REVERT: B 321 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9109 (mm) REVERT: B 357 TRP cc_start: 0.8828 (p90) cc_final: 0.8231 (p90) REVERT: C 197 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8448 (m-80) REVERT: C 227 ASN cc_start: 0.8472 (m-40) cc_final: 0.8171 (t0) REVERT: C 270 GLU cc_start: 0.9039 (tt0) cc_final: 0.8828 (tt0) REVERT: D 100 GLN cc_start: 0.9242 (mt0) cc_final: 0.8588 (mp10) REVERT: D 179 SER cc_start: 0.9343 (m) cc_final: 0.9027 (p) REVERT: D 196 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9049 (tt) REVERT: D 197 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: E 55 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7996 (t70) REVERT: E 197 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.8237 (t80) REVERT: E 229 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8174 (tp40) REVERT: E 355 LYS cc_start: 0.8989 (mttt) cc_final: 0.8503 (mmmt) REVERT: F 48 MET cc_start: 0.8149 (ttt) cc_final: 0.7786 (ttm) REVERT: G 196 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9330 (tt) REVERT: G 347 LEU cc_start: 0.9487 (tp) cc_final: 0.9256 (tt) REVERT: H 25 ASP cc_start: 0.8036 (p0) cc_final: 0.7676 (p0) REVERT: H 116 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7619 (mtt90) REVERT: H 225 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8542 (pp30) REVERT: I 75 MET cc_start: 0.8249 (tpp) cc_final: 0.7324 (mmm) REVERT: I 87 GLU cc_start: 0.9438 (OUTLIER) cc_final: 0.9166 (pp20) REVERT: I 176 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8610 (mtm) REVERT: I 270 GLU cc_start: 0.7717 (tt0) cc_final: 0.7344 (tt0) REVERT: J 322 GLU cc_start: 0.9285 (tp30) cc_final: 0.8826 (tp30) REVERT: a 6 TYR cc_start: 0.7142 (p90) cc_final: 0.6290 (p90) REVERT: a 47 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.6975 (p-80) REVERT: b 39 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7377 (tp30) REVERT: b 79 LYS cc_start: 0.8787 (tppt) cc_final: 0.7490 (ttpp) REVERT: d 1 MET cc_start: 0.4823 (mmt) cc_final: 0.4594 (mmp) outliers start: 164 outliers final: 123 residues processed: 371 average time/residue: 0.5256 time to fit residues: 342.8739 Evaluate side-chains 361 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 220 time to evaluate : 5.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 203 TYR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 227 ASN Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 340 THR Chi-restraints excluded: chain G residue 376 PHE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 225 GLN Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 276 GLU Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 355 MET Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 297 ASN Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain K residue 163 PHE Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 245 GLU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 126 HIS Chi-restraints excluded: chain L residue 147 CYS Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 226 SER Chi-restraints excluded: chain L residue 247 ASP Chi-restraints excluded: chain a residue 47 HIS Chi-restraints excluded: chain a residue 50 VAL Chi-restraints excluded: chain b residue 39 GLU Chi-restraints excluded: chain b residue 42 SER Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 424 optimal weight: 7.9990 chunk 682 optimal weight: 20.0000 chunk 416 optimal weight: 0.9990 chunk 323 optimal weight: 0.9980 chunk 474 optimal weight: 20.0000 chunk 716 optimal weight: 9.9990 chunk 659 optimal weight: 20.0000 chunk 570 optimal weight: 50.0000 chunk 59 optimal weight: 4.9990 chunk 440 optimal weight: 6.9990 chunk 349 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 187 GLN L 196 GLN L 209 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 50127 Z= 0.520 Angle : 0.806 18.086 68359 Z= 0.397 Chirality : 0.043 0.201 8136 Planarity : 0.005 0.062 9100 Dihedral : 5.102 54.187 7682 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.42 % Favored : 92.56 % Rotamer: Outliers : 3.94 % Allowed : 20.85 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.28 (0.12), residues: 4693 helix: 0.05 (0.12), residues: 1788 sheet: -0.93 (0.19), residues: 734 loop : -1.55 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 176 HIS 0.014 0.002 HIS J 344 PHE 0.040 0.002 PHE a 59 TYR 0.023 0.002 TYR H 143 ARG 0.014 0.001 ARG B 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9386 Ramachandran restraints generated. 4693 Oldfield, 0 Emsley, 4693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 233 time to evaluate : 4.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9358 (mmm) cc_final: 0.8553 (mmm) REVERT: A 174 PHE cc_start: 0.8818 (m-80) cc_final: 0.8536 (m-10) REVERT: A 210 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: A 227 ASN cc_start: 0.8864 (m110) cc_final: 0.8494 (t0) REVERT: A 325 ASP cc_start: 0.8876 (m-30) cc_final: 0.8421 (t0) REVERT: B 101 THR cc_start: 0.9469 (OUTLIER) cc_final: 0.9244 (p) REVERT: B 197 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8185 (m-80) REVERT: B 321 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9082 (mm) REVERT: B 357 TRP cc_start: 0.8666 (p90) cc_final: 0.8100 (p90) REVERT: C 376 PHE cc_start: 0.5719 (m-80) cc_final: 0.4671 (p90) REVERT: D 100 GLN cc_start: 0.9194 (mt0) cc_final: 0.8575 (mp10) REVERT: D 164 VAL cc_start: 0.9356 (OUTLIER) cc_final: 0.8911 (m) REVERT: D 197 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.7829 (m-80) REVERT: E 197 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8139 (t80) REVERT: E 229 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8266 (tp40) REVERT: E 355 LYS cc_start: 0.8975 (mttt) cc_final: 0.8476 (mmmt) REVERT: F 48 MET cc_start: 0.8038 (ttt) cc_final: 0.7499 (ttm) REVERT: G 197 TYR cc_start: 0.9169 (OUTLIER) cc_final: 0.8403 (t80) REVERT: G 361 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9243 (tttm) REVERT: H 16 MET cc_start: 0.8667 (mmm) cc_final: 0.7213 (pmm) REVERT: H 25 ASP cc_start: 0.8020 (p0) cc_final: 0.7650 (p0) REVERT: H 116 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7539 (mtt90) REVERT: H 132 MET cc_start: 0.9163 (ppp) cc_final: 0.8790 (ppp) REVERT: I 75 MET cc_start: 0.8075 (tpp) cc_final: 0.7228 (mmm) REVERT: I 87 GLU cc_start: 0.9412 (OUTLIER) cc_final: 0.8996 (pp20) REVERT: J 220 LEU cc_start: 0.9206 (pt) cc_final: 0.8599 (tp) REVERT: J 322 GLU cc_start: 0.9191 (tp30) cc_final: 0.8661 (tp30) REVERT: L 63 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7068 (p0) REVERT: a 6 TYR cc_start: 0.6798 (p90) cc_final: 0.6006 (p90) REVERT: a 47 HIS cc_start: 0.7357 (OUTLIER) cc_final: 0.7059 (p-80) REVERT: b 39 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7353 (tp30) REVERT: b 79 LYS cc_start: 0.8751 (tppt) cc_final: 0.7336 (tttp) REVERT: d 1 MET cc_start: 0.4728 (mmt) cc_final: 0.4507 (mmp) outliers start: 148 outliers final: 118 residues processed: 357 average time/residue: 0.5306 time to fit residues: 331.1081 Evaluate side-chains 355 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 223 time to evaluate : 5.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 340 THR Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 376 PHE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 276 GLU Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 353 GLN Chi-restraints excluded: chain H residue 355 MET Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 297 ASN Chi-restraints excluded: chain J residue 73 HIS Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain K residue 163 PHE Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 63 ASP Chi-restraints excluded: chain L residue 126 HIS Chi-restraints excluded: chain L residue 147 CYS Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 247 ASP Chi-restraints excluded: chain a residue 47 HIS Chi-restraints excluded: chain a residue 50 VAL Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain b residue 39 GLU Chi-restraints excluded: chain b residue 42 SER Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 453 optimal weight: 9.9990 chunk 607 optimal weight: 10.0000 chunk 174 optimal weight: 0.8980 chunk 525 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 158 optimal weight: 0.5980 chunk 571 optimal weight: 40.0000 chunk 239 optimal weight: 0.0970 chunk 586 optimal weight: 50.0000 chunk 72 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 298 GLN ** J 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 ASN K 162 GLN L 209 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.098810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.075526 restraints weight = 188759.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.073226 restraints weight = 134862.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.074226 restraints weight = 116528.230| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 50127 Z= 0.217 Angle : 0.612 14.635 68359 Z= 0.302 Chirality : 0.039 0.202 8136 Planarity : 0.004 0.065 9100 Dihedral : 4.512 56.607 7682 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 2.63 % Allowed : 22.36 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.62 (0.12), residues: 4693 helix: 0.66 (0.12), residues: 1792 sheet: -0.62 (0.18), residues: 762 loop : -1.22 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 357 HIS 0.006 0.001 HIS F 166 PHE 0.016 0.001 PHE K 33 TYR 0.021 0.002 TYR J 76 ARG 0.007 0.001 ARG B 373 =============================================================================== Job complete usr+sys time: 8983.54 seconds wall clock time: 164 minutes 13.42 seconds (9853.42 seconds total)