Starting phenix.real_space_refine on Wed Jun 26 21:05:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5h_19735/06_2024/8s5h_19735_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5h_19735/06_2024/8s5h_19735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5h_19735/06_2024/8s5h_19735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5h_19735/06_2024/8s5h_19735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5h_19735/06_2024/8s5h_19735_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5h_19735/06_2024/8s5h_19735_trim_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 8 7.16 5 P 8 5.49 5 S 176 5.16 5 C 20216 2.51 5 N 5536 2.21 5 O 5960 1.98 5 H 31792 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 245": "OD1" <-> "OD2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 245": "OD1" <-> "OD2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B ASP 309": "OD1" <-> "OD2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 245": "OD1" <-> "OD2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C ASP 309": "OD1" <-> "OD2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 329": "OE1" <-> "OE2" Residue "C ASP 388": "OD1" <-> "OD2" Residue "C GLU 404": "OE1" <-> "OE2" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ASP 120": "OD1" <-> "OD2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 245": "OD1" <-> "OD2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D ASP 309": "OD1" <-> "OD2" Residue "D PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D ASP 388": "OD1" <-> "OD2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ASP 120": "OD1" <-> "OD2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 245": "OD1" <-> "OD2" Residue "E GLU 292": "OE1" <-> "OE2" Residue "E GLU 304": "OE1" <-> "OE2" Residue "E ASP 309": "OD1" <-> "OD2" Residue "E PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E ASP 388": "OD1" <-> "OD2" Residue "E GLU 404": "OE1" <-> "OE2" Residue "E PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F ASP 120": "OD1" <-> "OD2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 245": "OD1" <-> "OD2" Residue "F GLU 292": "OE1" <-> "OE2" Residue "F GLU 304": "OE1" <-> "OE2" Residue "F ASP 309": "OD1" <-> "OD2" Residue "F PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 329": "OE1" <-> "OE2" Residue "F ASP 388": "OD1" <-> "OD2" Residue "F GLU 404": "OE1" <-> "OE2" Residue "F PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G ASP 120": "OD1" <-> "OD2" Residue "G GLU 131": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 245": "OD1" <-> "OD2" Residue "G GLU 292": "OE1" <-> "OE2" Residue "G GLU 304": "OE1" <-> "OE2" Residue "G ASP 309": "OD1" <-> "OD2" Residue "G PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 329": "OE1" <-> "OE2" Residue "G ASP 388": "OD1" <-> "OD2" Residue "G GLU 404": "OE1" <-> "OE2" Residue "G PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "H ASP 120": "OD1" <-> "OD2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H GLU 144": "OE1" <-> "OE2" Residue "H TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 245": "OD1" <-> "OD2" Residue "H GLU 292": "OE1" <-> "OE2" Residue "H GLU 304": "OE1" <-> "OE2" Residue "H ASP 309": "OD1" <-> "OD2" Residue "H PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 329": "OE1" <-> "OE2" Residue "H ASP 388": "OD1" <-> "OD2" Residue "H GLU 404": "OE1" <-> "OE2" Residue "H PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 63696 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7919 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 7919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7919 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 7919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7919 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 7919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7919 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 7919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7919 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 7919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7919 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 7919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7919 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 7919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7919 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.54, per 1000 atoms: 0.32 Number of scatterers: 63696 At special positions: 0 Unit cell: (152.985, 150.815, 254.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 8 26.01 S 176 16.00 P 8 15.00 O 5960 8.00 N 5536 7.00 C 20216 6.00 H 31792 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 39.68 Conformation dependent library (CDL) restraints added in 4.8 seconds 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7456 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 32 sheets defined 37.5% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.55 Creating SS restraints... Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.714A pdb=" N PHE A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 99' Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.866A pdb=" N HIS A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 259 through 271 removed outlier: 4.308A pdb=" N ILE A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 294 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 348 through 363 removed outlier: 3.714A pdb=" N LYS A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLN A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 388 through 394 Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 431 through 441 Processing helix chain 'A' and resid 461 through 470 Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 536 through 547 Processing helix chain 'B' and resid 60 through 62 No H-bonds generated for 'chain 'B' and resid 60 through 62' Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.714A pdb=" N PHE B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 99' Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 149 through 161 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 203 through 213 Processing helix chain 'B' and resid 226 through 234 removed outlier: 3.867A pdb=" N HIS B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 259 through 271 removed outlier: 4.307A pdb=" N ILE B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 294 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 328 through 342 Processing helix chain 'B' and resid 348 through 363 removed outlier: 3.713A pdb=" N LYS B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 388 through 394 Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 431 through 441 Processing helix chain 'B' and resid 461 through 470 Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 536 through 547 Processing helix chain 'C' and resid 60 through 62 No H-bonds generated for 'chain 'C' and resid 60 through 62' Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 95 through 99 removed outlier: 3.715A pdb=" N PHE C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 95 through 99' Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 121 through 132 Processing helix chain 'C' and resid 149 through 161 Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 203 through 213 Processing helix chain 'C' and resid 226 through 234 removed outlier: 3.867A pdb=" N HIS C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 259 through 271 removed outlier: 4.308A pdb=" N ILE C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 294 Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 328 through 342 Processing helix chain 'C' and resid 348 through 363 removed outlier: 3.714A pdb=" N LYS C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN C 362 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU C 363 " --> pdb=" O LYS C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 388 through 394 Processing helix chain 'C' and resid 399 through 403 Processing helix chain 'C' and resid 414 through 416 No H-bonds generated for 'chain 'C' and resid 414 through 416' Processing helix chain 'C' and resid 431 through 441 Processing helix chain 'C' and resid 461 through 470 Processing helix chain 'C' and resid 479 through 481 No H-bonds generated for 'chain 'C' and resid 479 through 481' Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 536 through 547 Processing helix chain 'D' and resid 60 through 62 No H-bonds generated for 'chain 'D' and resid 60 through 62' Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 95 through 99 removed outlier: 3.715A pdb=" N PHE D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 99' Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 121 through 132 Processing helix chain 'D' and resid 149 through 161 Processing helix chain 'D' and resid 175 through 183 Processing helix chain 'D' and resid 203 through 213 Processing helix chain 'D' and resid 226 through 234 removed outlier: 3.866A pdb=" N HIS D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 243 Processing helix chain 'D' and resid 259 through 271 removed outlier: 4.309A pdb=" N ILE D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 294 Processing helix chain 'D' and resid 317 through 319 No H-bonds generated for 'chain 'D' and resid 317 through 319' Processing helix chain 'D' and resid 328 through 342 Processing helix chain 'D' and resid 348 through 363 removed outlier: 3.713A pdb=" N LYS D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLN D 362 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLU D 363 " --> pdb=" O LYS D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 381 Processing helix chain 'D' and resid 388 through 394 Processing helix chain 'D' and resid 399 through 403 Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 431 through 441 Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'D' and resid 479 through 481 No H-bonds generated for 'chain 'D' and resid 479 through 481' Processing helix chain 'D' and resid 496 through 503 Processing helix chain 'D' and resid 536 through 547 Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 95 through 99 removed outlier: 3.715A pdb=" N PHE E 99 " --> pdb=" O ILE E 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 95 through 99' Processing helix chain 'E' and resid 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 121 through 132 Processing helix chain 'E' and resid 149 through 161 Processing helix chain 'E' and resid 175 through 183 Processing helix chain 'E' and resid 203 through 213 Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.867A pdb=" N HIS E 232 " --> pdb=" O ASN E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 259 through 271 removed outlier: 4.308A pdb=" N ILE E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 294 Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 328 through 342 Processing helix chain 'E' and resid 348 through 363 removed outlier: 3.713A pdb=" N LYS E 359 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN E 362 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLU E 363 " --> pdb=" O LYS E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 381 Processing helix chain 'E' and resid 388 through 394 Processing helix chain 'E' and resid 399 through 403 Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' Processing helix chain 'E' and resid 431 through 441 Processing helix chain 'E' and resid 461 through 470 Processing helix chain 'E' and resid 479 through 481 No H-bonds generated for 'chain 'E' and resid 479 through 481' Processing helix chain 'E' and resid 496 through 503 Processing helix chain 'E' and resid 536 through 547 Processing helix chain 'F' and resid 60 through 62 No H-bonds generated for 'chain 'F' and resid 60 through 62' Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 95 through 99 removed outlier: 3.715A pdb=" N PHE F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 95 through 99' Processing helix chain 'F' and resid 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 121 through 132 Processing helix chain 'F' and resid 149 through 161 Processing helix chain 'F' and resid 175 through 183 Processing helix chain 'F' and resid 203 through 213 Processing helix chain 'F' and resid 226 through 234 removed outlier: 3.867A pdb=" N HIS F 232 " --> pdb=" O ASN F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 243 Processing helix chain 'F' and resid 259 through 271 removed outlier: 4.308A pdb=" N ILE F 264 " --> pdb=" O THR F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 294 Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 328 through 342 Processing helix chain 'F' and resid 348 through 363 removed outlier: 3.713A pdb=" N LYS F 359 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLN F 362 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU F 363 " --> pdb=" O LYS F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 381 Processing helix chain 'F' and resid 388 through 394 Processing helix chain 'F' and resid 399 through 403 Processing helix chain 'F' and resid 414 through 416 No H-bonds generated for 'chain 'F' and resid 414 through 416' Processing helix chain 'F' and resid 431 through 441 Processing helix chain 'F' and resid 461 through 470 Processing helix chain 'F' and resid 479 through 481 No H-bonds generated for 'chain 'F' and resid 479 through 481' Processing helix chain 'F' and resid 496 through 503 Processing helix chain 'F' and resid 536 through 547 Processing helix chain 'G' and resid 60 through 62 No H-bonds generated for 'chain 'G' and resid 60 through 62' Processing helix chain 'G' and resid 80 through 82 No H-bonds generated for 'chain 'G' and resid 80 through 82' Processing helix chain 'G' and resid 95 through 99 removed outlier: 3.714A pdb=" N PHE G 99 " --> pdb=" O ILE G 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 95 through 99' Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 121 through 132 Processing helix chain 'G' and resid 149 through 161 Processing helix chain 'G' and resid 175 through 183 Processing helix chain 'G' and resid 203 through 213 Processing helix chain 'G' and resid 226 through 234 removed outlier: 3.867A pdb=" N HIS G 232 " --> pdb=" O ASN G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 243 Processing helix chain 'G' and resid 259 through 271 removed outlier: 4.309A pdb=" N ILE G 264 " --> pdb=" O THR G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 294 Processing helix chain 'G' and resid 317 through 319 No H-bonds generated for 'chain 'G' and resid 317 through 319' Processing helix chain 'G' and resid 328 through 342 Processing helix chain 'G' and resid 348 through 363 removed outlier: 3.713A pdb=" N LYS G 359 " --> pdb=" O ALA G 355 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN G 362 " --> pdb=" O VAL G 358 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU G 363 " --> pdb=" O LYS G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 381 Processing helix chain 'G' and resid 388 through 394 Processing helix chain 'G' and resid 399 through 403 Processing helix chain 'G' and resid 414 through 416 No H-bonds generated for 'chain 'G' and resid 414 through 416' Processing helix chain 'G' and resid 431 through 441 Processing helix chain 'G' and resid 461 through 470 Processing helix chain 'G' and resid 479 through 481 No H-bonds generated for 'chain 'G' and resid 479 through 481' Processing helix chain 'G' and resid 496 through 503 Processing helix chain 'G' and resid 536 through 547 Processing helix chain 'H' and resid 60 through 62 No H-bonds generated for 'chain 'H' and resid 60 through 62' Processing helix chain 'H' and resid 80 through 82 No H-bonds generated for 'chain 'H' and resid 80 through 82' Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.715A pdb=" N PHE H 99 " --> pdb=" O ILE H 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 95 through 99' Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 121 through 132 Processing helix chain 'H' and resid 149 through 161 Processing helix chain 'H' and resid 175 through 183 Processing helix chain 'H' and resid 203 through 213 Processing helix chain 'H' and resid 226 through 234 removed outlier: 3.866A pdb=" N HIS H 232 " --> pdb=" O ASN H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 243 Processing helix chain 'H' and resid 259 through 271 removed outlier: 4.308A pdb=" N ILE H 264 " --> pdb=" O THR H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 294 Processing helix chain 'H' and resid 317 through 319 No H-bonds generated for 'chain 'H' and resid 317 through 319' Processing helix chain 'H' and resid 328 through 342 Processing helix chain 'H' and resid 348 through 363 removed outlier: 3.713A pdb=" N LYS H 359 " --> pdb=" O ALA H 355 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLN H 362 " --> pdb=" O VAL H 358 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU H 363 " --> pdb=" O LYS H 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 381 Processing helix chain 'H' and resid 388 through 394 Processing helix chain 'H' and resid 399 through 403 Processing helix chain 'H' and resid 414 through 416 No H-bonds generated for 'chain 'H' and resid 414 through 416' Processing helix chain 'H' and resid 431 through 441 Processing helix chain 'H' and resid 461 through 470 Processing helix chain 'H' and resid 479 through 481 No H-bonds generated for 'chain 'H' and resid 479 through 481' Processing helix chain 'H' and resid 496 through 503 Processing helix chain 'H' and resid 536 through 547 Processing sheet with id= A, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.597A pdb=" N MET A 250 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE A 373 " --> pdb=" O MET A 250 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL A 252 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG A 276 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALA A 253 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 278 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS A 322 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ASP A 281 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE A 324 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 141 through 145 removed outlier: 6.410A pdb=" N ARG A 164 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLU A 144 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE A 166 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU A 187 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N MET A 169 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL A 189 " --> pdb=" O MET A 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 488 through 490 removed outlier: 3.738A pdb=" N GLY A 532 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS A 513 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL A 530 " --> pdb=" O HIS A 513 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLN A 515 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN A 528 " --> pdb=" O GLN A 515 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN A 517 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN A 526 " --> pdb=" O GLN A 517 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 445 through 449 Processing sheet with id= E, first strand: chain 'B' and resid 89 through 91 removed outlier: 6.596A pdb=" N MET B 250 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE B 373 " --> pdb=" O MET B 250 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL B 252 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG B 276 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALA B 253 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE B 278 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS B 322 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASP B 281 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE B 324 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 141 through 145 removed outlier: 6.409A pdb=" N ARG B 164 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLU B 144 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE B 166 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU B 187 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N MET B 169 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 189 " --> pdb=" O MET B 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 488 through 490 removed outlier: 3.738A pdb=" N GLY B 532 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS B 513 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL B 530 " --> pdb=" O HIS B 513 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLN B 515 " --> pdb=" O GLN B 528 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN B 528 " --> pdb=" O GLN B 515 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN B 517 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN B 526 " --> pdb=" O GLN B 517 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 445 through 449 Processing sheet with id= I, first strand: chain 'C' and resid 89 through 91 removed outlier: 6.597A pdb=" N MET C 250 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE C 373 " --> pdb=" O MET C 250 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL C 252 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG C 276 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALA C 253 " --> pdb=" O ARG C 276 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 278 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS C 322 " --> pdb=" O GLY C 279 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASP C 281 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE C 324 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 141 through 145 removed outlier: 6.410A pdb=" N ARG C 164 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLU C 144 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE C 166 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU C 187 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N MET C 169 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL C 189 " --> pdb=" O MET C 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 488 through 490 removed outlier: 3.738A pdb=" N GLY C 532 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N HIS C 513 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL C 530 " --> pdb=" O HIS C 513 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLN C 515 " --> pdb=" O GLN C 528 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLN C 528 " --> pdb=" O GLN C 515 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN C 517 " --> pdb=" O GLN C 526 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN C 526 " --> pdb=" O GLN C 517 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 445 through 449 Processing sheet with id= M, first strand: chain 'D' and resid 89 through 91 removed outlier: 6.597A pdb=" N MET D 250 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ILE D 373 " --> pdb=" O MET D 250 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL D 252 " --> pdb=" O ILE D 373 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG D 276 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ALA D 253 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE D 278 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS D 322 " --> pdb=" O GLY D 279 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASP D 281 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE D 324 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 141 through 145 removed outlier: 6.409A pdb=" N ARG D 164 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLU D 144 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE D 166 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU D 187 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N MET D 169 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL D 189 " --> pdb=" O MET D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 488 through 490 removed outlier: 3.738A pdb=" N GLY D 532 " --> pdb=" O VAL D 511 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N HIS D 513 " --> pdb=" O VAL D 530 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL D 530 " --> pdb=" O HIS D 513 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLN D 515 " --> pdb=" O GLN D 528 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLN D 528 " --> pdb=" O GLN D 515 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN D 517 " --> pdb=" O GLN D 526 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN D 526 " --> pdb=" O GLN D 517 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 445 through 449 Processing sheet with id= Q, first strand: chain 'E' and resid 89 through 91 removed outlier: 6.596A pdb=" N MET E 250 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ILE E 373 " --> pdb=" O MET E 250 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL E 252 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG E 276 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALA E 253 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE E 278 " --> pdb=" O ALA E 253 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS E 322 " --> pdb=" O GLY E 279 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ASP E 281 " --> pdb=" O LYS E 322 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE E 324 " --> pdb=" O ASP E 281 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 141 through 145 removed outlier: 6.410A pdb=" N ARG E 164 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLU E 144 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE E 166 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU E 187 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N MET E 169 " --> pdb=" O GLU E 187 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL E 189 " --> pdb=" O MET E 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 488 through 490 removed outlier: 3.738A pdb=" N GLY E 532 " --> pdb=" O VAL E 511 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N HIS E 513 " --> pdb=" O VAL E 530 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL E 530 " --> pdb=" O HIS E 513 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLN E 515 " --> pdb=" O GLN E 528 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN E 528 " --> pdb=" O GLN E 515 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN E 517 " --> pdb=" O GLN E 526 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN E 526 " --> pdb=" O GLN E 517 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 445 through 449 Processing sheet with id= U, first strand: chain 'F' and resid 89 through 91 removed outlier: 6.597A pdb=" N MET F 250 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE F 373 " --> pdb=" O MET F 250 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL F 252 " --> pdb=" O ILE F 373 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG F 276 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALA F 253 " --> pdb=" O ARG F 276 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE F 278 " --> pdb=" O ALA F 253 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS F 322 " --> pdb=" O GLY F 279 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASP F 281 " --> pdb=" O LYS F 322 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE F 324 " --> pdb=" O ASP F 281 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 141 through 145 removed outlier: 6.409A pdb=" N ARG F 164 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLU F 144 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE F 166 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU F 187 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N MET F 169 " --> pdb=" O GLU F 187 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL F 189 " --> pdb=" O MET F 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 488 through 490 removed outlier: 3.739A pdb=" N GLY F 532 " --> pdb=" O VAL F 511 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N HIS F 513 " --> pdb=" O VAL F 530 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL F 530 " --> pdb=" O HIS F 513 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLN F 515 " --> pdb=" O GLN F 528 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLN F 528 " --> pdb=" O GLN F 515 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN F 517 " --> pdb=" O GLN F 526 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN F 526 " --> pdb=" O GLN F 517 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 445 through 449 Processing sheet with id= Y, first strand: chain 'G' and resid 89 through 91 removed outlier: 6.597A pdb=" N MET G 250 " --> pdb=" O VAL G 371 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE G 373 " --> pdb=" O MET G 250 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL G 252 " --> pdb=" O ILE G 373 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG G 276 " --> pdb=" O LEU G 251 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ALA G 253 " --> pdb=" O ARG G 276 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE G 278 " --> pdb=" O ALA G 253 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS G 322 " --> pdb=" O GLY G 279 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASP G 281 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE G 324 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 141 through 145 removed outlier: 6.410A pdb=" N ARG G 164 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLU G 144 " --> pdb=" O ARG G 164 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE G 166 " --> pdb=" O GLU G 144 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU G 187 " --> pdb=" O ILE G 167 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N MET G 169 " --> pdb=" O GLU G 187 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL G 189 " --> pdb=" O MET G 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'G' and resid 488 through 490 removed outlier: 3.738A pdb=" N GLY G 532 " --> pdb=" O VAL G 511 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS G 513 " --> pdb=" O VAL G 530 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL G 530 " --> pdb=" O HIS G 513 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLN G 515 " --> pdb=" O GLN G 528 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLN G 528 " --> pdb=" O GLN G 515 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN G 517 " --> pdb=" O GLN G 526 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN G 526 " --> pdb=" O GLN G 517 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 445 through 449 Processing sheet with id= AC, first strand: chain 'H' and resid 89 through 91 removed outlier: 6.596A pdb=" N MET H 250 " --> pdb=" O VAL H 371 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ILE H 373 " --> pdb=" O MET H 250 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL H 252 " --> pdb=" O ILE H 373 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG H 276 " --> pdb=" O LEU H 251 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALA H 253 " --> pdb=" O ARG H 276 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE H 278 " --> pdb=" O ALA H 253 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS H 322 " --> pdb=" O GLY H 279 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASP H 281 " --> pdb=" O LYS H 322 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE H 324 " --> pdb=" O ASP H 281 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 141 through 145 removed outlier: 6.410A pdb=" N ARG H 164 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLU H 144 " --> pdb=" O ARG H 164 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE H 166 " --> pdb=" O GLU H 144 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU H 187 " --> pdb=" O ILE H 167 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N MET H 169 " --> pdb=" O GLU H 187 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL H 189 " --> pdb=" O MET H 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'H' and resid 488 through 490 removed outlier: 3.739A pdb=" N GLY H 532 " --> pdb=" O VAL H 511 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N HIS H 513 " --> pdb=" O VAL H 530 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL H 530 " --> pdb=" O HIS H 513 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLN H 515 " --> pdb=" O GLN H 528 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN H 528 " --> pdb=" O GLN H 515 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN H 517 " --> pdb=" O GLN H 526 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN H 526 " --> pdb=" O GLN H 517 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 445 through 449 904 hydrogen bonds defined for protein. 2640 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: 23.16 Time building geometry restraints manager: 42.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.08: 31712 1.08 - 1.32: 5464 1.32 - 1.55: 26872 1.55 - 1.79: 104 1.79 - 2.03: 208 Bond restraints: 64360 Sorted by residual: bond pdb=" OP4 LLP C 119 " pdb=" P LLP C 119 " ideal model delta sigma weight residual 1.726 1.647 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" OP4 LLP A 119 " pdb=" P LLP A 119 " ideal model delta sigma weight residual 1.726 1.648 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" OP4 LLP H 119 " pdb=" P LLP H 119 " ideal model delta sigma weight residual 1.726 1.648 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" OP4 LLP B 119 " pdb=" P LLP B 119 " ideal model delta sigma weight residual 1.726 1.648 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" OP4 LLP G 119 " pdb=" P LLP G 119 " ideal model delta sigma weight residual 1.726 1.648 0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 64355 not shown) Histogram of bond angle deviations from ideal: 88.89 - 106.68: 1158 106.68 - 124.47: 111649 124.47 - 142.26: 3929 142.26 - 160.06: 0 160.06 - 177.85: 16 Bond angle restraints: 116752 Sorted by residual: angle pdb=" O LLP A 119 " pdb=" C LLP A 119 " pdb=" N ASP A 120 " ideal model delta sigma weight residual 123.00 108.72 14.28 1.60e+00 3.91e-01 7.97e+01 angle pdb=" O LLP F 119 " pdb=" C LLP F 119 " pdb=" N ASP F 120 " ideal model delta sigma weight residual 123.00 108.73 14.27 1.60e+00 3.91e-01 7.95e+01 angle pdb=" O LLP E 119 " pdb=" C LLP E 119 " pdb=" N ASP E 120 " ideal model delta sigma weight residual 123.00 108.74 14.26 1.60e+00 3.91e-01 7.94e+01 angle pdb=" O LLP C 119 " pdb=" C LLP C 119 " pdb=" N ASP C 120 " ideal model delta sigma weight residual 123.00 108.75 14.25 1.60e+00 3.91e-01 7.94e+01 angle pdb=" O LLP D 119 " pdb=" C LLP D 119 " pdb=" N ASP D 120 " ideal model delta sigma weight residual 123.00 108.76 14.24 1.60e+00 3.91e-01 7.92e+01 ... (remaining 116747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 26525 17.40 - 34.79: 2284 34.79 - 52.19: 676 52.19 - 69.58: 259 69.58 - 86.98: 104 Dihedral angle restraints: 29848 sinusoidal: 16752 harmonic: 13096 Sorted by residual: dihedral pdb=" CA GLN G 528 " pdb=" C GLN G 528 " pdb=" N MET G 529 " pdb=" CA MET G 529 " ideal model delta harmonic sigma weight residual 180.00 -144.54 -35.46 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA GLN F 528 " pdb=" C GLN F 528 " pdb=" N MET F 529 " pdb=" CA MET F 529 " ideal model delta harmonic sigma weight residual -180.00 -144.55 -35.45 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA GLN E 528 " pdb=" C GLN E 528 " pdb=" N MET E 529 " pdb=" CA MET E 529 " ideal model delta harmonic sigma weight residual -180.00 -144.55 -35.45 0 5.00e+00 4.00e-02 5.03e+01 ... (remaining 29845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3192 0.029 - 0.057: 1127 0.057 - 0.086: 268 0.086 - 0.114: 291 0.114 - 0.143: 82 Chirality restraints: 4960 Sorted by residual: chirality pdb=" CA ILE E 516 " pdb=" N ILE E 516 " pdb=" C ILE E 516 " pdb=" CB ILE E 516 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ILE C 516 " pdb=" N ILE C 516 " pdb=" C ILE C 516 " pdb=" CB ILE C 516 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE A 516 " pdb=" N ILE A 516 " pdb=" C ILE A 516 " pdb=" CB ILE A 516 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 4957 not shown) Planarity restraints: 9496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LLP F 119 " -0.073 2.00e-02 2.50e+03 1.35e-01 1.83e+02 pdb=" C LLP F 119 " 0.234 2.00e-02 2.50e+03 pdb=" O LLP F 119 " -0.085 2.00e-02 2.50e+03 pdb=" N ASP F 120 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP D 119 " -0.073 2.00e-02 2.50e+03 1.35e-01 1.82e+02 pdb=" C LLP D 119 " 0.234 2.00e-02 2.50e+03 pdb=" O LLP D 119 " -0.085 2.00e-02 2.50e+03 pdb=" N ASP D 120 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP A 119 " 0.073 2.00e-02 2.50e+03 1.35e-01 1.82e+02 pdb=" C LLP A 119 " -0.234 2.00e-02 2.50e+03 pdb=" O LLP A 119 " 0.085 2.00e-02 2.50e+03 pdb=" N ASP A 120 " 0.076 2.00e-02 2.50e+03 ... (remaining 9493 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 3477 2.18 - 2.79: 131206 2.79 - 3.39: 183825 3.39 - 4.00: 237440 4.00 - 4.60: 368604 Nonbonded interactions: 924552 Sorted by model distance: nonbonded pdb=" O LEU E 268 " pdb=" H CYS E 272 " model vdw 1.581 1.850 nonbonded pdb=" O LEU H 268 " pdb=" H CYS H 272 " model vdw 1.581 1.850 nonbonded pdb=" O LEU B 268 " pdb=" H CYS B 272 " model vdw 1.582 1.850 nonbonded pdb=" O LEU C 268 " pdb=" H CYS C 272 " model vdw 1.582 1.850 nonbonded pdb=" O LEU G 268 " pdb=" H CYS G 272 " model vdw 1.582 1.850 ... (remaining 924547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.900 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: 0.700 Extract box with map and model: 5.800 Check model and map are aligned: 0.370 Set scattering table: 0.450 Process input model: 156.730 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 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 : 0.004 0.079 32568 Z= 0.250 Angle : 0.655 14.280 44232 Z= 0.347 Chirality : 0.040 0.143 4960 Planarity : 0.006 0.135 5656 Dihedral : 14.756 86.977 12120 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.59 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.14), residues: 4016 helix: 0.95 (0.15), residues: 1432 sheet: 0.11 (0.21), residues: 600 loop : 0.71 (0.15), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 208 HIS 0.006 0.001 HIS A 66 PHE 0.016 0.001 PHE H 531 TYR 0.029 0.002 TYR G 518 ARG 0.005 0.000 ARG E 527 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 3.776 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: B 474 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7740 (mp10) REVERT: C 126 MET cc_start: 0.8529 (mtp) cc_final: 0.8280 (mtp) REVERT: C 364 LEU cc_start: 0.6855 (mt) cc_final: 0.6461 (mt) REVERT: C 391 MET cc_start: 0.7833 (mmm) cc_final: 0.7560 (mmm) REVERT: F 126 MET cc_start: 0.8601 (mtp) cc_final: 0.8344 (mtp) REVERT: F 391 MET cc_start: 0.7851 (mmm) cc_final: 0.7609 (mmm) REVERT: G 505 MET cc_start: 0.7581 (mmt) cc_final: 0.7366 (mmp) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.9904 time to fit residues: 556.1373 Evaluate side-chains 240 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 6.9990 chunk 303 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 313 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 chunk 233 optimal weight: 0.5980 chunk 363 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 513 HIS D 517 GLN E 517 GLN F 517 GLN G 513 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 32568 Z= 0.254 Angle : 0.538 7.605 44232 Z= 0.272 Chirality : 0.042 0.145 4960 Planarity : 0.004 0.038 5656 Dihedral : 8.230 89.148 4448 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.77 % Favored : 98.03 % Rotamer: Outliers : 1.11 % Allowed : 11.83 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.14), residues: 4016 helix: 0.89 (0.14), residues: 1496 sheet: 0.17 (0.21), residues: 632 loop : 0.71 (0.15), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 208 HIS 0.005 0.001 HIS F 203 PHE 0.011 0.001 PHE E 531 TYR 0.020 0.002 TYR G 518 ARG 0.006 0.000 ARG F 548 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 236 time to evaluate : 3.866 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 129 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6724 (t0) REVERT: B 474 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7771 (mp10) REVERT: B 540 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8594 (tt) REVERT: C 126 MET cc_start: 0.8553 (mtp) cc_final: 0.8331 (mtp) REVERT: C 540 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8426 (tp) REVERT: D 429 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6597 (tt) REVERT: D 540 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8632 (tt) REVERT: E 391 MET cc_start: 0.8021 (mmm) cc_final: 0.7591 (mmt) REVERT: E 429 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6619 (tt) REVERT: E 540 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8649 (tt) REVERT: F 126 MET cc_start: 0.8532 (mtp) cc_final: 0.8313 (mtp) REVERT: F 458 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7500 (tpp) REVERT: F 540 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8434 (tp) REVERT: G 505 MET cc_start: 0.7859 (mmt) cc_final: 0.7633 (mmt) outliers start: 38 outliers final: 17 residues processed: 261 average time/residue: 0.8058 time to fit residues: 341.5801 Evaluate side-chains 239 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 213 time to evaluate : 4.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain H residue 402 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 302 optimal weight: 30.0000 chunk 247 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 363 optimal weight: 5.9990 chunk 393 optimal weight: 20.0000 chunk 324 optimal weight: 9.9990 chunk 360 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 ASN D 216 ASN E 513 HIS F 216 ASN F 489 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 32568 Z= 0.318 Angle : 0.566 6.521 44232 Z= 0.289 Chirality : 0.043 0.187 4960 Planarity : 0.004 0.043 5656 Dihedral : 7.921 89.381 4448 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.44 % Favored : 97.36 % Rotamer: Outliers : 2.10 % Allowed : 11.97 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 4016 helix: 0.64 (0.14), residues: 1496 sheet: -0.14 (0.22), residues: 568 loop : 0.59 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 208 HIS 0.007 0.001 HIS C 513 PHE 0.016 0.002 PHE C 332 TYR 0.016 0.002 TYR C 163 ARG 0.005 0.001 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 233 time to evaluate : 3.900 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 129 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.6868 (t0) REVERT: B 474 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7800 (mp-120) REVERT: C 126 MET cc_start: 0.8592 (mtp) cc_final: 0.8385 (mtp) REVERT: C 216 ASN cc_start: 0.7103 (OUTLIER) cc_final: 0.6824 (t0) REVERT: C 540 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8509 (tp) REVERT: D 216 ASN cc_start: 0.7194 (OUTLIER) cc_final: 0.6842 (t0) REVERT: D 302 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: D 429 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7077 (tt) REVERT: D 511 VAL cc_start: 0.9411 (t) cc_final: 0.9191 (m) REVERT: D 540 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8561 (tt) REVERT: E 171 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7862 (tm-30) REVERT: E 173 MET cc_start: 0.8596 (mmt) cc_final: 0.8304 (mmt) REVERT: E 302 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: E 328 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7282 (p0) REVERT: E 429 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7069 (tt) REVERT: F 126 MET cc_start: 0.8556 (mtp) cc_final: 0.8349 (mtp) REVERT: F 216 ASN cc_start: 0.7106 (OUTLIER) cc_final: 0.6838 (t0) REVERT: F 531 PHE cc_start: 0.7210 (m-10) cc_final: 0.7003 (m-10) REVERT: F 540 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8494 (tp) REVERT: H 129 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6758 (t0) outliers start: 72 outliers final: 45 residues processed: 285 average time/residue: 0.8042 time to fit residues: 369.4928 Evaluate side-chains 256 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 198 time to evaluate : 4.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 464 MET Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 359 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 173 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 365 optimal weight: 3.9990 chunk 386 optimal weight: 8.9990 chunk 190 optimal weight: 0.8980 chunk 346 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 32568 Z= 0.207 Angle : 0.505 6.187 44232 Z= 0.251 Chirality : 0.041 0.142 4960 Planarity : 0.003 0.037 5656 Dihedral : 7.297 88.374 4448 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.84 % Favored : 97.96 % Rotamer: Outliers : 1.58 % Allowed : 13.17 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.14), residues: 4016 helix: 0.88 (0.14), residues: 1496 sheet: -0.15 (0.22), residues: 600 loop : 0.59 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 208 HIS 0.006 0.001 HIS D 66 PHE 0.012 0.001 PHE C 531 TYR 0.010 0.001 TYR D 163 ARG 0.003 0.000 ARG G 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 210 time to evaluate : 3.845 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: A 129 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6752 (t0) REVERT: B 474 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7726 (mp-120) REVERT: B 540 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8456 (tt) REVERT: C 302 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: C 540 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8404 (tp) REVERT: D 171 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7858 (tm-30) REVERT: D 173 MET cc_start: 0.8584 (mmt) cc_final: 0.8273 (mmt) REVERT: D 302 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: D 464 MET cc_start: 0.7453 (mtm) cc_final: 0.7200 (mtm) REVERT: D 540 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8532 (tt) REVERT: E 171 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7809 (tm-30) REVERT: E 173 MET cc_start: 0.8563 (mmt) cc_final: 0.8259 (mmt) REVERT: E 302 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: E 540 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8557 (tt) REVERT: F 302 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: F 531 PHE cc_start: 0.7152 (m-10) cc_final: 0.6920 (m-10) REVERT: F 540 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8392 (tp) outliers start: 54 outliers final: 41 residues processed: 250 average time/residue: 0.8284 time to fit residues: 337.1071 Evaluate side-chains 254 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 203 time to evaluate : 3.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 328 ASP Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 322 optimal weight: 10.0000 chunk 219 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 347 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN E 513 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 32568 Z= 0.238 Angle : 0.510 6.581 44232 Z= 0.253 Chirality : 0.041 0.147 4960 Planarity : 0.003 0.037 5656 Dihedral : 6.847 88.541 4448 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.66 % Favored : 97.14 % Rotamer: Outliers : 1.72 % Allowed : 13.49 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 4016 helix: 0.93 (0.14), residues: 1488 sheet: -0.16 (0.22), residues: 584 loop : 0.64 (0.15), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 408 HIS 0.007 0.001 HIS D 66 PHE 0.013 0.001 PHE E 531 TYR 0.012 0.001 TYR H 163 ARG 0.003 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 214 time to evaluate : 3.866 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: A 129 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6845 (t0) REVERT: A 141 THR cc_start: 0.8607 (m) cc_final: 0.8346 (p) REVERT: C 302 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: D 171 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7895 (tm-30) REVERT: D 173 MET cc_start: 0.8604 (mmt) cc_final: 0.8289 (mmt) REVERT: D 302 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: D 464 MET cc_start: 0.7590 (mtm) cc_final: 0.7334 (mtm) REVERT: D 511 VAL cc_start: 0.9333 (t) cc_final: 0.9079 (m) REVERT: D 540 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8555 (tt) REVERT: E 171 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7807 (tm-30) REVERT: E 173 MET cc_start: 0.8599 (mmt) cc_final: 0.8297 (mmt) REVERT: E 216 ASN cc_start: 0.7602 (OUTLIER) cc_final: 0.7211 (t0) REVERT: E 302 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8232 (mp0) REVERT: F 302 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: F 531 PHE cc_start: 0.7172 (m-10) cc_final: 0.6928 (m-10) REVERT: F 540 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8594 (tp) outliers start: 59 outliers final: 45 residues processed: 260 average time/residue: 0.8280 time to fit residues: 346.8526 Evaluate side-chains 259 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 206 time to evaluate : 3.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 328 ASP Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 5.9990 chunk 348 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 227 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 387 optimal weight: 10.0000 chunk 321 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 32568 Z= 0.254 Angle : 0.513 6.539 44232 Z= 0.255 Chirality : 0.041 0.149 4960 Planarity : 0.003 0.038 5656 Dihedral : 6.804 87.462 4448 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.49 % Favored : 97.36 % Rotamer: Outliers : 2.04 % Allowed : 13.43 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 4016 helix: 0.91 (0.14), residues: 1488 sheet: -0.25 (0.22), residues: 600 loop : 0.60 (0.15), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 410 HIS 0.006 0.001 HIS D 66 PHE 0.013 0.001 PHE D 531 TYR 0.013 0.001 TYR F 518 ARG 0.006 0.000 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 205 time to evaluate : 3.755 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 129 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6863 (t0) REVERT: A 141 THR cc_start: 0.8607 (m) cc_final: 0.8354 (p) REVERT: A 314 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8610 (p) REVERT: B 474 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7674 (mp10) REVERT: C 302 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: C 314 VAL cc_start: 0.9357 (OUTLIER) cc_final: 0.9144 (p) REVERT: D 171 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7890 (tm-30) REVERT: D 173 MET cc_start: 0.8604 (mmt) cc_final: 0.8310 (mmt) REVERT: D 302 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: D 391 MET cc_start: 0.7961 (mmm) cc_final: 0.7679 (mmt) REVERT: D 464 MET cc_start: 0.7521 (mtm) cc_final: 0.7298 (mtm) REVERT: D 540 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8560 (tt) REVERT: E 171 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7863 (tm-30) REVERT: E 173 MET cc_start: 0.8615 (mmt) cc_final: 0.8301 (mmt) REVERT: E 302 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8271 (mp0) REVERT: F 132 ARG cc_start: 0.8535 (ttm110) cc_final: 0.8151 (ttp80) REVERT: F 302 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: F 531 PHE cc_start: 0.7216 (m-10) cc_final: 0.6947 (m-10) REVERT: F 540 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8517 (tp) REVERT: H 129 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6767 (t0) outliers start: 70 outliers final: 46 residues processed: 259 average time/residue: 0.7948 time to fit residues: 335.1410 Evaluate side-chains 259 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 203 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 506 ASP Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 328 ASP Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 373 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 220 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 325 optimal weight: 8.9990 chunk 216 optimal weight: 3.9990 chunk 385 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 32568 Z= 0.463 Angle : 0.635 7.948 44232 Z= 0.327 Chirality : 0.045 0.174 4960 Planarity : 0.005 0.051 5656 Dihedral : 7.384 88.249 4448 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.25 % Allowed : 14.02 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.13), residues: 4016 helix: 0.20 (0.13), residues: 1488 sheet: -0.80 (0.22), residues: 568 loop : 0.34 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 208 HIS 0.007 0.001 HIS C 203 PHE 0.027 0.002 PHE C 385 TYR 0.018 0.002 TYR H 163 ARG 0.004 0.001 ARG G 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 193 time to evaluate : 3.739 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 129 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.6953 (t0) REVERT: A 314 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8609 (p) REVERT: A 458 MET cc_start: 0.7723 (ptm) cc_final: 0.7514 (ptt) REVERT: B 474 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7732 (mp10) REVERT: C 314 VAL cc_start: 0.9433 (OUTLIER) cc_final: 0.9187 (p) REVERT: C 529 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6477 (mtp) REVERT: D 173 MET cc_start: 0.8662 (mmt) cc_final: 0.8345 (mmt) REVERT: D 302 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8254 (mp0) REVERT: D 391 MET cc_start: 0.7926 (mmm) cc_final: 0.7708 (mmt) REVERT: D 540 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8761 (tt) REVERT: E 173 MET cc_start: 0.8670 (mmt) cc_final: 0.8354 (mmt) REVERT: E 216 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7364 (t0) REVERT: E 302 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: E 391 MET cc_start: 0.7901 (mmm) cc_final: 0.7677 (mmt) REVERT: F 314 VAL cc_start: 0.9415 (OUTLIER) cc_final: 0.9172 (p) REVERT: F 531 PHE cc_start: 0.7383 (m-10) cc_final: 0.7154 (m-80) REVERT: F 540 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8551 (tp) REVERT: H 129 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6862 (t0) REVERT: H 314 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8546 (p) outliers start: 77 outliers final: 59 residues processed: 257 average time/residue: 0.8248 time to fit residues: 345.9421 Evaluate side-chains 256 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 185 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain F residue 506 ASP Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 328 ASP Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 238 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 230 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 245 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 303 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 32568 Z= 0.172 Angle : 0.502 6.710 44232 Z= 0.245 Chirality : 0.041 0.144 4960 Planarity : 0.003 0.038 5656 Dihedral : 6.670 89.673 4448 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.84 % Favored : 97.96 % Rotamer: Outliers : 1.55 % Allowed : 14.54 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.14), residues: 4016 helix: 0.91 (0.14), residues: 1456 sheet: -0.57 (0.22), residues: 584 loop : 0.65 (0.15), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 408 HIS 0.006 0.001 HIS D 66 PHE 0.016 0.001 PHE E 531 TYR 0.016 0.001 TYR F 518 ARG 0.004 0.000 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 210 time to evaluate : 3.771 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: A 141 THR cc_start: 0.8529 (m) cc_final: 0.8195 (p) REVERT: A 314 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8580 (p) REVERT: B 474 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7799 (mp10) REVERT: C 302 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: C 314 VAL cc_start: 0.9368 (OUTLIER) cc_final: 0.9136 (p) REVERT: C 529 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6407 (mtp) REVERT: D 144 GLU cc_start: 0.7594 (tp30) cc_final: 0.7292 (tp30) REVERT: D 169 MET cc_start: 0.9137 (ptp) cc_final: 0.8896 (ptp) REVERT: D 171 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7904 (tm-30) REVERT: D 173 MET cc_start: 0.8571 (mmt) cc_final: 0.8286 (mmt) REVERT: D 302 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8252 (mp0) REVERT: E 171 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7899 (tm-30) REVERT: E 173 MET cc_start: 0.8574 (mmt) cc_final: 0.8273 (mmt) REVERT: E 302 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: F 302 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: F 314 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.9111 (p) REVERT: F 531 PHE cc_start: 0.7344 (m-10) cc_final: 0.7100 (m-80) REVERT: F 540 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8501 (tp) REVERT: H 314 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8529 (p) outliers start: 53 outliers final: 38 residues processed: 252 average time/residue: 0.8259 time to fit residues: 341.5711 Evaluate side-chains 249 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 201 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 350 optimal weight: 10.0000 chunk 369 optimal weight: 9.9990 chunk 336 optimal weight: 0.7980 chunk 359 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 282 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 324 optimal weight: 9.9990 chunk 339 optimal weight: 0.9990 chunk 358 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN F 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 32568 Z= 0.207 Angle : 0.501 6.632 44232 Z= 0.246 Chirality : 0.041 0.142 4960 Planarity : 0.003 0.038 5656 Dihedral : 6.603 89.588 4448 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 1.49 % Allowed : 14.54 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 4016 helix: 0.97 (0.14), residues: 1480 sheet: -0.48 (0.22), residues: 584 loop : 0.67 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 208 HIS 0.006 0.001 HIS D 66 PHE 0.014 0.001 PHE E 531 TYR 0.017 0.001 TYR F 518 ARG 0.003 0.000 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 210 time to evaluate : 4.847 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: A 141 THR cc_start: 0.8530 (m) cc_final: 0.8179 (p) REVERT: A 314 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8567 (p) REVERT: B 474 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7812 (mp10) REVERT: C 302 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: C 314 VAL cc_start: 0.9372 (OUTLIER) cc_final: 0.9134 (p) REVERT: C 529 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6567 (mtp) REVERT: D 144 GLU cc_start: 0.7546 (tp30) cc_final: 0.7054 (tp30) REVERT: D 169 MET cc_start: 0.9145 (ptp) cc_final: 0.8886 (ptp) REVERT: D 171 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7914 (tm-30) REVERT: D 173 MET cc_start: 0.8588 (mmt) cc_final: 0.8306 (mmt) REVERT: D 302 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: D 464 MET cc_start: 0.7575 (mtm) cc_final: 0.7338 (mtm) REVERT: E 171 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7903 (tm-30) REVERT: E 173 MET cc_start: 0.8598 (mmt) cc_final: 0.8297 (mmt) REVERT: E 302 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: F 302 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: F 314 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9128 (p) REVERT: F 434 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8713 (p) REVERT: F 531 PHE cc_start: 0.7364 (m-10) cc_final: 0.7109 (m-80) REVERT: F 540 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8494 (tp) REVERT: H 314 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8503 (p) outliers start: 51 outliers final: 35 residues processed: 252 average time/residue: 0.8194 time to fit residues: 337.9621 Evaluate side-chains 251 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 205 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 464 MET Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 235 optimal weight: 2.9990 chunk 379 optimal weight: 8.9990 chunk 231 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 398 optimal weight: 7.9990 chunk 366 optimal weight: 5.9990 chunk 317 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 194 optimal weight: 0.3980 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 ASN D 216 ASN ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 32568 Z= 0.263 Angle : 0.525 6.728 44232 Z= 0.260 Chirality : 0.042 0.152 4960 Planarity : 0.003 0.039 5656 Dihedral : 6.724 89.771 4448 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.39 % Favored : 96.51 % Rotamer: Outliers : 1.64 % Allowed : 14.72 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 4016 helix: 0.85 (0.14), residues: 1480 sheet: -0.62 (0.23), residues: 568 loop : 0.60 (0.15), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 208 HIS 0.005 0.001 HIS D 66 PHE 0.015 0.001 PHE E 531 TYR 0.012 0.001 TYR H 163 ARG 0.005 0.000 ARG D 527 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 206 time to evaluate : 3.885 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: A 141 THR cc_start: 0.8535 (m) cc_final: 0.8186 (p) REVERT: A 314 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8564 (p) REVERT: C 314 VAL cc_start: 0.9389 (OUTLIER) cc_final: 0.9143 (p) REVERT: C 434 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8739 (p) REVERT: C 529 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6686 (mtp) REVERT: D 144 GLU cc_start: 0.7597 (tp30) cc_final: 0.7071 (tp30) REVERT: D 171 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7955 (tm-30) REVERT: D 173 MET cc_start: 0.8615 (mmt) cc_final: 0.8339 (mmt) REVERT: D 216 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7330 (t0) REVERT: D 302 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: E 171 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7934 (tm-30) REVERT: E 173 MET cc_start: 0.8621 (mmt) cc_final: 0.8326 (mmt) REVERT: E 302 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: F 314 VAL cc_start: 0.9366 (OUTLIER) cc_final: 0.9130 (p) REVERT: F 531 PHE cc_start: 0.7395 (m-10) cc_final: 0.7103 (m-80) REVERT: F 540 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8512 (tp) REVERT: H 129 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6793 (t0) REVERT: H 314 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8531 (p) outliers start: 56 outliers final: 42 residues processed: 256 average time/residue: 0.8484 time to fit residues: 359.2970 Evaluate side-chains 253 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 200 time to evaluate : 3.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 506 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 506 ASP Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 252 optimal weight: 0.9990 chunk 338 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 292 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 317 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 326 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 489 GLN D 216 ASN ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.110455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.087128 restraints weight = 228494.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.087238 restraints weight = 161766.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.088378 restraints weight = 160856.650| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.222 32568 Z= 0.323 Angle : 0.639 59.110 44232 Z= 0.344 Chirality : 0.042 0.155 4960 Planarity : 0.003 0.039 5656 Dihedral : 6.735 89.673 4448 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.54 % Favored : 96.36 % Rotamer: Outliers : 1.81 % Allowed : 14.75 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 4016 helix: 0.82 (0.14), residues: 1480 sheet: -0.63 (0.23), residues: 568 loop : 0.58 (0.15), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 208 HIS 0.006 0.001 HIS D 66 PHE 0.017 0.001 PHE E 531 TYR 0.011 0.001 TYR H 163 ARG 0.004 0.000 ARG D 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8554.25 seconds wall clock time: 150 minutes 20.18 seconds (9020.18 seconds total)